1BUD

ACUTOLYSIN A FROM SNAKE VENOM OF AGKISTRODON ACUTUS AT PH 5.0


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structures of acutolysin A, a three-disulfide hemorrhagic zinc metalloproteinase from the snake venom of Agkistrodon acutus.

Gong, W.Zhu, X.Liu, S.Teng, M.Niu, L.

(1998) J.Mol.Biol. 283: 657-668

  • DOI: 10.1006/jmbi.1998.2110
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Acutolysin A alias AaHI, a 22 kDa hemorrhagic toxin isolated from the snake venom of Agkistrodon acutus, is a member of the adamalysin subfamily of the metzincin family and is a snake venom zinc metalloproteinase possessing only one catalytic domain. ...

    Acutolysin A alias AaHI, a 22 kDa hemorrhagic toxin isolated from the snake venom of Agkistrodon acutus, is a member of the adamalysin subfamily of the metzincin family and is a snake venom zinc metalloproteinase possessing only one catalytic domain. Acutolysin A was found to have a high-activity and a low-activity under weakly alkaline and acidic conditions, respectively. With the adamalysin II structure as the initial trial-and-error model, the crystal structures were solved to the final crystallographic R-factors of 0. 168 and 0.171, against the diffraction data of crystals grown under pH 5.0 and pH 7.5 conditions to 1.9 A and 1.95 A resolution, respectively. One zinc ion, binding in the active-site, one structural calcium ion and some water molecules were localized in both of the structures. The catalytic zinc ion is coordinated in a tetrahedral manner with one catalytic water molecule anchoring to an intermediate glutamic acid residue (Glu143) and three imidazole Nepsilon2 atoms of His142, His146 and His152 in the highly conserved sequence H142E143XXH146XXGXXH152. There are two new disulfide bridges (Cys157-Cys181 and Cys159-Cys164) in acutolysin A in addition to the highly conserved disulfide bridge Cys117-Cys197. The calcium ion occurs on the molecular surface. The superposition showed that there was no significant conformational changes between the two structures except for a few slight changes of some flexible residue side-chains on the molecular surface, terminal residues and the active-site cleft. The average contact distance between the catalytic water molecule and oxygen atoms of the Glu143 carboxylate group in the weakly alkaline structure was also found to be closer than that in the weakly acidic structure. By comparing the available structural information of the members of the adamalysin subfamily, it seems that, when lowering the pH value, the polarization capability of the Glu143 carboxylate group to the catalytic water molecule become weaker, which might be the structural reason why the snake venom metalloproteinases are inactive or have a low activity under acidic conditions.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Diffraction Studies of Haehorrhagin I from the Snake Venom of Agkistrodon Acutus
      Gong, W.,Zhu, Z.,Niu, L.,Teng, M.
      (1996) Acta Crystallogr.,Sect.D 52: 201


    Organizational Affiliation

    Department of Molecular Biology and Cell Biology and Laboratory of Structural Biology, School of Life Science, University of Science and Technology of China, Hefei, Anhui, 230026, P.R. China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (ACUTOLYSIN A)
A
197Deinagkistrodon acutusMutation(s): 0 
EC: 3.4.24.-
Find proteins for Q9PW35 (Deinagkistrodon acutus)
Go to UniProtKB:  Q9PW35
Small Molecules
Ligands 2 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
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Work: 0.169 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 63.470α = 90.00
b = 63.470β = 90.00
c = 95.490γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORphasing
SCALEPACKdata scaling
X-PLORrefinement
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-09-07
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-04-04
    Type: Data collection