› 2qjm

X-ray diffraction
2.2Å resolution

Crystal structure of the K271E mutant of Mannonate dehydratase from Novosphingobium aromaticivorans complexed with Mg and D-mannonate

Released:
DOI: 10.2210/pdb2qjm/pdb
PDB entry 2qjm coloured by chain, front view.
PDB entry 2qjm coloured by chain, side view.
PDB entry 2qjm coloured by chain, top view.
Source organism: Novosphingobium aromaticivorans
Primary publication:
Evolution of enzymatic activities in the enolase superfamily: D-Mannonate dehydratase from Novosphingobium aromaticivorans.
Rakus JF, Fedorov AA, Fedorov EV, Glasner ME, Vick JE, Babbitt PC, Almo SC, Gerlt JA
Biochemistry 46 12896-908 (2007)
PMID: 17944491

Function and Biology Details

Reaction catalysed: 
D-mannonate = 2-dehydro-3-deoxy-D-gluconate + H(2)O
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
homo dimer (preferred)
homo octamer
Assembly name:
PDBe Complex ID:
PDB-CPX-107482 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
D-mannonate dehydratase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 402 amino acids
Theoretical weight: 45.3 KDa
Source organism: Novosphingobium aromaticivorans
Expression system: Escherichia coli
UniProt:
  • Canonical: A4XF23 (Residues: 1-402; Coverage: 100%)
Gene names: Saro_3675, manD
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand MG 4 x MG
Ligand CS2 4 x CS2
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X4A
Spacegroup: C2221
Unit cell:
a: 116.254Å b: 165.312Å c: 166.853Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.168 0.168 0.206
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Divergent evolution in enolase superfamily: strategies for assigning functions.
Gerlt et al. (2012)
17 other articles

1 mention without citation

Discovery of function in the enolase superfamily: D-mannonate and d-gluconate dehydratases in the D-mannonate dehydratase subgroup.
Wichelecki et al. (2014)