6C07

Crystal Structure of S-Adenosylmethionine synthetase (MetK/Mat) from Cryptosporidium parvum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.160 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of a critical metabolic enzyme: S-adenosylmethionine synthetase from Cryptosporidium parvum.

Ohren, J.Parungao, G.G.Viola, R.E.

(2019) Acta Crystallogr F Struct Biol Commun 75: 290-298

  • DOI: https://doi.org/10.1107/S2053230X19002772
  • Primary Citation of Related Structures:  
    6C07

  • PubMed Abstract: 

    S-Adenosyl-L-methionine (AdoMet), the primary methyl donor in most biological methylation reactions, is produced from ATP and methionine in a multistep reaction catalyzed by AdoMet synthetase. The diversity of group-transfer reactions that involve AdoMet places this compound at a key crossroads in amino-acid, nucleic acid and lipid metabolism, and disruption of its synthesis has adverse consequences for all forms of life. The family of AdoMet synthetases is highly conserved, and structures of this enzyme have been determined from organisms ranging from bacteria to humans. Here, the structure of an AdoMet synthetase from the infectious parasite Cryptosporidium parvum has been determined as part of an effort to identify structural differences in this enzyme family that can guide the development of species-selective inhibitors. This enzyme form has a less extensive subunit interface than some previously determined structures, and contains some key structural differences from the human enzyme in an allosteric site, presenting an opportunity for the design of selective inhibitors against the AdoMet synthetase from this organism.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
S-adenosylmethionine synthase
A, B, C, D
406Cryptosporidium parvum Iowa IIMutation(s): 0 
Gene Names: cgd7_2650
EC: 2.5.1.6
UniProt
Find proteins for Q5CYE4 (Cryptosporidium parvum (strain Iowa II))
Explore Q5CYE4 
Go to UniProtKB:  Q5CYE4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5CYE4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download Ideal Coordinates CCD File 
J [auth C]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A],
K [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth B]
I [auth B]
L [auth C]
F [auth A],
G [auth A],
H [auth B],
I [auth B],
L [auth C],
M [auth C],
N [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.160 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.39α = 90
b = 62.06β = 90.65
c = 191.583γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-16
    Type: Initial release
  • Version 1.1: 2019-04-17
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description