› 2ydy

X-ray diffraction
2.25Å resolution

Crystal structure of human S-adenosylmethionine synthetase 2, beta subunit in Orthorhombic crystal form

Released:
DOI: 10.2210/pdb2ydy/pdb
PDB entry 2ydy coloured by chain, front view.
PDB entry 2ydy coloured by chain, side view.
PDB entry 2ydy coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Insight into S-adenosylmethionine biosynthesis from the crystal structures of the human methionine adenosyltransferase catalytic and regulatory subunits.
Shafqat N, Muniz JR, Pilka ES, Papagrigoriou E, von Delft F, Oppermann U, Yue WW
Biochem J 452 27-36 (2013)
PMID: 23425511

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-192763 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Methionine adenosyltransferase 2 subunit beta Chain: A
Molecule details ›
Chain: A
Length: 315 amino acids
Theoretical weight: 35.83 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9NZL9 (Residues: 28-334; Coverage: 92%)
Gene names: MAT2B, MSTP045, Nbla02999, TGR, UNQ2435/PRO4995
Sequence domains: RmlD substrate binding domain
Structure domains: NAD(P)-binding Rossmann-like Domain

Ligands and Environments

2 bound ligands:
Ligand SO4 3 x SO4
Ligand CL 1 x CL
1 modified residue:
Ligand MSE 6 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: C2221
Unit cell:
a: 40.98Å b: 111.77Å c: 123.12Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.177 0.175 0.218
Expression system: Escherichia coli BL21(DE3)

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Citations

5 review citations

Evolutionary Limitation and Opportunities for Developing tRNA Synthetase Inhibitors with 5-Binding-Mode Classification.
Fang et al. (2015)
4 more

4 mentions without citation

Insight into S-adenosylmethionine biosynthesis from the crystal structures of the human methionine adenosyltransferase catalytic and regulatory subunits.
Shafqat et al. (2013)
3 more