PDBsum entry 1k41

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protein Protein-protein interface(s) links
Isomerase PDB id
Protein chains
121 a.a. *
Waters ×41
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Crystal structure of ksi y57s mutant
Structure: Ketosteroid isomerase. Chain: a, b. Synonym: steroid delta-isomerase. Engineered: yes. Mutation: yes
Source: Pseudomonas putida. Organism_taxid: 303. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Tetramer (from PQS)
2.20Å     R-factor:   0.235     R-free:   0.315
Authors: S.S.Cha,B.H.Oh,G.H.Nam,D.S.Jang,T.H.Lee,K.Y.Choi
Key ref:
G.H.Nam et al. (2001). Maintenance of alpha-helical structures by phenyl rings in the active-site tyrosine triad contributes to catalysis and stability of ketosteroid isomerase from Pseudomonas putida biotype B. Biochemistry, 40, 13529-13537. PubMed id: 11695900 DOI: 10.1021/bi015547k
05-Oct-01     Release date:   16-Oct-02    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P07445  (SDIS_PSEPU) -  Steroid Delta-isomerase
131 a.a.
121 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Steroid Delta-isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: A 3-oxo-Delta5-steroid = a 3-oxo-Delta4-steroid
= 3-oxo-Delta(4)-steroid
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   1 term 
  Biological process     transport   3 terms 
  Biochemical function     isomerase activity     2 terms  


    Added reference    
DOI no: 10.1021/bi015547k Biochemistry 40:13529-13537 (2001)
PubMed id: 11695900  
Maintenance of alpha-helical structures by phenyl rings in the active-site tyrosine triad contributes to catalysis and stability of ketosteroid isomerase from Pseudomonas putida biotype B.
G.H.Nam, D.S.Jang, S.S.Cha, T.H.Lee, D.H.Kim, B.H.Hong, Y.S.Yun, B.H.Oh, K.Y.Choi.
Ketosteroid isomerase (KSI) from Pseudomonas putida biotype B is a homodimeric enzyme catalyzing an allylic rearrangement of Delta5-3-ketosteroids at rates comparable with the diffusion-controlled limit. The tyrosine triad (Tyr14.Tyr55.Tyr30) forming a hydrogen-bond network in the apolar active site of KSI has been characterized in an effort to identify the roles of the phenyl rings in catalysis, stability, and unfolding of the enzyme. The replacement of Tyr14, a catalytic residue, with serine resulted in a 33-fold decrease of kcat, while the replacements of Tyr30 and Tyr55 with serine decreased kcat by 4- and 51-fold, respectively. The large decrease of kcat for Y55S could be due to the structural perturbation of alpha-helix A3, which results in the reorientation of the active-site residues as judged by the crystal structure of Y55S determined at 2.2 A resolution. Consistent with the analysis of the Y55S crystal structure, the far-UV circular dichroism spectra of Y14S, Y30S, and Y55S indicated that the elimination of the phenyl ring of the tyrosine reduced significantly the content of alpha-helices. Urea-induced equilibrium unfolding experiments revealed that the DeltaG(U)H2O values of Y14S, Y30S, and Y55S were significantly decreased by 11.9, 13.7, and 9.5 kcal/mol, respectively, as compared with that of the wild type. A characterization of the unfolding kinetics based on PhiU-value analysis indicates that the interactions mediated by the tyrosine triad in the native state are very resistant to unfolding. Taken together, our results demonstrate that the internal packing by the phenyl rings in the active-site tyrosine triad contributes to the conformational stability and catalytic activity of KSI by maintaining the structural integrity of the alpha-helices.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20080683 D.A.Kraut, P.A.Sigala, T.D.Fenn, and D.Herschlag (2010).
Dissecting the paradoxical effects of hydrogen bond mutations in the ketosteroid isomerase oxyanion hole.
  Proc Natl Acad Sci U S A, 107, 1960-1965.
PDB code: 3ipt
16689794 I.K.Kim, C.J.Lee, M.K.Kim, J.M.Kim, J.H.Kim, H.S.Yim, S.S.Cha, and S.O.Kang (2006).
Crystal structure of the DNA-binding domain of BldD, a central regulator of aerial mycelium formation in Streptomyces coelicolor A3(2).
  Mol Microbiol, 60, 1179-1193.
PDB code: 2ewt
15819891 Y.S.Yun, G.H.Nam, Y.G.Kim, B.H.Oh, and K.Y.Choi (2005).
Small exterior hydrophobic cluster contributes to conformational stability and steroid binding in ketosteroid isomerase from Pseudomonas putida biotype B.
  FEBS J, 272, 1999-2011.
PDB code: 1w6y
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.