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PDBsum entry 2hdj

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
2hdj
Jmol
Contents
Protein chain
322 a.a. *
Ligands
SO4 ×4
NDP ×2
EDO ×6
Waters ×548
* Residue conservation analysis
PDB id:
2hdj
Name: Oxidoreductase
Title: Crystal structure of human type 3 3alpha-hydroxysteroid dehydrogenase in complex with NADP(h)
Structure: Aldo-keto reductase family 1 member c2. Chain: a, b. Synonym: trans-1,2- dihydrobenzene-1,2-diol dehydrogenase, type iii 3- alpha-hydroxysteroid dehydrogenase, 3-alpha- hsd3, chlordecone reductase homolog hakrd, dihydrodiol dehydrogenase/bile acid-binding protein, dd/babp, dihydrodiol dehydrogenase 2, dd2. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: akr1c2, ddh2. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.00Å     R-factor:   0.196     R-free:   0.226
Authors: F.Faucher,K.Pereira De Jesus-Tran,L.Cantin,V.Luu-The, F.Labrie,R.Breton
Key ref:
F.Faucher et al. (2006). Crystal structures of mouse 17alpha-hydroxysteroid dehydrogenase (apoenzyme and enzyme-NADP(H) binary complex): identification of molecular determinants responsible for the unique 17alpha-reductive activity of this enzyme. J Mol Biol, 364, 747-763. PubMed id: 17034817 DOI: 10.1016/j.jmb.2006.09.030
Date:
20-Jun-06     Release date:   05-Dec-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P52895  (AK1C2_HUMAN) -  Aldo-keto reductase family 1 member C2
Seq:
Struc:
323 a.a.
322 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 1: E.C.1.1.1.357  - 3-alpha-hydroxysteroid 3-dehydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: A 3-alpha-hydroxysteroid + NAD(P)(+) = a 3-oxosteroid + NAD(P)H
3-alpha-hydroxysteroid
+
NAD(P)(+)
Bound ligand (Het Group name = NDP)
corresponds exactly
= 3-oxosteroid
+ NAD(P)H
   Enzyme class 2: E.C.1.3.1.20  - Trans-1,2-dihydrobenzene-1,2-diol dehydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Trans-1,2-dihydrobenzene-1,2-diol + NADP+ = catechol + NADPH
Trans-1,2-dihydrobenzene-1,2-diol
Bound ligand (Het Group name = EDO)
matches with 50.00% similarity
+
NADP(+)
Bound ligand (Het Group name = NDP)
corresponds exactly
= catechol
+ NADPH
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     daunorubicin metabolic process   14 terms 
  Biochemical function     oxidoreductase activity     9 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2006.09.030 J Mol Biol 364:747-763 (2006)
PubMed id: 17034817  
 
 
Crystal structures of mouse 17alpha-hydroxysteroid dehydrogenase (apoenzyme and enzyme-NADP(H) binary complex): identification of molecular determinants responsible for the unique 17alpha-reductive activity of this enzyme.
F.Faucher, K.Pereira de Jésus-Tran, L.Cantin, V.Luu-The, F.Labrie, R.Breton.
 
  ABSTRACT  
 
Very recently, the mouse 17alpha-hydroxysteroid dehydrogenase (m17alpha-HSD), a member of the aldo-keto reductase (AKR) superfamily, has been characterized and identified as the unique enzyme able to catalyze efficiently and in a stereospecific manner the conversion of androstenedione (Delta4) into epitestosterone (epi-T), the 17alpha-epimer of testosterone. Indeed, the other AKR enzymes that significantly reduce keto groups situated at position C17 of the steroid nucleus, the human type 3 3alpha-HSD (h3alpha-HSD3), the human and mouse type 5 17beta-HSD, and the rabbit 20alpha-HSD, produce only 17beta-hydroxy derivatives, although they possess more than 70% amino acid identity with m17alpha-HSD. Structural comparisons of these highly homologous enzymes thus offer an excellent opportunity of identifying the molecular determinants responsible for their 17alpha/17beta-stereospecificity. Here, we report the crystal structure of the m17alpha-HSD enzyme in its apo-form (1.9 A resolution) as well as those of two different forms of this enzyme in binary complex with NADP(H) (2.9 A and 1.35 A resolution). Interestingly, one of these binary complex structures could represent a conformational intermediate between the apoenzyme and the active binary complex. These structures provide a complete picture of the NADP(H)-enzyme interactions involving the flexible loop B, which can adopt two different conformations upon cofactor binding. Structural comparison with binary complexes of other AKR1C enzymes has also revealed particularities of the interaction between m17alpha-HSD and NADP(H), which explain why it has been possible to crystallize this enzyme in its apo form. Close inspection of the m17alpha-HSD steroid-binding cavity formed upon cofactor binding leads us to hypothesize that the residue at position 24 is of paramount importance for the stereospecificity of the reduction reaction. Mutagenic studies have showed that the m17alpha-HSD(A24Y) mutant exhibited a completely reversed stereospecificity, producing testosterone only from Delta4, whereas the h3alpha-HSD3(Y24A) mutant acquires the capacity to metabolize Delta4 into epi-T.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Electron density maps corresponding to the NADP(H) molecule bound to the m17α-HSD enzyme. Electron density maps (2F[o]–F[c]) of NADP(H) in the m17α-HSD binary complexes in (a) the open conformation and (b) the closed conformation (see the text). The maps were computed with 2.9 Å and 1.35 Å resolution data, respectively, and contoured at the 1σ level. Figure 3. Electron density maps corresponding to the NADP(H) molecule bound to the m17α-HSD enzyme. Electron density maps (2F[o]–F[c]) of NADP(H) in the m17α-HSD binary complexes in (a) the open conformation and (b) the closed conformation (see the text). The maps were computed with 2.9 Å and 1.35 Å resolution data, respectively, and contoured at the 1σ level. The Figure was drawn using MOLSCRIPT and Raster3D.[3]^[34.]^ and [4]^[35.]
Figure 5.
Figure 5. Loop B rearrangement following NADP(H) binding to the m17α-HSD enzyme. (a) The surface of the m17α-HSD in its apo form or in binary complex with the cofactor in (b) open conformation and (c) closed conformation is coloured according to electrostatic potential: blue for positive and red for negative. Loop B (residues Gly217–Glu238) with the side-chain of Trp227 drawn to illustrate the amplitude of the movement undergone by this structure. The broken green line indicates the “mature” steroid-binding site (see the text). Phosphorus atoms are depicted in orange, carbon atoms in white, oxygen atoms in red, and nitrogen atoms in blue. Figure 5. Loop B rearrangement following NADP(H) binding to the m17α-HSD enzyme. (a) The surface of the m17α-HSD in its apo form or in binary complex with the cofactor in (b) open conformation and (c) closed conformation is coloured according to electrostatic potential: blue for positive and red for negative. Loop B (residues Gly217–Glu238) with the side-chain of Trp227 drawn to illustrate the amplitude of the movement undergone by this structure. The broken green line indicates the “mature” steroid-binding site (see the text). Phosphorus atoms are depicted in orange, carbon atoms in white, oxygen atoms in red, and nitrogen atoms in blue. The Figure was generated with Swiss-PdbViewer.[3]^33
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 364, 747-763) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21217827 J.W.Arthur, and J.K.Reichardt (2010).
Modeling single nucleotide polymorphisms in the human AKR1C1 and AKR1C2 genes: implications for functional and genotyping analyses.
  PLoS One, 5, e15604.  
20124700 U.Dhagat, S.Endo, H.Mamiya, A.Hara, and O.El-Kabbani (2010).
Studies on a Tyr residue critical for the binding of coenzyme and substrate in mouse 3(17)alpha-hydroxysteroid dehydrogenase (AKR1C21): structure of the Y224D mutant enzyme.
  Acta Crystallogr D Biol Crystallogr, 66, 198-204.
PDB code: 3fjn
  17909281 U.Dhagat, V.Carbone, R.P.Chung, C.Schulze-Briese, S.Endo, A.Hara, and O.El-Kabbani (2007).
Structure of 3(17)alpha-hydroxysteroid dehydrogenase (AKR1C21) holoenzyme from an orthorhombic crystal form: an insight into the bifunctionality of the enzyme.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 825-830.
PDB code: 2p5n
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.