1QUA

CRYSTAL STRUCTURE OF ACUTOLYSIN-C, A HEMORRHAGIC TOXIN FROM THE SNAKE VENOM OF AGKISTRODON ACUTUS, AT 2.2 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.176 

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This is version 1.3 of the entry. See complete history

Literature

Structure of acutolysin-C, a haemorrhagic toxin from the venom of Agkistrodon acutus, providing further evidence for the mechanism of the pH-dependent proteolytic reaction of zinc metalloproteinases.

Zhu, X.Teng, M.Niu, L.

(1999) Acta Crystallogr.,Sect.D 55: 1834-1841

  • DOI: 10.1107/s0907444999010306

  • PubMed Abstract: 
  • The structure of acutolysin-C, a haemorrhagic zinc metalloproteinase from the venom of Agkistrodon acutus, has been analyzed and refined at 2.2 A resolution. The space group of the crystal is P2(1)2(1)2(1), with unit-cell dimensions a = 46.84, b = 49 ...

    The structure of acutolysin-C, a haemorrhagic zinc metalloproteinase from the venom of Agkistrodon acutus, has been analyzed and refined at 2.2 A resolution. The space group of the crystal is P2(1)2(1)2(1), with unit-cell dimensions a = 46.84, b = 49.52, c = 95.34 A. One molecule was found in each asymmetric unit. The phasing problem was solved by the molecular-replacement program AMoRe. Crystallographic refinement was performed using X-PLOR, leading to final R and free R factors of 0.176 and 0.272, respectively. The residue sequence of acutolysin-C was determined mainly by electron density. No density was found for the first residue at the N--terminus and the last two residues at the C-terminus, which was also the case for most other P-I class snake-venom metalloproteinases (SVMPs). Acutolysin-C has two highly conserved characteristic sequences His142-Glu143-X-X-His146-X-X-Gly149-X-X-His15 2 and Cys162-Ile163-Met164. The enzyme has three disulfide bridges: Cys117-Cys195, Cys157-Cys179 and Cys159-Cys162. The entire structure shows good agreement with that of other reported P-I class SVMPs and has two subdomains with a cleft in which one catalytic zinc ion is localized. However, the local conformation (especially the disulfide configurations), the coordination of the catalytic water molecules and some residue side chains differ compared with other P-I class SVMPs. The proteolytic activities of SVMPs are sensitive to the pH value. The molecular superpositions around the proteolytic active sites of all the P-I class SVMP crystal structures show that the distances between the zinc ion and its ligands are not correlated with the crystallization pH values, although the contact distances between the catalytic water molecule and the O atoms of the Glu143 carboxylate group in the neutral and weakly alkaline structures are shorter than those in weakly acidic structures, and the closer the crystallization pH value of one enzyme is to its optimal activity pH value, the shorter the contact distances. Overall, all P-I class SVMPs have similar conformations in the active-site cleft. The size of the active site is not correlated with the crystallization pH values or the proteolytic activities. The disulfide bridge Cys117-Cys195 is conserved in all crystal structures of P-I class SVMPs, whereas the conformation and number of disulfide bridges in the C-terminal subdomain differ. Acutolysin-C has no structural calcium ion, which may not affect the proteolytic activity or haemorrhagic activity directly.


    Related Citations: 
    • Preliminary X-Ray Diffraction Analysis of Hemorrhagin III from the Snake Venom of Agkistrodon Acutus
      Gong, W.,Zhu, Z.,Niu, L.,Teng, M.
      (1996) CHIN.SCI.BULL. 41: 544


    Organizational Affiliation

    Department of Molecular Biology, Laboratory of Structural Biology, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, People's Republic of China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ACUTOLYSIN-C
A
197Deinagkistrodon acutusMutation(s): 0 
EC: 3.4.24.-
Find proteins for P60244 (Deinagkistrodon acutus)
Go to UniProtKB:  P60244
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 46.838α = 90.00
b = 49.524β = 90.00
c = 95.343γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
SCALEPACKdata scaling
AMoREphasing
DENZOdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-07-05
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-04-04
    Type: Data collection