4AXQ | pdb_00004axq

CRYSTAL STRUCTURE OF ARCHAEMETZINCIN (AMZA) FROM ARCHAEOGLOBUS FULGIDUS AT 1.4 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb4AXQ/pdb
• Entry: 4AXQ supersedes: 2XHQ

• Classification: HYDROLASE
• Organism(s): Archaeoglobus fulgidus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-06-13 Released: 2012-06-27 
• Deposition Author(s): Graef, C., Schacherl, M., Baumann, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.186 (Depositor), 0.192 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

Crystal Structures of Archaemetzincin Reveal a Moldable Substrate-Binding Site.

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

(2012) PLoS One 7: 43863

• PubMed: 22937112 
• DOI: https://doi.org/10.1371/journal.pone.0043863
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 18.33 kDa 
• Atom Count: 1,609 
• Modeled Residue Count: 163 
• Deposited Residue Count: 163 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ARCHAEMETZINCIN	A	163	Archaeoglobus fulgidus	Mutation(s): 0  EC: 3 (PDB Primary Data), 3.4 (UniProt)
UniProt
Find proteins for O29917 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O29917  Go to UniProtKB:  O29917

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.186 (Depositor), 0.192 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.339	α = 90
b = 88.339	β = 90
c = 50.275	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-27 
Deposition Author(s): Graef, C., Schacherl, M., Baumann, U.
• This entry supersedes: 2XHQ

Revision History  

• Version 1.0: 2012-06-27
  Type: Initial release
  
• Version 1.1: 2012-09-12
  Changes: Database references
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary