4GJJ

Crystal structure of Pseudomonas stutzeri L-rhamnose isomerase mutant H101N in complex with D-allopyranose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 3.0 of the entry. See complete history

Literature

Structure of l-rhamnose isomerase in complex with l-rhamnopyranose demonstrates the sugar-ring opening mechanism and the role of a substrate sub-binding site.

Yoshida, H.Yoshihara, A.Teraoka, M.Yamashita, S.Izumori, K.Kamitori, S.

(2013) FEBS Open Bio 3: 35-40

  • DOI: 10.1016/j.fob.2012.11.008
  • Primary Citation of Related Structures:  4GJI

  • PubMed Abstract: 
  • l-Rhamnose isomerase (l-RhI) catalyzes the reversible isomerization of l-rhamnose to l-rhamnulose. Previously determined X-ray structures of l-RhI showed a hydride-shift mechanism for the isomerization of substrates in a linear form, but the mechanis ...

    l-Rhamnose isomerase (l-RhI) catalyzes the reversible isomerization of l-rhamnose to l-rhamnulose. Previously determined X-ray structures of l-RhI showed a hydride-shift mechanism for the isomerization of substrates in a linear form, but the mechanism for opening of the sugar-ring is still unclear. To elucidate this mechanism, we determined X-ray structures of a mutant l-RhI in complex with l-rhamnopyranose and d-allopyranose. Results suggest that a catalytic water molecule, which acts as an acid/base catalyst in the isomerization reaction, is likely to be involved in pyranose-ring opening, and that a newly found substrate sub-binding site in the vicinity of the catalytic site may recognize different anomers of substrates.


    Related Citations: 
    • 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
    • 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
    • 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


    Organizational Affiliation

    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 isomerase
A, B, C, D
438Pseudomonas stutzeriGene Names: L-RhI
Find proteins for Q75WH8 (Pseudomonas stutzeri)
Go to UniProtKB:  Q75WH8
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B, C, D
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
AOS
Query on AOS

Download SDF File 
Download CCD File 
A, C, D
D-ALLOSE
C6 H12 O6
GZCGUPFRVQAUEE-BGPJRJDNSA-N
 Ligand Interaction
AFD
Query on AFD

Download SDF File 
Download CCD File 
B
Alpha-D-Allopyranose
C6 H12 O6
WQZGKKKJIJFFOK-UKFBFLRUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 74.650α = 90.00
b = 104.381β = 107.91
c = 113.972γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
CNSrefinement
MOLREPphasing
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-12-12
    Type: Initial release
  • Version 1.1: 2014-05-28
    Type: Database references
  • Version 2.0: 2017-11-15
    Type: Advisory, Atomic model, Structure summary
  • Version 3.0: 2017-11-22
    Type: Advisory, Atomic model, Derived calculations