PDBsum entry: 1dmq

Isomerase

PDB id: 1dmq

Contents

Protein chain

123 a.a. *

Waters ×47

* Residue conservation analysis

PDB id:

1dmq

Name:

Isomerase

Title:

Crystal structure of mutant enzyme y32f of ketosteroid isomerase from pseudomonas putida biotype b

Structure:

Steroid delta-isomerase. Chain: a. Engineered: yes. Mutation: yes

Source:

Pseudomonas putida. Organism_taxid: 303. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PDB file)

Resolution:

2.15Å R-factor: 0.182 R-free: 0.234

Authors:

D.H.Kim,D.S.Jang,G.H.Nam,B.H.Oh,K.Y.Choi

Key ref:

D.H.Kim et al. (2000). Contribution of the hydrogen-bond network involving a tyrosine triad in the active site to the structure and function of a highly proficient ketosteroid isomerase from Pseudomonas putida biotype B. Biochemistry, 39, 4581-4589. PubMed id: 10769113 DOI: 10.1021/bi992119u

Date:

14-Dec-99 Release date: 23-May-00

Protein chain

P07445  (SDIS_PSEPU) -  Steroid Delta-isomerase

Seq: 131 a.a.

Struc: 123 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.5.3.3.1 - Steroid Delta-isomerase.
• Reaction: A 3-oxo-Delta₅-steroid = a 3-oxo-Delta₄-steroid

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Cellular component: intracellular (1 term)
• Biological process: transport (3 terms)
• Biochemical function: isomerase activity (2 terms)

Added reference

DOI no: 10.1021/bi992119u

Biochemistry 39:4581-4589 (2000)

PubMed id: 10769113

Contribution of the hydrogen-bond network involving a tyrosine triad in the active site to the structure and function of a highly proficient ketosteroid isomerase from Pseudomonas putida biotype B.

D.H.Kim, D.S.Jang, G.H.Nam, G.Choi, J.S.Kim, N.C.Ha, M.S.Kim, B.H.Oh, K.Y.Choi.

ABSTRACT

Delta(5)-3-Ketosteroid isomerase from Pseudomonas putida biotype B is one of the most proficient enzymes catalyzing an allylic isomerization reaction at rates comparable to the diffusion limit. The hydrogen-bond network (Asp99... Wat504...Tyr14...Tyr55...Tyr30) which links the two catalytic residues, Tyr14 and Asp99, to Tyr30, Tyr55, and a water molecule in the highly apolar active site has been characterized in an effort to identify its roles in function and stability. The DeltaG(U)(H2O) determined from equilibrium unfolding experiments reveals that the elimination of the hydroxyl group of Tyr14 or Tyr55 or the replacement of Asp99 with leucine results in a loss of conformational stability of 3.5-4.4 kcal/mol, suggesting that the hydrogen bonds of Tyr14, Tyr55, and Asp99 contribute significantly to stability. While decreasing the stability by about 6.5-7.9 kcal/mol, the Y55F/D99L or Y30F/D99L double mutation also reduced activity significantly, exhibiting a synergistic effect on k(cat) relative to the respective single mutations. These results indicate that the hydrogen-bond network is important for both stability and function. Additionally, they suggest that Tyr14 cannot function efficiently alone without additional support from the hydrogen bonds of Tyr55 and Asp99. The crystal structure of Y55F as determined at 1.9 A resolution shows that Tyr14 OH undergoes an alteration in orientation to form a new hydrogen bond with Tyr30. This observation supports the role of Tyr55 OH in positioning Tyr14 properly to optimize the hydrogen bond between Tyr14 and C3-O of the steroid substrate. No significant structural changes were observed in the crystal structures of Y30F and Y30F/Y55F, which allowed us to estimate approximately the interaction energies mediated by the hydrogen bonds Tyr30...Tyr55 and Tyr14...Tyr55. Taken together, our results demonstrate that the hydrogen-bond network provides the structural support that is needed for the enzyme to maintain the active-site geometry optimized for both function and stability.