3CIA

Crystal structure of cold-aminopeptidase from Colwellia psychrerythraea


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.249 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structure of the Cold-active Aminopeptidase from Colwellia psychrerythraea, a Close Structural Homologue of the Human Bifunctional Leukotriene A4 Hydrolase.

Bauvois, C.Jacquamet, L.Huston, A.L.Borel, F.Feller, G.Ferrer, J.L.

(2008) J.Biol.Chem. 283: 23315-23325

  • DOI: 10.1074/jbc.M802158200

  • PubMed Abstract: 
  • The crystal structure of a cold-active aminopeptidase (ColAP) from Colwellia psychrerythraea strain 34H has been determined, extending the number of crystal structures of the M1 metallopeptidase family to four among the 436 members currently identifi ...

    The crystal structure of a cold-active aminopeptidase (ColAP) from Colwellia psychrerythraea strain 34H has been determined, extending the number of crystal structures of the M1 metallopeptidase family to four among the 436 members currently identified. In agreement with their sequence similarity, the overall structure of ColAP displayed a high correspondence with leukotriene A4 hydrolase (LTA4H), a human bifunctional enzyme that converts leukotriene A4 (LTA4) in the potent chemoattractant leukotriene B4. Indeed, both enzymes are composed of three domains, an N-terminal saddle-like domain, a catalytic thermolysin-like domain, and a less conserved C-terminal alpha-helical flat spiral domain. Together, these domains form a deep cavity harboring the zinc binding site formed by residues included in the conserved HEXXHX(18)H motif. A detailed structural comparison of these enzymes revealed several plausible determinants of ColAP cold adaptation. The main differences involve specific amino acid substitutions, loop content and solvent exposure, complexity and distribution of ion pairs, and differential domain flexibilities. Such elements may act synergistically to allow conformational flexibility needed for an efficient catalysis in cold environments. Furthermore, the region of ColAP corresponding to the aminopeptidase active site of LTA4H is much more conserved than the suggested LTA4 substrate binding region. This observation supports the hypothesis that this region of the LTA4H active site has evolved in order to fit the lipidic substrate.


    Organizational Affiliation

    Laboratoire de Microbiologie, Université Libre de Bruxelles, B-1070 Bruxelles, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cold-active aminopeptidase
A, B, C, D
605Colwellia psychrerythraea (strain 34H / ATCC BAA-681)Mutation(s): 0 
Find proteins for Q7WVY1 (Colwellia psychrerythraea (strain 34H / ATCC BAA-681))
Go to UniProtKB:  Q7WVY1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.249 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 81.370α = 88.83
b = 87.100β = 70.68
c = 116.360γ = 88.43
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance