› 5tjy

X-ray diffraction
2.4Å resolution

Structure of 4-Hydroxy-tetrahydrodipicolinate Reductase from Mycobacterium tuberculosis with 2,6 Pyridine Dicarboxylic Acid and NADH

Released:
DOI: 10.2210/pdb5tjy/pdb
PDB entry 5tjy coloured by chain, front view.
PDB entry 5tjy coloured by chain, side view.
PDB entry 5tjy coloured by chain, top view.
Source organism: Mycobacterium tuberculosis H37Ra
Primary publication:
Comparative structural and mechanistic studies of 4-hydroxy-tetrahydrodipicolinate reductases from Mycobacterium tuberculosis and Vibrio vulnificus.
Pote S, Kachhap S, Mank NJ, Daneshian L, Klapper V, Pye S, Arnette AK, Shimizu LS, Borowski T, Chruszcz M
Biochim Biophys Acta Gen Subj 1865 129750 (2021)
PMID: 32980502

Function and Biology Details

Reaction catalysed: 
(S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + NAD(P)(+) + H(2)O = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + NAD(P)H
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-107745 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
4-hydroxy-tetrahydrodipicolinate reductase Chain: A
Molecule details ›
Chain: A
Length: 245 amino acids
Theoretical weight: 25.68 KDa
Source organism: Mycobacterium tuberculosis H37Ra
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A5U6C6 (Residues: 1-244; Coverage: 100%)
Gene names: MRA_2798, dapB
Sequence domains:

Ligands and Environments


Cofactor: Ligand NAI 1 x NAI
8 bound ligands:
Ligand PDC 1 x PDC
Ligand SO4 1 x SO4
Ligand BEZ 1 x BEZ
Ligand IMD 1 x IMD
Ligand PG4 1 x PG4
Ligand NA 1 x NA
Ligand EDO 6 x EDO
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P6222
Unit cell:
a: 66.421Å b: 66.421Å c: 249.363Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.148 0.146 0.195
Expression system: Escherichia coli BL21(DE3)

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Citations

2 mentions without citation

Boulton-Katritzky Rearrangement of 5-Substituted Phenyl-3-[2-(morpholin-1-yl)ethyl]-1,2,4-oxadiazoles as a Synthetic Path to Spiropyrazoline Benzoates and Chloride with Antitubercular Properties.
Kayukova et al. (2021)
1 more