› 8pf8

X-ray diffraction
2.23Å resolution

Structure of Mycobacterium tuberculosis beta-oxidation trifunctional enzyme in complex with Fragment-M-72

Released:
DOI: 10.2210/pdb8pf8/pdb
PDB entry 8pf8 coloured by chain, front view.
PDB entry 8pf8 coloured by chain, side view.
PDB entry 8pf8 coloured by chain, top view.
Source organism: Mycobacterium tuberculosis H37Rv
Primary publication:
Crystallographic fragment-binding studies of the Mycobacterium tuberculosis trifunctional enzyme suggest binding pockets for the tails of the acyl-CoA substrates at its active sites and a potential substrate-channeling path between them.
Dalwani S, Metz A, Huschmann FU, Weiss MS, Wierenga RK, Venkatesan R
Acta Crystallogr D Struct Biol (2024)
PMID: 39012716

Function and Biology Details

Reaction catalysed: 
(S)-3-hydroxyacyl-CoA + NAD(+) = 3-oxoacyl-CoA + NADH
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-129474 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Probable fatty oxidation protein FadB Chains: A, B
Molecule details ›
Chains: A, B
Length: 736 amino acids
Theoretical weight: 78.01 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O53872 (Residues: 1-720; Coverage: 100%)
Gene names: Rv0860, fadB
Sequence domains:
Putative acyltransferase Rv0859 Chains: C, D
Molecule details ›
Chains: C, D
Length: 403 amino acids
Theoretical weight: 42.46 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O53871 (Residues: 1-403; Coverage: 100%)
Gene names: Rv0859, fadA
Sequence domains:

Ligands and Environments

6 bound ligands:
Ligand SO4 23 x SO4
Ligand GOL 1 x GOL
Ligand YMK 1 x YMK
Ligand YLZ 2 x YLZ
Ligand YLN 2 x YLN
Ligand JXL 6 x JXL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: C2
Unit cell:
a: 250.961Å b: 134.614Å c: 119.974Å
α: 90° β: 110.44° γ: 90°
R-values:
R R work R free
0.191 0.189 0.219
Expression system: Escherichia coli BL21(DE3)

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