Crystal structure of Archaemetzincin (AmzA) from Archaeoglobus fulgidus at 1.4 A resolution complexed with malonate

Experimental Data Snapshot

  • Resolution: 1.40 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.144 

Starting Model: experimental
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Crystal Structures of Archaemetzincin Reveal a Moldable Substrate-Binding Site.

Graef, C.Schacherl, M.Waltersperger, S.Baumann, U.

(2012) PLoS One 7: 43863

  • DOI: https://doi.org/10.1371/journal.pone.0043863
  • Primary Citation of Related Structures:  
    3ZVS, 4A3W, 4AXQ

  • PubMed Abstract: 

    Archaemetzincins are metalloproteases occurring in archaea and some mammalia. They are distinct from all the other metzincins by their extended active site consensus sequence HEXXHXXGXXHCX(4)CXMX(17)CXXC featuring four conserved cysteine residues. Very little is known about their biological importance and structure-function relationships. Here we present three crystal structures of the archaemetzincin AfAmzA (Uniprot O29917) from Archaeoglobus fulgidus, revealing a metzincin architecture featuring a zinc finger-like structural element involving the conserved cysteines of the consensus motif. The active sites in all three structures are occluded to different extents rendering the enzymes proteolytically inactive against a large variety of tested substrates. Owing to the different ligand binding there are significant differences in active site architecture, revealing a large flexibility of the loops covering the active site cleft. The crystal structures of AfAmzA provide the structural basis for the lack of activity in standard proteolytic assays and imply a triggered activity onset upon opening of the active site cleft.

  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C
160Archaeoglobus fulgidusMutation(s): 0 
EC: 3
Find proteins for O29917 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16))
Explore O29917 
Go to UniProtKB:  O29917
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO29917
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MLI

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
J [auth B],
M [auth C]
C3 H2 O4
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
H [auth B]
I [auth B]
K [auth C]
D [auth A],
E [auth A],
H [auth B],
I [auth B],
K [auth C],
L [auth C]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.40 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.144 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.302α = 71.39
b = 63.49β = 86.68
c = 64.533γ = 82.67
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-08
    Type: Initial release
  • Version 1.1: 2012-09-12
    Changes: Database references, Other
  • Version 2.0: 2023-12-20
    Changes: Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description