2DW1

Crystal structure of VAP2 from Crotalus atrox venom (Form 2-2 crystal)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of catrocollastatin/VAP2B reveal a dynamic, modular architecture of ADAM/adamalysin/reprolysin family proteins

Igarashi, T.Araki, S.Mori, H.Takeda, S.

(2007) Febs Lett. 581: 2416-2422

  • DOI: 10.1016/j.febslet.2007.04.057
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Catrocollastatin/vascular apoptosis-inducing protein (VAP)2B is a metalloproteinase from Crotalus atrox venom, possessing metalloproteinase/disintegrin/cysteine-rich (MDC) domains that bear the typical domain architecture of a disintegrin and metallo ...

    Catrocollastatin/vascular apoptosis-inducing protein (VAP)2B is a metalloproteinase from Crotalus atrox venom, possessing metalloproteinase/disintegrin/cysteine-rich (MDC) domains that bear the typical domain architecture of a disintegrin and metalloproteinase (ADAM)/adamalysin/reprolysin family proteins. Here we describe crystal structures of catrocollastatin/VAP2B in three different crystal forms, representing the first reported crystal structures of a member of the monomeric class of this family of proteins. The overall structures show good agreement with both monomers of atypical homodimeric VAP1. Comparison of the six catrocollastatin/VAP2B monomer structures and the structures of VAP1 reveals a dynamic, modular architecture that may be important for the functions of ADAM/adamalysin/reprolysin family proteins.


    Related Citations: 
    • Crystallization and preliminary X-ray crystallographic analysis of two vascular apoptosis-inducing proteins (VAPs) from Crotalus atrox venom.
      Igarashi, T.,Oishi, Y.,Araki, S.,Mori, H.,Takeda, S.
      (2006) ACTA CRYSTALLOGR.,SECT.F 62: 688
    • Two vascular apoptosis-inducing proteins from snake venom are members of the metalloprotease/disintegrin family
      Masuda, S.,Hayashi, H.,Araki, S.
      (1998) Eur.J.Biochem. 253: 36
    • Crystal structures of VAP1 reveal ADAMs' MDC domain architecture and its unique C-shaped scaffold
      Takeda, S.,Igarashi, T.,Mori, H.,Araki, S.
      (2006) Embo J. 25: 2388
    • cDNA cloning and some additional peptide characterization of a single-chain vascular apoptosis-inducing protein, VAP2
      Masuda, S.,Maeda, H.,Miao, J.Y.,Hayashi, H.,Araki, S.
      (2007) ENDOTHELIUM 14: 89


    Organizational Affiliation

    Department of Cardiac Physiology, National Cardiovascular Center Research Institute 5-7-1 Fujishiro-dai, Suita, Osaka 565-8565, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Catrocollastatin
A, B
419Crotalus atroxMutation(s): 0 
EC: 3.4.24.-
Find proteins for Q90282 (Crotalus atrox)
Go to UniProtKB:  Q90282
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

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Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
FUC
Query on FUC

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Download CCD File 
B
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
BMA
Query on BMA

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B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
GM6
Query on GM6

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Download CCD File 
A, B
3-(N-HYDROXYCARBOXAMIDO)-2-ISOBUTYLPROPANOYL-TRP-METHYLAMIDE
GM6001
C20 H28 N4 O4
NITYDPDXAAFEIT-DYVFJYSZSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.227 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 57.670α = 90.00
b = 118.180β = 90.00
c = 138.460γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
HKL-2000data reduction
CNSrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-07-10
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance