3M0H

Crystal structure of Pseudomonas stutzeri L-rhamnose isomerase mutant S329F in complex with L-rhamnose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Elucidation of the role of Ser329 and the C-terminal region in the catalytic activity of Pseudomonas stutzeri L-rhamnose isomerase

Yoshida, H.Takeda, K.Izumori, K.Kamitori, S.

(2010) Protein Eng Des Sel 23: 919-927

  • DOI: 10.1093/protein/gzq077
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Pseudomonas stutzeri l-rhamnose isomerase (l-RhI) is capable of catalyzing the isomerization between various aldoses and ketoses, showing high catalytic activity with broad substrate-specificity compared with Escherichia coli l-RhI. In a previous stu ...

    Pseudomonas stutzeri l-rhamnose isomerase (l-RhI) is capable of catalyzing the isomerization between various aldoses and ketoses, showing high catalytic activity with broad substrate-specificity compared with Escherichia coli l-RhI. In a previous study, the crystal structure of P. stutzeri l-RhI revealed an active site comparable with that of E. coli l-RhI and d-xylose isomerases (d-XIs) with structurally conserved amino acids, but also with a different residue seemingly responsible for the specificity of P. stutzeri l-RhI, though the residue itself does not interact with the bound substrate. This residue, Ser329, corresponds to Phe336 in E. coli l-RhI and Lys294 in Actinoplanes missouriensis d-XI. To elucidate the role of Ser329 in P. stutzeri l-RhI, we constructed mutants, S329F (E. coli l-RhI type), S329K (A. missouriensis d-XI type), S329L and S329A. Analyses of the catalytic activity and crystal structure of the mutants revealed a hydroxyl group of Ser329 to be crucial for catalytic activity via interaction with a water molecule. In addition, in complexes with substrate, the mutants S329F and S329L exhibited significant electron density in the C-terminal region not observed in the wild-type P. stutzeri l-RhI. The C-terminal region of P. stutzeri l-RhI has flexibility and shows a flip-flop movement at the inter-molecular surface of the dimeric form.


    Related Citations: 
    • The structures of L-rhamnose isomerase from Pseudomonas stutzeri in complexes with L-rhamnose and D-allose provide insights into broad substrate specificity
      Yoshida, H., Yamada, M., Ohyama, Y., Takada, G., Izumori, K., Kamitori, S.
      (2007) J Mol Biol 365: 1505
    • Catalytic reaction mechanism of Pseudomonas stutzeri L-rhamnose isomerase deduced from X-ray structures
      Yoshida, H., Yamaji, M., Ishii, T., Izumori, K., Kamitori, S.
      (2010) FEBS J 277: 1045

    Organizational Affiliation

    Division of Structural Biology, Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
L-rhamnose isomeraseA, B, C, D438Pseudomonas stutzeriMutation(s): 2 
Gene Names: L-RhI
EC: 5.3.1.14
Find proteins for Q75WH8 (Pseudomonas stutzeri)
Explore Q75WH8 
Go to UniProtKB:  Q75WH8
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RNS
Query on RNS

Download CCD File 
A, B, C, D
L-RHAMNOSE
C6 H12 O5
PNNNRSAQSRJVSB-BXKVDMCESA-N
 Ligand Interaction
MN
Query on MN

Download CCD File 
A, B, C, D
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.161 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.476α = 90
b = 104.457β = 107.26
c = 108.2γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance