1IUP

meta-Cleavage product hydrolase from Pseudomonas fluorescens IP01 (CumD) S103A mutant complexed with isobutyrates


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structures of a meta-cleavage product hydrolase from Pseudomonas fluorescens IP01 (CumD) complexed with cleavage products

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

(2002) Protein Sci 11: 2184-2195

  • DOI: 10.1110/ps.0209602
  • Primary Citation of Related Structures:  
    1IUP, 1IUO, 1IUN

  • PubMed Abstract: 
  • 2-Hydroxy-6-oxo-7-methylocta-2,4-dienoate hydrolase (CumD) from Pseudomonas fluorescens IP01 hydrolyzes a meta-cleavage product generated in the cumene (isopropylbenzene) degradation pathway. The crystal structures of the inactive S103A mutant of the CumD enzyme complexed with isobutyrate and acetate ions were determined at 1 ...

    2-Hydroxy-6-oxo-7-methylocta-2,4-dienoate hydrolase (CumD) from Pseudomonas fluorescens IP01 hydrolyzes a meta-cleavage product generated in the cumene (isopropylbenzene) degradation pathway. The crystal structures of the inactive S103A mutant of the CumD enzyme complexed with isobutyrate and acetate ions were determined at 1.6 and 2.0 A resolution, respectively. The isobutyrate and acetate ions were located at the same position in the active site, and occupied the site for a part of the hydrolysis product with CumD, which has the key determinant group for the substrate specificity of related hydrolases. One of the oxygen atoms of the carboxyl group of the isobutyrate ion was hydrogen bonded with a water molecule and His252. Another oxygen atom of the carboxyl group was situated in an oxyanion hole formed by the two main-chain N atoms. The isopropyl group of the isobutyric acid was recognized by the side-chains of the hydrophobic residues. The substrate-binding pocket of CumD was long, and the inhibition constants of various organic acids corresponded well to it. In comparison with the structure of BphD from Rhodococcus sp. RHA1, the structural basis for the substrate specificity of related hydrolases, is revealed.


    Related Citations: 
    • Purification, characterization, and steady-state kinetics of a meta-cleavage compound hydrolase from Pseudomonas fluorescens IP01
      Saku, T., Fushinobu, S., Jun, S.-Y., Ikeda, N., Nojiri, H., Yamane, H., Omori, T., Wakagi, T.
      (2002) J Biosci Bioeng 93: 568
    • Analysis of cumene (isopropylbenzene) degradation genes from Pseudomonas fluorescens IP01
      Habe, H., Kasuga, K., Nojiri, H., Yamane, H., Omori, T.
      (1996) Appl Environ Microbiol 62: 4471

    Organizational Affiliation

    Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan. asfushi@mail.ecc.u-tokyo.ac.jp



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
meta-Cleavage product hydrolaseA282Pseudomonas fluorescensMutation(s): 1 
Gene Names: cumD
EC: 3.7.1.9
Find proteins for P96965 (Pseudomonas fluorescens)
Explore P96965 
Go to UniProtKB:  P96965
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ALQ
Query on ALQ

Download Ideal Coordinates CCD File 
B [auth A], C [auth A], D [auth A]2-METHYL-PROPIONIC ACID
C4 H8 O2
KQNPFQTWMSNSAP-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ISBKi :  2900000   nM  PDBBind
ALQKi:  2900000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.35α = 90
b = 116.584β = 90
c = 78.721γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
CNSrefinement
MOSFLMdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-09-18
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance