Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 31770.92 
• Atom Count: 2157 
• Residue Count: 282 
• Unique protein chains: 1

1IUP

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

• DOI: 10.2210/pdb1IUP/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas fluorescens
• Expression System: Escherichia coli
• Mutation(s): 1 


• Deposited: 2002-03-06 Released: 2002-09-18 
• Deposition Author(s): Fushinobu, S., Saku, T., Hidaka, M., Jun, S.-Y., Nojiri, H., Yamane, H., Shoun, H., Omori, T., Wakagi, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.6 Å
• R-Value Free: 0.219 
• R-Value Work: 0.188 

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

• PubMed: 12192074 
• DOI: 10.1110/ps.0209602
• Primary Citation of Related Structures:  
  1IUO, 1IUN
• Also Cited By: 2D0D


• 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 1.6 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.

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Related Citations: 

• 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
• 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




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Organizational Affiliation: 

Department of Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
meta-Cleavage product hydrolase	A	282	Pseudomonas fluorescens	Mutation(s): 1  Gene Names: cumD
Find proteins for P96965 (Pseudomonas fluorescens) Go to UniProtKB:  P96965

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ALQ	A	2-METHYL-PROPIONIC ACID C4 H8 O2 KQNPFQTWMSNSAP-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
ALQ	Ki: 2900000 nM BINDINGMOAD
ISB	Ki: 2900000 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.6 Å
• R-Value Free: 0.219 
• R-Value Work: 0.188 
• Space Group: C 2 2 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 77.350	α = 90.00
b = 116.584	β = 90.00
c = 78.721	γ = 90.00

Software Package:

Software Name	Purpose
MOSFLM	data reduction
CNS	refinement
MOLREP	phasing
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-03-06 
• Released Date: 2002-09-18 
• Deposition Author(s): Fushinobu, S., Saku, T., Hidaka, M., Jun, S.-Y., Nojiri, H., Yamane, H., Shoun, H., Omori, T., Wakagi, T.

Revision History 

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