› 9evv

X-ray diffraction
2.44Å resolution

His579Leu variant of L-arabinonate dehydratase co-crystallized with 2-oxobutyrate

Released:
DOI: 10.2210/pdb9evv/pdb
PDB entry 9evv coloured by chain, front view.
PDB entry 9evv coloured by chain, side view.
PDB entry 9evv coloured by chain, top view.
Source organism: Rhizobium leguminosarum bv. trifolii
Primary publication:
Unveiling the importance of the C-terminus in the sugar acid dehydratase of the IlvD/EDD superfamily.
Ren Y, Vettenranta E, Penttinen L, Blomster Andberg M, Koivula A, Rouvinen J, Hakulinen N
Appl Microbiol Biotechnol 108 436 (2024)
PMID: 39126499

Function and Biology Details

Reactions catalysed: 
L-arabinonate = 2-dehydro-3-deoxy-L-arabinonate + H(2)O
D-galactonate = 2-dehydro-3-deoxy-D-galactonate + H(2)O
D-fuconate = 2-dehydro-3-deoxy-D-fuconate + H(2)O
Biochemical function:
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-110304 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
L-arabinonate dehydratase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 588 amino acids
Theoretical weight: 63.83 KDa
Source organism: Rhizobium leguminosarum bv. trifolii
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: B5ZZ34 (Residues: 2-579; Coverage: 100%)
Gene names: Rleg2_2909, araD
Sequence domains: Dehydratase family

Ligands and Environments

3 bound ligands:
Ligand MG 4 x MG
Ligand FES 4 x FES
Ligand 2KT 1 x 2KT
1 modified residue:
Ligand KCX 4 x KCX

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID30B
Spacegroup: P212121
Unit cell:
a: 107.947Å b: 148.211Å c: 165.025Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.186 0.185 0.237
Expression system: Escherichia coli BL21(DE3)

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