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PDBsum entry 2ipj

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
2ipj
Jmol
Contents
Protein chain
321 a.a. *
Ligands
SO4 ×3
NAP ×2
FFA ×2
BME ×3
EDO ×7
Waters ×613
* Residue conservation analysis
PDB id:
2ipj
Name: Oxidoreductase
Title: Crystal structure of h3alpha-hydroxysteroid dehydrogenase ty mutant y24a in complex with NADP+ and epi-testosterone
Structure: Aldo-keto reductase family 1 member c2. Chain: a, b. Synonym: trans-1,2- dihydrobenzene-1,2-diol dehydrogenase, 3- alpha-hydroxysteroid dehydrogenase, 3-alpha-hsd3, chlord reductase homolog hakrd, dihydrodiol dehydrogenase/bile aci protein, dd/babp, dihydrodiol dehydrogenase 2, dd2. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: akr1c2. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.80Å     R-factor:   0.204     R-free:   0.228
Authors: F.Faucher,L Cantin,K.Pereira De Jesus-Tran,V.Luu-The,F.Labri R.Breton
Key ref:
F.Faucher et al. (2007). Mouse 17alpha-Hydroxysteroid Dehydrogenase (AKR1C21) Binds Steroids Differently from other Aldo-keto Reductases: Identification and Characterization of Amino Acid Residues Critical for Substrate Binding. J Mol Biol, 369, 525-540. PubMed id: 17442338 DOI: 10.1016/j.jmb.2007.03.058
Date:
12-Oct-06     Release date:   19-Jun-07    
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.
321 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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
Bound ligand (Het Group name = FFA)
corresponds exactly
+
NAD(P)(+)
Bound ligand (Het Group name = NAP)
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 = NAP)
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.2007.03.058 J Mol Biol 369:525-540 (2007)
PubMed id: 17442338  
 
 
Mouse 17alpha-Hydroxysteroid Dehydrogenase (AKR1C21) Binds Steroids Differently from other Aldo-keto Reductases: Identification and Characterization of Amino Acid Residues Critical for Substrate Binding.
F.Faucher, L.Cantin, K.Pereira de Jésus-Tran, M.Lemieux, V.Luu-The, F.Labrie, R.Breton.
 
  ABSTRACT  
 
The mouse 17alpha-hydroxysteroid dehydrogenase (m17alpha-HSD) is the unique known member of the aldo-keto reductase (AKR) superfamily able to catalyze efficiently and in a stereospecific manner the conversion of androstenedione (Delta4) into epi-testosterone (epi-T), the 17alpha-epimer of testosterone. Structural and mutagenic studies had already identified one of the residues delineating the steroid-binding cavity, A24, as the major molecular determinant for the stereospecificity of m17alpha-HSD. We report here a ternary complex crystal structure (m17alpha-HSD:NADP(+):epi-T) determined at 1.85 A resolution that confirms this and reveals a unique steroid-binding mode for an AKR enzyme. Indeed, in addition to the interactions found in all other AKRs (van der Waals contacts stabilizing the core of the steroid and the hydrogen bonds established at the catalytic site by the Y55 and H117 residues with the oxygen atom of the ketone group to be reduced), m17alpha-HSD establishes with the other extremity of the steroid nucleus an additional interaction involving K31. By combining direct mutagenesis and kinetic studies, we found that the elimination of this hydrogen bond did not affect the affinity of the enzyme for its steroid substrate but led to a slight but significant increase of its catalytic efficiency (k(cat)/K(m)), suggesting a role for K31 in the release of the steroidal product at the end of the reaction. This previously unobserved steroid-binding mode for an AKR is similar to that adopted by other steroid-binding proteins, the hydroxysteroid dehydrogenases of the short-chain dehydrogenases/reductases (SDR) family and the steroid hormone nuclear receptors. Mutagenesis and structural studies made on the human type 3 3alpha-HSD, a closely related enzyme that shares 73% amino acids identity with the m17alpha-HSD, also revealed that the residue at position 24 of these two enzymes directly affects the binding and/or the release of NADPH, in addition to its role in their 17alpha/17beta stereospecificity.
 
  Selected figure(s)  
 
Figure 1.
Figure 6.
Figure 6. Comparison of the steroid-binding cavity of the m17α-HSD with the more spacious one of the h3α-HSD3. Superposition of the residues making the hydrophobic contacts between the enzyme and the steroid (m17α-HSD with epi-T (in standard CPK color set) and h3α-HSD3 with T (in orange)). Except for the position 24, the side-chain of the residues in the m17α-HSD are generally much bulkier than residues at the same position in the h3α-HSD3 structure. Residues of the m17α-HSD enzyme are identified with the one letter code and the corresponding residue in the h3α-HSD3 sequence is in parenthesis when it differs. The Figure was generated with Pymol (DeLano Scientific).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 369, 525-540) copyright 2007.  
  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
20003443 P.Veliça, N.J.Davies, P.P.Rocha, H.Schrewe, J.P.Ride, and C.M.Bunce (2009).
Lack of functional and expression homology between human and mouse aldo-keto reductase 1C enzymes: implications for modelling human cancers.
  Mol Cancer, 8, 121.  
19237748 U.Dhagat, S.Endo, H.Mamiya, A.Hara, and O.El-Kabbani (2009).
Structure of the G225P/G226P mutant of mouse 3(17)alpha-hydroxysteroid dehydrogenase (AKR1C21) ternary complex: implications for the binding of inhibitor and substrate.
  Acta Crystallogr D Biol Crystallogr, 65, 257-265.
PDB code: 3cv6
18949601 O.A.Barski, S.M.Tipparaju, and A.Bhatnagar (2008).
The aldo-keto reductase superfamily and its role in drug metabolism and detoxification.
  Drug Metab Rev, 40, 553-624.  
  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.