› 5xv2

X-ray diffraction
2Å resolution

Crystal structure of Rib7 mutant D33A from Methanosarcina mazei

Released:
DOI: 10.2210/pdb5xv2/pdb
PDB entry 5xv2 coloured by chain, front view.
PDB entry 5xv2 coloured by chain, side view.
PDB entry 5xv2 coloured by chain, top view.
Source organism: Methanosarcina mazei Go1
Primary publication:
Evolution of archaeal Rib7 and eubacterial RibG reductases in riboflavin biosynthesis: Substrate specificity and cofactor preference.
Chen SC, Yen TM, Chang TH, Liaw SH
Biochem Biophys Res Commun 503 195-201 (2018)
PMID: 29864427

Function and Biology Details

Reaction catalysed: 
2,5-diamino-6-(5-phospho-D-ribitylamino)pyrimidin-4(3H)-one + NAD(P)(+) = 2,5-diamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one + NAD(P)H
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-185828 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate reductase Chain: A
Molecule details ›
Chain: A
Length: 240 amino acids
Theoretical weight: 26.06 KDa
Source organism: Methanosarcina mazei Go1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8PYN5 (Residues: 1-228; Coverage: 100%)
Gene name: MM_0826
Sequence domains: RibD C-terminal domain
Structure domains: Dihydrofolate Reductase, subunit A

Ligands and Environments


Cofactor: Ligand NAP 1 x NAP
No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSRRC BEAMLINE BL13B1
Spacegroup: P6422
Unit cell:
a: 70.147Å b: 70.147Å c: 217.458Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.236 0.235 0.252
Expression system: Escherichia coli

Quick links

Citations

1 citations in other articles

Crystal structures of Aspergillus oryzae Rib2 deaminase: the functional mechanism involved in riboflavin biosynthesis.
Chen et al. (2021)