› 2qjj

X-ray diffraction
1.8Å resolution

Crystal structure of D-Mannonate dehydratase from Novosphingobium aromaticivorans

Released:
DOI: 10.2210/pdb2qjj/pdb
PDB entry 2qjj coloured by chain, front view.
PDB entry 2qjj coloured by chain, side view.
PDB entry 2qjj 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
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

1 bound ligand:
Ligand MG 4 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X4A
Spacegroup: C2221
Unit cell:
a: 117.465Å b: 167.711Å c: 166.441Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.18 0.178 0.192
Expression system: Escherichia coli

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Citations

1 review citation

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

5 mentions without citation

Structural adaptation of extreme halophilic proteins through decrease of conserved hydrophobic contact surface.
Siglioccolo et al. (2011)
4 more