› 1rya

X-ray diffraction
1.3Å resolution

Crystal Structure of the E. coli GDP-mannose mannosyl hydrolase in complex with GDP and MG

Released:
DOI: 10.2210/pdb1rya/pdb
PDB entry 1rya coloured by chain, front view.
PDB entry 1rya coloured by chain, side view.
PDB entry 1rya coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Structure and mechanism of GDP-mannose glycosyl hydrolase, a Nudix enzyme that cleaves at carbon instead of phosphorus.
Gabelli SB, Bianchet MA, Azurmendi HF, Xia Z, Sarawat V, Mildvan AS, Amzel LM
Structure 12 927-35 (2004)
PMID: 15274914

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-542614 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
GDP-mannose mannosyl hydrolase Chains: A, B
Molecule details ›
Chains: A, B
Length: 160 amino acids
Theoretical weight: 18.42 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P32056 (Residues: 1-159; Coverage: 100%)
Gene names: JW5335, b2051, gmm, nudD, wcaH, yefC
Sequence domains: NUDIX domain
Structure domains: Nucleoside Triphosphate Pyrophosphohydrolase

Ligands and Environments

4 bound ligands:
Ligand MG 2 x MG
Ligand GDP 2 x GDP
Ligand TRS 2 x TRS
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X6A
Spacegroup: P212121
Unit cell:
a: 50.069Å b: 81.363Å c: 98.974Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.17 0.169 0.191
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Structures and mechanisms of Nudix hydrolases.
Mildvan et al. (2005)
14 other articles

3 mentions without citation

The evolution of function within the Nudix homology clan.
Srouji et al. (2017)
2 more