4BG9

Apo form of a putative sugar kinase MK0840 from Methanopyrus kandleri (orthorhombic space group)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural Characterization of the Ribonuclease H-Like Type Askha Superfamily Kinase Mk0840 from Methanopyrus Kandleri

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

(2013) Acta Crystallogr D Biol Crystallogr 69: 2440

  • DOI: https://doi.org/10.1107/S0907444913022683
  • Primary Citation of Related Structures:  
    4BG8, 4BG9, 4BGA, 4BGB

  • PubMed Abstract: 

    Murein recycling is a process in which microorganisms recover peptidoglycan-degradation products in order to utilize them in cell wall biosynthesis or basic metabolic pathways. Methanogens such as Methanopyrus kandleri contain pseudomurein, which differs from bacterial murein in its composition and branching. Here, four crystal structures of the putative sugar kinase MK0840 from M. kandleri in apo and nucleotide-bound states are reported. MK0840 shows high similarity to bacterial anhydro-N-acetylmuramic acid kinase, which is involved in murein recycling. The structure shares a common fold with panthothenate kinase and the 2-hydroxyglutaryl-CoA dehydratase component A, both of which are members of the ASKHA (acetate and sugar kinases/Hsc70/actin) superfamily of phosphotransferases. Local conformational changes in the nucleotide-binding site between the apo and holo forms are observed upon nucleotide binding. Further insight is given into domain movements and putative active-site residues are identified.


  • Organizational Affiliation

    Institute of Biochemistry, University of Cologne, Otto-Fischer-Strasse 12-14, 50674 Cologne, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PREDICTED MOLECULAR CHAPERONE DISTANTLY RELATED TO HSP70-F OLD METALLOPROTEASES361Methanopyrus kandleri AV19Mutation(s): 0 
UniProt
Find proteins for Q8TX37 (Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938))
Explore Q8TX37 
Go to UniProtKB:  Q8TX37
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TX37
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.043α = 90
b = 115.967β = 90
c = 48.363γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-27
    Type: Initial release
  • Version 1.1: 2013-12-18
    Changes: Database references
  • Version 1.2: 2019-03-06
    Changes: Data collection, Derived calculations, Experimental preparation, Other
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description