6HRG

Structure of Igni18, a novel metallo hydrolase from the hyperthermophilic archaeon Ignicoccus hospitalis KIN4/I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A promiscuous ancestral enzyme s structure unveils protein variable regions of the highly diverse metallo-beta-lactamase family.

Perez-Garcia, P.Kobus, S.Gertzen, C.G.W.Hoeppner, A.Holzscheck, N.Strunk, C.H.Huber, H.Jaeger, K.E.Gohlke, H.Kovacic, F.Smits, S.H.J.Streit, W.R.Chow, J.

(2021) Commun Biol 4: 132-132

  • DOI: https://doi.org/10.1038/s42003-021-01671-8
  • Primary Citation of Related Structures:  
    6HRG

  • PubMed Abstract: 

    The metallo-β-lactamase fold is an ancient protein structure present in numerous enzyme families responsible for diverse biological processes. The crystal structure of the hyperthermostable crenarchaeal enzyme Igni18 from Ignicoccus hospitalis was solved at 2.3 Å and could resemble a possible first archetype of a multifunctional metallo-β-lactamase. Ancestral enzymes at the evolutionary origin are believed to be promiscuous all-rounders. Consistently, Igni18´s activity can be cofactor-dependently directed from β-lactamase to lactonase, lipase, phosphodiesterase, phosphotriesterase or phospholipase. Its core-domain is highly conserved within metallo-β-lactamases from Bacteria, Archaea and Eukarya and gives insights into evolution and function of enzymes from this superfamily. Structural alignments with diverse metallo-β-lactamase-fold-containing enzymes allowed the identification of Protein Variable Regions accounting for modulation of activity, specificity and oligomerization patterns. Docking of different substrates within the active sites revealed the basis for the crucial cofactor dependency of this enzyme superfamily.


  • Organizational Affiliation

    Department of Microbiology and Biotechnology, University of Hamburg, Ohnhorststrasse 18, 22609, Hamburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UPF0173 metal-dependent hydrolase Igni_1254261Ignicoccus hospitalisMutation(s): 0 
Gene Names: Igni_1254
UniProt
Find proteins for A8ABX8 (Ignicoccus hospitalis (strain KIN4/I / DSM 18386 / JCM 14125))
Explore A8ABX8 
Go to UniProtKB:  A8ABX8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8ABX8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.189 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.42α = 90
b = 67.42β = 90
c = 253.77γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-09
    Type: Initial release
  • Version 1.1: 2021-03-17
    Changes: Database references, Derived calculations