› 5udt

X-ray diffraction
3.19Å resolution

LarE, a sulfur transferase involved in synthesis of the cofactor for lactate racemase, in complex with AMP

Released:
DOI: 10.2210/pdb5udt/pdb
PDB entry 5udt coloured by chain, front view.
PDB entry 5udt coloured by chain, side view.
PDB entry 5udt coloured by chain, top view.
Source organism: Lactiplantibacillus plantarum WCFS1
Primary publication:
Structural insights into the catalytic mechanism of a sacrificial sulfur insertase of the N-type ATP pyrophosphatase family, LarE.
Fellner M, Desguin B, Hausinger RP, Hu J
Proc Natl Acad Sci U S A 114 9074-9079 (2017)
PMID: 28784764

Function and Biology Details

Reaction catalysed: 
(1a) ATP + pyridinium-3,5-dicarboxylate mononucleotide = diphosphate + 5-carboxy-1-(5-O-phospho-beta-D-ribofuranosyl)pyridinium-3-carbonyl adenylate
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-123801 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Pyridinium-3,5-bisthiocarboxylic acid mononucleotide synthase Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 286 amino acids
Theoretical weight: 31.72 KDa
Source organism: Lactiplantibacillus plantarum WCFS1
Expression system: Escherichia coli
UniProt:
  • Canonical: F9UST4 (Residues: 1-276; Coverage: 100%)
Gene names: larE, lp_0109
Sequence domains: NAD synthase

Ligands and Environments

2 bound ligands:
Ligand AMP 3 x AMP
Ligand PO4 6 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: P3121
Unit cell:
a: 166.299Å b: 166.299Å c: 124.925Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.21 0.207 0.273
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Structure, function, and biosynthesis of nickel-dependent enzymes.
Alfano et al. (2020)
4 more

1 mention without citation

Structural insights into the catalytic mechanism of a sacrificial sulfur insertase of the N-type ATP pyrophosphatase family, LarE.
Fellner et al. (2017)