Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 31.77 kDa 
• Atom Count: 2542 
• Modelled Residue Count: 271 
• Deposited Residue Count: 282 
• Unique protein chains: 1

1IUP

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

• PDB DOI: 10.2210/pdb1IUP/pdb

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


• 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.

---

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 

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:  
  1IUN, 1IUO, 1IUP


• 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.

---

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. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
meta-Cleavage product hydrolase	A	282	Pseudomonas fluorescens	Mutation(s): 1  Gene Names: cumD EC: 3.7.1.9
UniProt
Find proteins for P96965 (Pseudomonas fluorescens) Explore P96965  Go to UniProtKB:  P96965

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ALQ	B [auth A], C [auth A], D [auth A]	2-METHYL-PROPIONIC ACID C4 H8 O2 KQNPFQTWMSNSAP-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ALQ	Binding MOAD:  1IUP	Ki: 2.90e+6 (nM) from 1 assay(s)

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 = 77.35	α = 90
b = 116.584	β = 90
c = 78.721	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
CNS	refinement
MOSFLM	data reduction
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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-10
  Changes: Database references, Derived calculations