› 3c8g

X-ray diffraction
2.5Å resolution

Crystal structure of a possible transciptional regulator YggD from Shigella flexneri 2a str. 2457T

Released:
DOI: 10.2210/pdb3c8g/pdb
PDB entry 3c8g coloured by chain, front view.
PDB entry 3c8g coloured by chain, side view.
PDB entry 3c8g coloured by chain, top view.
Source organism: Shigella flexneri 2a str. 2457T
Primary publication:
The mannitol operon repressor MtlR belongs to a new class of transcription regulators in bacteria.
Tan K, Clancy S, Borovilos M, Zhou M, Hörer S, Moy S, Volkart LL, Sassoon J, Baumann U, Joachimiak A
J Biol Chem 284 36670-36679 (2009)
PMID: 19840941

Function and Biology Details

Reaction catalysed: 
(S)-malate = fumarate + H(2)O
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assemblies composition:
homo dimer (preferred)
hetero dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-182955 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Fumarase E Chains: A, C
Molecule details ›
Chains: A, C
Length: 172 amino acids
Theoretical weight: 19.89 KDa
Source organism: Shigella flexneri 2a str. 2457T
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q83Q96 (Residues: 1-169; Coverage: 100%)
Gene names: AJR24_04990, S3120, SF2919, fumE, yggD
Sequence domains: Mannitol repressor
Structure domains: Nucleotidyltransferases domain 2
Fumarase E Chain: B
Molecule details ›
Chain: B
Length: 172 amino acids
Theoretical weight: 19.89 KDa
Source organism: Shigella flexneri 2a str. 2457T
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q83Q96 (Residues: 1-169; Coverage: 100%)
Gene names: AJR24_04990, S3120, SF2919, fumE, yggD
Sequence domains: Mannitol repressor
Structure domains: Nucleotidyltransferases domain 2
Fumarase E Chain: D
Molecule details ›
Chain: D
Length: 172 amino acids
Theoretical weight: 19.84 KDa
Source organism: Shigella flexneri 2a str. 2457T
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q83Q96 (Residues: 1-169; Coverage: 100%)
Gene names: AJR24_04990, S3120, SF2919, fumE, yggD
Sequence domains: Mannitol repressor
Structure domains: Nucleotidyltransferases domain 2

Ligands and Environments

1 bound ligand:
Ligand ACT 1 x ACT
2 modified residues:
Ligand MSE 20 x MSE
Ligand MLY 22 x MLY

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-BM
Spacegroup: C2
Unit cell:
a: 71.365Å b: 70.946Å c: 159.037Å
α: 90° β: 90.43° γ: 90°
R-values:
R R work R free
0.212 0.207 0.27
Expression system: Escherichia coli BL21

Quick links

Citations

1 review citation

Challenges in enzymatic route of mannitol production.
Bhatt et al. (2013)
8 other articles

3 mentions without citation

Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing.
Anantharaman et al. (2013)
2 more