1UKA

Crystal structure of a meta-cleavage product hydrolase (CumD) complexed with (S)-2-methylbutyrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A Series of Crystal Structures of a meta-Cleavage Product Hydrolase from Pseudomonas fluorescens IP01 (CumD) Complexed with Various Cleavage Products

Fushinobu, S.Jun, S.-Y.Hidaka, M.Nojiri, H.Yamane, H.Shoun, H.Omori, T.Wakagi, T.

(2005) BIOSCI.BIOTECHNOL.BIOCHEM. 69: 491-498

  • DOI: 10.1271/bbb.69.491
  • Primary Citation of Related Structures:  
  • Also Cited By: 2D0D

  • PubMed Abstract: 
  • Meta-cleavage product hydrolase (MCP-hydrolase) is one of the key enzymes in the microbial degradation of aromatic compounds. MCP-hydrolase produces 2-hydroxypenta-2,4-dienoate and various organic acids, according to the C6 substituent of the substra ...

    Meta-cleavage product hydrolase (MCP-hydrolase) is one of the key enzymes in the microbial degradation of aromatic compounds. MCP-hydrolase produces 2-hydroxypenta-2,4-dienoate and various organic acids, according to the C6 substituent of the substrate. Comprehensive analysis of the substrate specificity of the MCP-hydrolase from Pseudomonas fluorescens IP01 (CumD) was carried out by determining the kinetic parameters for nine substrates and crystal structures complexed with eight cleavage products. CumD preferred substrates with long non-branched C6 substituents, but did not effectively hydrolyze a substrate with a phenyl group. Superimposition of the complex structures indicated that benzoate was bound in a significantly different direction than other aliphatic cleavage products. The directions of the bound organic acids appeared to be related with the k(cat) values of the corresponding substrates. The Ile139 and Trp143 residues on helix alpha4 appeared to cause steric hindrance with the aromatic ring of the substrate, which hampers base-catalyzed attack by water.


    Organizational Affiliation

    Department of Biotechnology, The University of Tokyo, Japan. asfushi@mail.ecc.u-tokyo.ac.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2-hydroxy-6-oxo-7-methylocta-2,4-dienoate hydrolase
A
282Pseudomonas fluorescensMutation(s): 1 
Gene Names: cumD
Find proteins for P96965 (Pseudomonas fluorescens)
Go to UniProtKB:  P96965
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SMB
Query on SMB

Download SDF File 
Download CCD File 
A
2-METHYLBUTANOIC ACID
C5 H10 O2
WLAMNBDJUVNPJU-BYPYZUCNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.179 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 77.019α = 90.00
b = 116.444β = 90.00
c = 78.562γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
CNSphasing
CNSrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-09-14
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance