8TFO

Structure of MKvar


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.208 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Characterization of novel mevalonate kinases from the tardigrade Ramazzottius varieornatus and the psychrophilic archaeon Methanococcoides burtonii.

Esquirol, L.Newman, J.Nebl, T.Scott, C.Vickers, C.Sainsbury, F.Peat, T.S.

(2024) Acta Crystallogr D Struct Biol 80: 203-215

  • DOI: https://doi.org/10.1107/S2059798324001360
  • Primary Citation of Related Structures:  
    8TEB, 8TFO

  • PubMed Abstract: 

    Mevalonate kinase is central to the isoprenoid biosynthesis pathway. Here, high-resolution X-ray crystal structures of two mevalonate kinases are presented: a eukaryotic protein from Ramazzottius varieornatus and an archaeal protein from Methanococcoides burtonii. Both enzymes possess the highly conserved motifs of the GHMP enzyme superfamily, with notable differences between the two enzymes in the N-terminal part of the structures. Biochemical characterization of the two enzymes revealed major differences in their sensitivity to geranyl pyrophosphate and farnesyl pyrophosphate, and in their thermal stabilities. This work adds to the understanding of the structural basis of enzyme inhibition and thermostability in mevalonate kinases.


  • Organizational Affiliation

    Environment, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT 2601, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mevalonate kinase
A, B
416Ramazzottius varieornatusMutation(s): 0 
Gene Names: RvY_15762-1
EC: 2.7.1.36
UniProt
Find proteins for A0A1D1VW28 (Ramazzottius varieornatus)
Explore A0A1D1VW28 
Go to UniProtKB:  A0A1D1VW28
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1D1VW28
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.081α = 90
b = 80.705β = 90
c = 207.467γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government--

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-13
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Structure summary