› 4fwi

X-ray diffraction
2.89Å resolution

Crystal structure of the nucleotide-binding domain of a dipeptide ABC transporter

Released:
DOI: 10.2210/pdb4fwi/pdb
PDB entry 4fwi coloured by chain, front view.
PDB entry 4fwi coloured by chain, side view.
PDB entry 4fwi coloured by chain, top view.
Source organism: Caldanaerobacter subterraneus subsp. tengcongensis MB4
Primary publication:
Structure of the nucleotide-binding domain of a dipeptide ABC transporter reveals a novel iron-sulfur cluster-binding domain.
Li X, Zhuo W, Yu J, Ge J, Gu J, Feng Y, Yang M, Wang L, Wang N
Acta Crystallogr D Biol Crystallogr 69 256-65 (2013)
PMID: 23385461

Function and Biology Details

Reaction catalysed: 
ATP + H(2)O + a dipeptide-[dipeptide-binding protein](Side 1) = ADP + phosphate + a dipeptide(Side 2) + [dipeptide-binding protein](Side 1)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-185966 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Dipeptide transport ATP-binding protein DppD Chain: B
Molecule details ›
Chain: B
Length: 334 amino acids
Theoretical weight: 37.48 KDa
Source organism: Caldanaerobacter subterraneus subsp. tengcongensis MB4
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8RDH4 (Residues: 1-326; Coverage: 100%)
Gene names: TTE0057, dppD
Sequence domains:
Structure domains: P-loop containing nucleotide triphosphate hydrolases

Ligands and Environments

3 bound ligands:
Ligand SF4 1 x SF4
Ligand ATP 1 x ATP
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P4322
Unit cell:
a: 64.247Å b: 64.247Å c: 320.608Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.215 0.212 0.268
Expression system: Escherichia coli

Quick links

Citations

1 review citation

The Abc of Phosphonate Breakdown: A Mechanism for Bacterial Survival.
Manav et al. (2018)
3 other articles

5 mentions without citation

Structural insights into the bacterial carbon-phosphorus lyase machinery.
Seweryn et al. (2015)
4 more