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Department of Molecular Medicine and Surgery (T.R., A.W.), Center for Molecular Medicine, L8:02, Karolinska Institutet/Karolinska University Hospital, S-171 76 Stockholm, Sweden; The Department of Physics, Chemistry and Biology (IFM Bioinformatics) (J.C., B.P.) and Molecular Biotechnology (M.S.), Linköping University, S-581 83 Linköping, Sweden; Department of Cell and Molecular Biology (B.P.), Programme for Genomics and Bioinformatics, Karolinska Institutet, S-171 77 Stockholm, Sweden
Address all correspondence and requests for reprints to: Tiina Robins, Department of Molecular Medicine and Surgery, Center for Molecular Medicine (CMM) L8:02, Karolinska Institutet/Karolinska University Hospital, S-171 76 Stockholm, Sweden. E-mail: tiina.robins{at}ki.se.
| ABSTRACT |
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| INTRODUCTION |
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Congenital adrenal hyperplasia (CAH) comprises a group of recessively inherited syndromes characterized by impaired cortisol secretion, increased feedback secretion of ACTH from the pituitary gland, and subsequent hyperplasia of the adrenal cortex. In humans, CAH has been correlated with mutations in the genes encoding four different CYPs involved in the synthesis of the steroid hormone cortisol in the adrenal cortex (CYP11A1, CYP11B1, CYP17, and CYP21A2). CYP11A1 and CYP11B1 are located in the mitochondria, whereas CYP17 and CYP21A2 are microsomal, belonging to the class II enzymes. Depending on the enzyme affected, synthesis of the other adrenal steroid hormones, mineralocorticoids and sex steroids, are deranged in different ways. The vast majority of all cases of CAH are due to steroid 21-hydroxylase (CYP21A2) deficiency (21OHD), which causes reduced production of cortisol and aldosterone, together with an excessive secretion of adrenal androgens (9). CAH due to 21OHD has an incidence of around 1/10 000 (10) and presents with a wide spectrum of severity. The syndrome has traditionally been divided into three clinical forms, the most severe form being salt wasting (SW), with a life-threatening salt loss during the neonatal period together with prenatal virilization of external genitalia in affected females. The simple virilizing (SV) form does not include overt SW: affected girls present with prenatal genital virilization and boys are often diagnosed due to accelerated growth and precocious pseudopuberty during early childhood. The mildest form, nonclassic (NC) CAH, is usually not recognized until later in childhood or adulthood, with hyperandrogenic symptoms such as accelerated somatic growth, precocious pseudopuberty, hirsutism, and/or decreased fertility.
The CYP21 gene is part of a complicated structure, referred to as the RCCX-module located in the human leukocyte antigen class III locus on chromosome 6 (band 6p21.3) (11). Also present in this locus, approximately 30 kb upstream of CYP21 is a 98% identical pseudogene (CYP21A1/CYP21P), which does not encode a functionally active protein due to numerous deleterious mutations that have been gathered throughout the gene during evolution. The proximity of CYP21 and CYP21P predisposes to sequence exchanges between the two genes. Misalignment during meiosis followed by recombination can lead to a net deletion of CYP21, and deleterious sequences can be transferred from CYP21P to CYP21 in apparent gene-conversion events. CYP21 gene deletion together with nine pseudogene-derived mutations are responsible for around 95% of all alleles involved in CAH. The remaining 5% of affected alleles harbor rare mutations, the number of which has increased dramatically during the last decade (12). To date, more than 80 non-pseudogene-derived disease-causing mutations have been reported. Around 50 of these are missense mutations or combinations of such. In CAH due to 21OHD, there are clear genotype-phenotype relationships. Thus, the degree of disease presentation is largely dependent on each patients underlying combination of mutations, and CYP21 genotyping has therefore become a valuable diagnostic tool. Activities of mutant enzymes, when expressed in cultured cells, also generally correlate with disease severity. All reported disease-causing CYP21A2 mutations together with (when known) associated clinical disease severity and in vitro enzyme activity, are listed on the home page of The Human Cytochrome P450 (CYP) Allele Nomenclature at http://www.imm.ki.se/CYPalleles/cyp21.htm.
The substantial number of known missense mutations, for which corresponding clinical phenotypes as well as in vitro enzyme activities are known, provides a unique background enabling analysis of clinically relevant functional and structural relationships of the CYP21 protein. A number of different prokaryotic CYP enzymes were initially crystallized and their structures were determined. The bacterial CYP102 (formerly called P450BM-3) was originally proposed as the most accurate prototype for microsomal CYPs (13) and, in the absence of determined mammalian P450 cytochrome structures, it was used as the main template for modeling mammalian CYP structures (14) including human CYP21 (15, 16). A model of the CYP21 active site using the bacterial CYP101 as the template has also been reported (17). However, in the past few years, an increasing number of CYP structures have been resolved and deposited in the Protein Data Bank (PDB) (18) of which five are mammalian, including three human proteins (CYP2C5, CYP2B4 and CYP2C9, CYP2C8, CYP3A4, respectively) (19, 20, 21, 22, 23, 24). The first eukaryotic P450 structure solved, CYP2C5, is a progesterone 21-hydroxylase expressed in rabbit microsomes. Because CYP21 has progesterone as one of its substrates, it is intriguing to compare CYP21 with respect to CYP2C5. Sequence comparisons also reveal that CYP2C5 is among the closest homologs of CYP21. Furthermore, extensive structural evaluation of CYP2C5 has been undertaken (21, 25, 26, 27, 28), as it is the first membrane-bound CYP structure determined by x-ray diffraction. Thus, it represents an improved template structure for the modeling of human cytochrome P450 enzymes.
In the present study bioinformatic techniques have been used to analyze naturally occurring CYP21 mutants and normal variants to improve understanding of structure-function relationships of the protein and to better understand the molecular causes of CAH due to 21OHD. A structural model of human CYP21 was calculated based upon the known structure of rabbit CYP2C5. Furthermore, individual models were calculated to investigate molecular mechanisms of all known allelic variants of CYP21. Finally, seven novel CYP21 missense mutations detected in CAH patients, V139E, C147R, R233G, T295N, L308F, R366C, and M473I, are reported, and the present models have been used to predict functional and structural consequences of each mutation.
| RESULTS |
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60%) of the heme-binding residues are conserved between CYP21 and CYP2C5. The steroid-binding site was defined by homology with CYP51, for which the complex with its steroid substrate (estriol) bound has been structurally determined (29). Totally 16 residues were found within a 5Å sphere around the steroid: S108 and L109 in the loop between helix B' and C, residues 203207 located in the loop connecting helix F and G', D287 and residues 290292 and 294295 in the central part of helix I, and finally V359, L363 and P364 in the loop between helix K and ß14. All 16 substrate-binding residues are indicated in Fig. 3
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-helix A, the second loop extends between strand 1 and 2 of ß-sheet 1 (ß11 and ß12), and the third loop is positioned between a break in the
-helix G, dividing the helix into what we denote G' and G, and helix G'' (Fig. 3
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70%) are located in the C-terminal half (Fig. 3
Molecular modeling has been carried out in an attempt to explain the structural effects for all reported mutations resulting in amino acid substitutions (Table 4![]()
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). Predicted distances to the heme and steroid are also given together with hydrophobicity changes. Amino acid residues present in the protein core are usually of structural importance, and they are consequently often conserved among different species. More than 50% of all identical or closely homologous residues compared with CYP2C5 are found in the inner core of our CYP21 model (accessibility to surface
20%) indicating a conserved structural core. Furthermore, it can be seen that nearly all of the SW and SV mutants affect residues that are buried in the three-dimensional structure and strictly conserved between higher eukaryotes (Table 3
). Many of these severe mutants are also located close to the heme- and steroid-binding sites (Table 3
). The remaining severe mutants mainly cause large changes in residue hydrophobicity or size.
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Prediction of Severity of Novel Mutants
Seven novel mutations in CYP21 have also been investigated (Table 5
). By combining information from modeling and residue properties, predictions of to which severity class each mutation belongs have been done. The information used for prediction was energy, surface accessibility, evolutionary conservation, changes in polarity, distances to heme and steroid, and structural information from visual inspection of the model.
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-helix might cause instabilities. The conclusion is that it fits in the NC class. T295N is most likely deleterious (SW) because it is close to both the heme and the steroid. L308F is buried but leads to only a small polarity change, most likely making it moderately harmful (NC or SV). R366C causes a considerable polarity change that leads to lost electrostatic interactions. However, the residue is not conserved, and it has some access to the surface, which implies that it can be either SV or SW. A classical example of a harmless alteration (N) is M473I: it affects a fully exposed residue, which is only partly conserved, and causes a rather low polarity change, and the allelic form (isoleucine) is identical to the corresponding residue in the mouse and rat sequence. | DISCUSSION |
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Functional characterization of new mutants using site-directed mutagenesis followed by in vitro expression has been done on numerous mutants and has shown that there is generally a good agreement between degree of enzymatic impairment in vitro and clinical disease presentation [for overview see http://www.imm.ki.se/CYPalleles/cyp21.htm (12)]. However, these are laborious and time-consuming methods and cannot provide clinically useful information within a reasonable time frame when a novel mutation is encountered in a patient. Therefore, the use of bioinformatic techniques would be valuable to predict consequences of mutations.
Molecular Model of Human CYP21A2
The present extensive evaluation of the correlation between clinical and structural data shows that the molecular model of human CYP21A2 can be used to judge the physiological effects of patient-occurring mutations. To obtain an accurate structural model, a sequence identity of more than 30% between the known structure and the modeled sequence is usually required (35). However, even though the residue identity between the CYP21 sequence and the sequence of the template amounts to only 29%, it should be remembered that in the cytochrome P450 superfamily, low sequence identity in pair-wise comparisons is common. In spite of this, the three-dimensional structures experimentally determined so far are clearly similar, especially around the heme-binding region, where the structures are easily superimposable. Thus, it can be expected that the core region of our model is valid, even though some uncertainties might occur at the exterior loops. However, this would not change our conclusions regarding heme and steroid binding. The same has been shown for other enzyme families with distant relationships, e.g. the short-chain dehydrogenases/reductases, with pair-wise identity of typically 20% (36).
The N-terminal membrane-spanning part was not modeled, because no experimentally solved three-dimensional structure has any structural information for this part due to methodological difficulties. However, it is believed to form an
-helix that anchors the P450 molecule in the membrane and that this helix should not affect the overall structure of the globular part.
Structural Domains of CYP21 and Naturally Occurring Mutants in These Regions
Meander and the ERR-Triad.
The meander is a highly conserved region in all cytochrome P450s and consists of a stretch approximately 20 amino acid residues long between the K' helix and the Cys pocket (37). In the present model, this region consists entirely of residues exposed to the molecular surface, with the exception of the two buried prolines (P401 and P406) that are practically invariant in all CYPs. An additional notable position in the meander of CYP21 is position 408, which is a highly conserved arginine (varies between arginine, histidine, and asparagine in all other CYPs) and has been reported to clinically result in SW CAH when mutated to cysteine (R408C; CYP21A2*73) (38). This residue is the third amino acid residue in the so-called ERR-triad, also consisting of glutamate and arginine that are located in the K-helix (E351 and R354) and that are strictly conserved in all CYPs. The ERR-triad acts as a folding motif in the meander and assists in stabilizing the three-dimensional structure of this region, locking the Cys-pocket in a position that assures covalent binding of heme with the CYP (37). Several site-directed mutagenesis experiments of the ERR-triad residues in various CYPs have confirmed their significance for enzyme function (39, 40, 41, 42). Because the hydroxylation activity of CYP21 is dependent on heme binding, it is not surprising that an interruption of the ERR-motif leads to a severe form of CAH. Modeling of R408C made it evident that this surface residue completely changes the hydrophilicity when becoming nonpolar, and thereby loses its function as a structural stabilizer. Two naturally occurring CYP21 mutants have also been reported in the first arginine of the ERR-triad, (R354H; CYP21A*54) (43, 44) and (R354C; CYP21A2*59) (85), both of which are clinically associated with SW CAH. Our model shows that substitutions to either histidine or cysteine in this position result in loss of the naturally occurring interactions with E351 and E403, essential for maintaining the structure. Recently, a missense mutation in the most N-terminal residue of the ERR-triad (E351K; CYP21A2*96) was reported in a SV CAH patient, and functional studies confirmed the diagnosis, with severe, but not a complete, loss of in vitro activity. Structural changes induced by the glutamate to lysine exchange as well as other artificial mutants at position 351 of CYP21 have also been shown by modeling to interfere with correct folding, although direct heme binding with C428 was not believed to be disturbed (46). In our novel model, a substitution of the negatively charged glutamate to the positively charged lysine results in loss of the strong interaction with the first arginine in the ERR-triad (R354) and, moreover, induces electrostatic repulsion between the two interacting residues. Thus, the structural features shown in the model highly correlate with the clinical consequences of CYP21 mutations in the ERR-motif and support the importance of the meander being a fundamental structural domain.
The Cys-Pocket and the Heme-Binding Region.
The present investigation has identified the same residues central to heme binding as for the template CYP2C5. These heme-binding residues are identical to the predicted residues in the previous model of CYP21 (16), based on the prokaryotic CYP102 (13). Thus, this novel model demonstrates that the heme-binding region is maintained in CYP21, as suspected, because the three-dimensional structure of this site is highly conserved throughout all domains of life from prokaryotic to human CYPs, despite low sequence identity.
All amino acid residues in the Cys-pocket (amino acid residues 421428) are conserved between CYP21 and the template. The heme iron is sulfide bonded by C428 in the loop connecting helix K to helix L, and the propionates of the heme interact with the side chains of W116 and K120 in helix C, H365 in ß14, and F421 and R426 in the Cys-pocket. C428 in CYP21 has also been shown experimentally to be heme iron binding, and experimental mutants (W428, M428, S428) have, in expression studies in mammalian and yeast cells, been shown to lose all enzymatic activity for conversion of 17OHP (47). CYP21 mutants involved in the Cys-pocket and heme binding are G424S (CYP21A2*55), R426H (CYP21A2*82), and H365Y (CYP21A2*99), and the reported clinical features (SV CAH) correlate well with the structural data presented here. The G424S mutant has been suggested to be a founder mutation with Mulatto origin, and several unrelated patients confirm its association to SV CAH (48). This glycine is important for structural maintenance of the Cys-pocket, because it enables a sharp turn where no other residue with a larger side chain can fit spatially. The R426H mutant was first reported in three hemizygous sisters, all with severe virilization of external genitalia but without any salt-wasting symptoms (49). However, recently we found this mutation in a young SV CAH girl with latent salt-wasting symptoms, and functional analyses revealed residual in vitro activity below 1% (50). The H365Y mutant (51) was recently detected in a CAH patient, but information of the clinical severity was not presented. Based on the present modeling studies of this mutant, it most probably results in classical CAH (SW or SV), because it is a residue directly involved in heme binding.
The Active Site; Substrate Binding and Catalysis.
The substrate-binding region is usually one of the most difficult regions to predict in modeling studies of CYPs, because it is the site of expected structural divergence depending on the substrate specificity of different proteins. Significant structural differences between substrate-binding sites have also been demonstrated (22, 23). Therefore, it is reasonable to believe that by using a template structure which catalyzes a related substrate, a more accurate model can be obtained regarding this specific matter. Rabbit CYP2C5, which was used as a template for the present modeling, utilizes several substrates including progesterone, which is also used by CYP21. Due to the lack of three-dimensional structures determined with bound CYP21 substrates (progesterone and 17OHP) in the active site, data from CYP51 were also used, which is the experimentally determined structure-ligand complex available with the most similar substrate, the steroid estriol (29). Residues identified as steroid binding in CYP51 correlate well with the putative substrate-binding site of docked progesterone in CYP21. Thus, we believe that our CYP21 model in this respect is an improvement over previous models based on prokaryotic CYP structures.
A conserved region among CYPs in the middle of helix I (corresponding to SRS 4) starts with a few hydrophobic residues followed by charged and polar amino acid residues that are believed to act as proton acceptors and donors in proton transfer to the ironbound oxygen. The present model shows that the conserved G291 and T295 are the corresponding residues in CYP21 that are connected by hydrogen bonding, shown in prokaryotic (13, 52) as well as mammalian (21) structures to form an oxygen-binding pocket. These helix I-interacting residues are furthermore involved in CAH-causing mutations. T295N is one of the novel mutants that are reported in this study, whereas three different mutations have been observed for G291. They are of missense type: G291S (CYP21A2*23) (53, 54), G291C (CYP21A2*53) (43, 55), and G291R (CYP21A2*77) (56), and all are correlated with severe, classical CAH. It has also previously been suspected that G291 may be part of catalysis, supported by experimental data from functional studies showing enzymatic activity in vitro of below 1% for both 17OHP and progesterone for the G291S mutant, whereas the half-life of the mutant was comparable to that of the normal protein (53). Among the identified substrate-binding residues, another disease-causing mutation is found between the K-helix and strand 4 of ß-sheet 1, corresponding to SRS5. The L363W mutant (CYP21A2*66) has been associated with SV CAH (57), which correlates well with the presented structural data suggesting this residue to be involved in steroid and heme binding. All these above-mentioned residues have been predicted to be involved with substrate binding in CYP2C5, which is also true for the substrate-binding residues S108, L109, D287, and V359 in our model.
Redox Partner Interactions
Electrostatic mechanisms are considered significant to orient the positively charged surface of the CYP-dipole toward the negative surface of the redox partner, whereas hydrophobic forces are likely to mediate the functional electron transfer between the two proteins. It is believed that hydrophobic interactions between the ER membrane and the CYP are significant to achieve proper alignment of the CYP and its redox partner (5).
Experimental evidence indicates that basic residues on the proximal face (with respect to heme) of various CYPs interact with acidic residues on the surface of the redox partner (5). A cluster of basic residues, mostly arginines, in CYP21 are prone to mutate resulting in CAH (58). The mutants consist of R339H, R341P/W, R354H, and R356Q/W/P and are part of the segment corresponding to residues 338361 in CYP21 that is believed to be involved in redox partner interaction according to the crystal structure of CYP102 (13). Modeling of the related CYP17 as well as experimental work has shown that arginines R358 and R347 are important for interaction with the corresponding redox partner. R347, in particular, is evidently a crucial component of the redox partner interaction site (32, 33). The corresponding residue in CYP21 is the completely conserved R339. A naturally occurring missense mutation in this position, R339H (CYP21A2*24), is associated with NC CAH (59). It seems likely that R339 is crucial for redox partner interaction, such that even the minor change of the side chain properties from arginine to histidine leads to mild disease. The R358 in CYP17 does not correspond to a basic residue in CYP21, but to alanine (A350). Thus, it seems likely that some other residue in CYP21 fulfils the function of R358. One of the candidates might be R341, corresponding to R349 in CYP17, which is located close to the important R339 (R347 in CYP17) (cf. Fig. 2
). All arginine residues in this region of CYP21 (R339, R341, R354, and R356) have been affected by disease-causing mutations, which most likely cause electrostatic disturbances as concluded from the present modeling studies (Table 3
).
Large Hydrophobic Area
Two mutants, G64E and V211L, have so far been identified in the large hydrophobic surface of CYP21. The G64E mutant (CYP21A2*47) is positioned in the loop between the two first strands of ß-sheet 1 and has been associated with the most severe form of the disease (SW) and complete loss of activity in vitro (60). Modeling shows that this residue substitution may lead to structural hindrance due to very constricted space, because the small side chain of glycine is the only possible amino acid to make the sharp turn seen in this loop. The V211L variant (CYP21A2*21) (61) affects the first residue C-terminally of helix G' that is exposed to the surface. Although reported as a CYP21 sequence variant, it has not been claimed to be responsible for CAH. Data deduced from the present model supports the fact that this residue alteration is of no significance to disease, but rather a normal variant of CYP21, because it does not confer any change in hydrophobicity. However, because this position is part of the hydrophobic patch that seems to be important for membrane association, a different change might result in unfavorable interactions causing disease.
Protein Stability Correlation
The stability dependence can give useful information about the mutant in combination with other information, e.g. about surface accessibility. In our case all amino acid residues affected by the normal variations have access to the solvent. The deleterious mutations associated with residue exchanges on the surface, in most cases, affect residues close to the active site and, consequently, they do not need to significantly affect the stability of the protein. Thus, when we looked at the stability dependence for the mutants affecting residues in the core, a greater separation between SV and SW was observed (data not shown).
Prediction of Clinical Effect of Novel CYP21 Mutations
The V139E mutation was found in a compound heterozygous patient (V139E/I2 splice) diagnosed with SW CAH. The structural prediction of V139E resulting in classical (SV/SW) CAH thus correlates well with the patients diagnosis. The 7-yr-old boy with genotype C147R/Q318X was diagnosed with NC CAH or possibly SV CAH. The prediction based on modeling is that C147R is associated with classical CAH, and the boy most likely has SV rather than NC CAH. This is hence a good example where a structural prediction based on the present model is of value in classifying a novel mutation. Because this patient is a boy, it is difficult to distinguish between SV and NC CAH based on clinical evaluation, because the presence or absence of virilization of external genitalia cannot be used. The ability to distinguish between NC and SV CAH is important in these boys, because it has impact both on treatment and genetic counseling to the family. The female patient with genotype R233G/R233G or R233G/del was diagnosed with NC CAH, which matches the predictions for this novel mutation. The boy with genotype T295N/I172N was diagnosed with SV CAH. The structural prediction is that T295N is associated with the most severe form of the disease, SW CAH, and his slightly less severe clinical phenotype thus reflects I172N (CYP21A2*11), which is associated with SV CAH. Structural prediction of L308F revealed this mutation to be most likely associated with moderately severe CAH (NC/SV), again in agreement with the clinical diagnosis of this SV girl. The Finnish girl with genotype R366C/V281L was diagnosed with NC CAH. R366C cannot be classified based on clinical evaluation, because the mild V281L (CYP21A2*15) mutation is responsible for this form of the disease. The present modeling shows that the novel mutant R366C is most likely associated with SV/SW CAH. Thus, R366C, in combination with a severe allele, would most probably result in classical CAH. Regarding M473I, we suggest that it is not a disease-causing mutation but rather a normal CYP21 variant. Consequently, the girl with genotype M473I/V281L is most likely a heterozygous carrier rather than a girl affected by a mild form of CAH. In conclusion, the predicted mutant severities were in good agreement with degree of disease presentation and, in several cases, provided additional clinically useful information that could not be resolved by examining the patients.
Normal Variants of CYP21
The present models include six normal variants of CYP21, which are not associated with disease. These are K102R, D183E, V211L, M239K, S268T, and N493S (Table 4![]()
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). As observed, they all affect nonconserved amino acid residues that are accessible to the surface to a higher degree than most disease-causing mutants. None of these alterations changes the electrostatic charge, except for M239K (CYP21A2*14), in which nonpolar methionine is exchanged for the positively charged lysine. It has recently been shown, by in vitro expression and functional analysis, that M239K is not disease causing on its own, but rather a normal CYP21 variant, with an activity of 95/98% for conversion of 17OHP and progesterone, respectively, compared with the normal enzyme. In combination with I236N and V237E, it forms the common Cluster E6 mutation, which is correlated to SW CAH and causes abolished enzyme function in vitro (62). M239K is also the only normal CYP21 variant in which modeling reveals some notable characteristics; the new mutant residue gains interaction with E238, as well as causes repulsion to R242 in the present model, which could be expected to result in structural disturbance. However, because this surface-exposed residue is found in the short loop between helix G and G'', which is not part of any domain of importance for enzyme function/structure, the introduced molecular interactions are unlikely to disturb overall protein structure.
Mutants of Unclear Severity
The present model has enabled structural explanations for all reported missense mutations, with the exception of G178A and E380D. The E380D mutant (CYP21A2*35) has been reported to be associated with SW CAH, although functional data have shown a reduction of normal enzyme activity to 30% (63, 64) that is usually associated with a NC phenotype. However, the modeling shows that there are only minor differences between a glutamate and an aspartate residue at this position. It has been speculated that this residue might be in electrostatic contact with residues in the membrane-binding helix (16), which is, however, not included in this model, and it thus remains speculative. G178A (CYP21A2*52) (43, 55), just as E380D, is also grouped among the unclear mutants in Table 4![]()
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, because the reported clinical phenotypes are not in agreement with functional data.
In conclusion, the work presented here shows evidence as to how the joint evaluation of a clinical mutation data bank with structural and bioinformatical analysis can provide both enhanced knowledge of structure-function relationships of the native protein and better understanding of the molecular mechanisms of CAH due to 21-hydroxylase deficiency. The strong coherence between the degree of disturbed structural parameters with the physiological manifestations of the mutation is striking and could provide a new bioinformatic route for the prediction of clinical consequences of novel disease-causing mutations. Because biochemical and biophysical evaluation of a mutant protein in vitro is both time consuming and often impractical due to folding and/or solubility problems of mutant proteins, novel routes toward in silico analysis of the effects of patient mutations open up for high-throughput analysis of genetic data. To achieve efficient individualized therapies in mutation-linked diseases, such as CAH due to 21-hydroxylase deficiency, which was the case analyzed here, and in mutation-generating disorders, such as cancer and antibiotics resistance, such efforts will be crucial for success.
| MATERIALS AND METHODS |
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Homology Modeling
A molecular model was calculated based upon the structure of rabbit cytochrome P450 2C5 (27) at 2.3 Å resolution and with an R-value of 0.257 (PDB accession no. 1N6B) using the program ICM (version 3.2, Molsoft LLC, La Jolla, CA). The sequence identity is 31.1% on the aligned part of the chain. ICM uses the alignment to tether the CYP21 sequence to the template structure. A Monte-Carlo procedure is used to energy minimize the structure. The calculations are performed both globally over the entire protein and locally on loops between regular secondary structure elements. The Monte-Carlo method is optimized using biases toward regions with high energy and using common side chain conformations, so called rotamers (68). The quality of the model was evaluated using several methods. The widely used evaluation method Procheck (69, 70) gives an overall G value for the model of 0.01. This is well above the threshold 1.00 for a bad structure and 0.50 for a poor one. Procheck evaluates geometrical and stereochemical properties, i.e. close contacts, bond distances, bond angles, torsion angles, and chirality. Another evaluation method, considering energy strain (71), results in an average normalized residue energy for the model of only 0.74, which is in the better half of the theoretical models in PDB. It is also useful to look at the Ramachandran plot in which the model has only nine nonglycine outliers compared with six for the template crystal structure. Finally there are very few clashes, i.e. atoms too close to each other causing high van der Waals interaction energies. Thus, we consider the CYP21 model to be of appropriate quality for the investigations in this study.
For comparison, we also calculated a model based upon the CYP2B4 structure (PDB code 1PO5, 1.6 Å resolution, R-value 0.217) (20), which has 28.5% sequence identity to CYP21. However, this model was considered inferior to the one based upon CYP2C5, as judged by the quality evaluations mentioned above.
Human CYP21 is a membrane-bound protein with an N-terminal membrane-attaching segment of 26 amino acid residues that was excluded from the model. The first residue in the present homology model is thus leucine 27, with residue numbering according to the native full-length protein. The alignment was manually adjusted at a few places where gaps interrupting regular secondary structure elements could be shifted a limited number of residues.
Analyses of CYP21 Mutants and Normal Variants
Structural analyses were performed for all reported mutations affecting CYP21 except nonsense, frame shift, splice site, and promoter mutations. A total of 66 different missense mutations, including seven novel mutations and six normal variants, were studied. The analyses of two reported missense mutations, M1I (CYP21A2*83) (72) and A15T (CYP21A2*74) (73) are lacking, because the very N-terminal transmembrane part of the protein was not included in the present model. Allelic variants were grouped according to their reported clinical classification (12), dividing the phenotypes into the three groups of disease severity, SW (n = 16), SV (n = 11), and NC CAH (n =18), as well as N for normal CYP21 variants (n = 6). For mutants that have been functionally investigated, in vitro enzyme activities below 1% of normal were considered to correspond to a SW phenotype, activities between 1% and 15% were classified as SV, and residual activity greater than 20% was considered typical of mutations associated with NC CAH. Thirteen mutants are presented separately because seven of these are novel, and functional information (associated clinical symptoms and correlated in vitro enzyme activity) is lacking for the remaining six. The structure corresponding to each mutant was individually modeled in triplicate using ICM, as detailed above. The molecular free energy was calculated according to the ECEPP/3 forcefield (74) parameters for van der Waals interactions, hydrogen bonds, electrostatic interactions, and torsion energies using algorithms implemented in ICM. The molecular free energy was used in comparisons between the structures. Hydrophobicity changes were calculated using the Kyte and Doolittle parameters (75). Distances between the amino acid residues corresponding to the mutants and the heme- and steroid-binding sites were measured in ICM.
Patients with Novel CYP21 Mutations 2
The novel mutations (V139E, C147R, R233G, T295N, L308F, R366C, and M473I) were detected at the Clinical Genetics Unit, Karolinska University Hospital, Sweden, by sequencing of the entire coding region of CYP21 from Scandinavian patients investigated for CAH.
V139E (accession no. AM183945) was found in trans with the intron 2 splice mutation (CYP21*9, genotype V139E/I2 splice) in a Swedish boy who was diagnosed with CAH through neonatal screening. His sodium levels started to fall before treatment was begun, and he was diagnosed with SW CAH.
The C147R mutation (AM183946) was found in trans with Q318X (CYP21A2*17) in a Swedish boy who presented with accelerated growth and premature adrenarche at the age of 7 yr. He was diagnosed with NC CAH, although the SV form cannot be ruled out in this boy.
R233G (AM183947) was found in hemi- or homozygous form (genotype R233G/deletion or R233G/R233G) in a Swedish female born in 1960. She reported hyperandrogenic symptoms such as hirsutism and oligomenorrhea from the age of 20, and had been diagnosed with polycystic ovary syndrome at this age. At the age of 32, she was reinvestigated for infertility, and elevated 17-hydroxyprogesterone (17OHP) (293 nmol/liter) and slight clitoromegaly were found. She was diagnosed with NC CAH.
T295N (AM183948) was found in trans with I172N (CYP21A2*11) in a Swedish boy who was also found through the neonatal screening (17OHP was 127 nmol/liter, reference value 75 nmol/liter). A few days later, serum 17OHP was 500 nmol/liter. Treatment was promptly instituted during the first week of life, and the patient was diagnosed with SV CAH, although SW cannot be ruled out in this patient.
L308F (AM183949) was found in trans with Q318X (CYP21A2*17) in a Russian female immigrant who came to Sweden at the age of 16 yr. Medical records were incomplete, but she had been diagnosed with CAH at the age of 4 months although treatment had not been instituted until she was 2 yr of age. She had undergone genital surgery at the age of 5 yr. She was classified as having SV CAH.
R366C (AM183950) was found in trans with V281L (CYP21A2*15) in a Finnish girl who came to medical attention because of growth acceleration and pubic hair growth at the age of 7.5 yr. She was diagnosed with NC CAH.
M473I (AM183951) was found in trans with V218L (CYP21A2*15) in a Norwegian girl who was investigated due to pubic and axillary hair growth from 9 yr of age. She had slightly increased 17OHP (20 nmol/liter basally, 95.6 after ACTH stimulation), and was considered either to have a very mild form of NC CAH or to be a heterozygous carrier.
Redox Partner Interaction
The redox partner of CYP21 is known to be the cytochrome P450 NADPH oxidoreductase (31), which docks to the protein and transfers electrons from NADPH to the heme iron. For the homolog CYP2B4, showing 28.5% pair-wise identity with CYP21, the redox partner-binding site is well studied (76, 77, 78, 79, 80). The CYP2B4 structure was superimposed onto the CYP21 model using ICM, and, subsequently, the residues considered important for redox binding in CYP2B4 were mapped in the CYP21 model.
Hydrophobic Areas
Searches for large hydrophobic areas that might interact with other molecules using the Optimal Docking Area method (34), available as a web service at http://www.molsoft.com/oda, was also performed. The ODA algorithm generates protein surface of different sizes to analyze their docking surface energy. The energy calculations are based on atomic solvation parameters, for each type of atom exposed to the solvent, previously derived form octanol-water transfer experiments. Areas with low docking surface energy correspond to regions likely to be buried in the interaction with other proteins.
Steroid-Binding Region
In a search for a homologous protein structure containing bound progesterone at the active site, a steroid that is hydroxylated by CYP21, CYP51 with the steroid estriol bound was the closest match found. The CYP51-estriol complex has been structurally determined at 1.55Å resolution with an R-value of 0.206 (pdb-ID 1X8V) (29). The two steroids, estriol and progesterone, have similar structures and sizes, and the two proteins, CYP21 and CYP51, are homologous with 22% pair-wise sequence identity. Based on the structure of CYP51, the probable steroid-binding site in CYP21 was mapped by superimposing the two proteins using the heme groups as guidelines The heme groups superimposed with an root mean square deviation of 0.63 Å, thus showing good agreement. After superimposing in ICM, the estriol molecule was transferred to the CYP21 model and subsequently changed to progesterone. The complex structure was energy minimized to avoid clashes, predominantly between the steroid and the heme group. From the resulting model, the amino acid residues within a sphere of 5Å radius from the progesterone were considered as steroid binding. Similarly, the amino acid residues close to the heme group were classified as heme binding (cf. Fig. 1
).
| ACKNOWLEDGMENTS |
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| FOOTNOTES |
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Disclosure statement: The authors have nothing to disclose.
First Published Online June 20, 2006
1 T.R. and J.C. contributed equally to this work. ![]()
Abbreviations: CAH, Congenital adrenal hyperplasia; CYP, cytochrome P450; CYP21A2, CYP21, steroid 21-hydroxylase; CYP21A2, CYP21, the gene encoding steroid 21-hydroxylase; CYP21A1, CYP21P, the CYP21 pseudogene; ER, endoplasmic reticulum; G6PD, glucose-6 phosphate 1-dehydrogenase; NADPH, reduced nicotinamide adenine dinucleotide phosphate; NC, non-classic; 21OHD, steroid 21-hydroxylase deficiency; 17OHP, 17-hydroxyprogesterone; PDB, Protein Data Bank; SRS, steroid recognition site; SV, simple virilizing; SW, salt wasting.
2 Novel nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under the GenBank accession numbers: AM183945 (CYP21-V139E), AM183946 (CYP21-C147R), AM183947 (CYP21-R233G), AM183948 (CYP21-T295N), AM183949 (CYP21-L308F), AM183950 (CYP21-R366C), and 183951 (CYP21-M473I). ![]()
Received for publication April 24, 2006. Accepted for publication June 12, 2006.
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