2ISA

Crystal Structure of Vibrio salmonicida catalase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The first structure of a cold-active catalase from Vibrio salmonicida at 1.96A reveals structural aspects of cold adaptation

Riise, E.K.Lorentzen, M.S.Helland, R.Smalas, A.O.Leiros, H.K.S.Willassen, N.P.

(2007) Acta Crystallogr D Biol Crystallogr 63: 135-148

  • DOI: 10.1107/S0907444906043812
  • Primary Citation of Related Structures:  
    2ISA

  • PubMed Abstract: 
  • The cold-adapted catalase from the fish-pathogenic bacterium Vibrio salmonicida (VSC) has recently been characterized and shown to be two times more catalytically efficient compared with catalase from the mesophilic human pathogen Proteus mirabilis [ ...

    The cold-adapted catalase from the fish-pathogenic bacterium Vibrio salmonicida (VSC) has recently been characterized and shown to be two times more catalytically efficient compared with catalase from the mesophilic human pathogen Proteus mirabilis [PMC; Lorentzen et al. (2006), Extremophiles, 10, 427-440]. VSC is also less temperature-stable, with a half-life of 5 min at 333 K compared with 50 min for PMC. This was the background for solving the crystal structure of the cold-adapted VSC to 1.96 A and performing an extensive structural comparison of VSC and PMC. The comparison revealed that the entrance (the major channel) leading to the catalytically essential haem group, is locally more flexible and slightly wider in VSC. This might explain the enhanced catalytic efficiency of the nearly diffusion-controlled degradation of hydrogen peroxide into water and molecular oxygen in VSC. The reduced thermal stability of the cold-adapted VSC may be explained by a reduced number of ion-pair networks. The four C-terminal alpha-helices are displaced in the structures, probably owing to missing ionic interactions in VSC compared with PMC, and this is postulated as an initiation site for unfolding the cold-adapted enzyme. VSC is the first crystal structure reported of a cold-adapted monofunctional haem-containing catalase.


    Organizational Affiliation

    The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, Faculty of Science, University of Tromsø, N-9037 Tromsø, Norway.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CatalaseABCDEFGH483Aliivibrio salmonicida LFI1238Mutation(s): 1 
Gene Names: catAVSAL_II0215
EC: 1.11.1.6
Find proteins for Q3LSM1 (Aliivibrio salmonicida (strain LFI1238))
Explore Q3LSM1 
Go to UniProtKB:  Q3LSM1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download CCD File 
A, B, C, D, E, F, G, H
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A, B, C, D, E, F, G, H
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
B, D, F, H
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OMT
Query on OMT
A,B,C,D,E,F,G,HL-PEPTIDE LINKINGC5 H11 N O4 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.151 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.15α = 90
b = 217.76β = 110.48
c = 99.28γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MAR345data collection
XDSdata reduction
CCP4data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-01-23
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Advisory, Refinement description