1OPY

KSI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

High-resolution crystal structures of delta5-3-ketosteroid isomerase with and without a reaction intermediate analogue.

Kim, S.W.Cha, S.S.Cho, H.S.Kim, J.S.Ha, N.C.Cho, M.J.Joo, S.Kim, K.K.Choi, K.Y.Oh, B.H.

(1997) Biochemistry 36: 14030-14036

  • DOI: 10.1021/bi971546+
  • Primary Citation of Related Structures:  1OH0, 4TSU
  • Also Cited By: 1W00, 1W01, 1W02

  • PubMed Abstract: 
  • Bacterial Delta5-3-ketosteroid isomerase (KSI) catalyzes a stereospecific isomerization of steroid substrates at an extremely fast rate, overcoming a large disparity of pKa values between a catalytic residue and its target. The crystal structures of ...

    Bacterial Delta5-3-ketosteroid isomerase (KSI) catalyzes a stereospecific isomerization of steroid substrates at an extremely fast rate, overcoming a large disparity of pKa values between a catalytic residue and its target. The crystal structures of KSI from Pseudomonas putida and of the enzyme in complex with equilenin, an analogue of the reaction intermediate, have been determined at 1.9 and 2.5 A resolution, respectively. The structures reveal that the side chains of Tyr14 and Asp99 (a newly identified catalytic residue) form hydrogen bonds directly with the oxyanion of the bound inhibitor in a completely apolar milieu of the active site. No water molecule is found at the active site, and the access of bulk solvent is blocked by a layer of apolar residues. Asp99 is surrounded by six apolar residues, and consequently, its pKa appears to be elevated as high as 9.5 to be consistent with early studies. No interaction was found between the bound inhibitor and the residue 101 (phenylalanine in Pseudomonas testosteroni and methionine in P. putida KSI) which was suggested to contribute significantly to the rate enhancement based on mutational analysis. This observation excludes the residue 101 as a potential catalytic residue and requires that the rate enhancement should be explained solely by Tyr14 and Asp99. Kinetic analyses of Y14F and D99L mutant enzymes demonstrate that Tyr14 contributes much more significantly to the rate enhancement than Asp99. Previous studies and the structural analysis strongly suggest that the low-barrier hydrogen bond of Tyr14 (>7.1 kcal/mol), along with a moderate strength hydrogen bond of Asp99 ( approximately 4 kcal/mol), accounts for the required energy of 11 kcal/mol for the transition-state stabilization.


    Organizational Affiliation

    Department of Life Science and School of Environmental Engineering, Pohang University of Science and Technology, Pohang, Kyungbuk, 790-784, South Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DELTA5-3-KETOSTEROID IOSMERASE
A
131Pseudomonas putidaGene Names: ksi
EC: 5.3.3.1
Find proteins for P07445 (Pseudomonas putida)
Go to UniProtKB:  P07445
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.199 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 36.400α = 90.00
b = 96.120β = 90.00
c = 74.400γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-04-08
    Type: Initial release
  • Version 1.1: 2008-03-04
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance