› 6u1d

X-ray diffraction
1.9Å resolution

Thermus thermophilus D-alanine-D-alanine ligase in complex with ATP, D-alanine-D-alanine, Mg2+ and Rb+

Released:
DOI: 10.2210/pdb6u1d/pdb
PDB entry 6u1d coloured by chain, front view.
PDB entry 6u1d coloured by chain, side view.
PDB entry 6u1d coloured by chain, top view.
Source organism: Thermus thermophilus HB8
Primary publication:
d-Alanine-d-alanine ligase as a model for the activation of ATP-grasp enzymes by monovalent cations.
Pederick JL, Thompson AP, Bell SG, Bruning JB
J Biol Chem 295 7894-7904 (2020)
PMID: 32335509

Function and Biology Details

Reaction catalysed: 
ATP + 2 D-alanine = ADP + phosphate + D-alanyl-D-alanine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-177919 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
D-alanine--D-alanine ligase Chains: A, B
Molecule details ›
Chains: A, B
Length: 327 amino acids
Theoretical weight: 35.79 KDa
Source organism: Thermus thermophilus HB8
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q5SHZ3 (Residues: 1-319; Coverage: 100%)
Gene names: TTHA1587, ddl
Sequence domains:

Ligands and Environments

4 bound ligands:
Ligand DAL 4 x DAL
Ligand MG 4 x MG
Ligand RB 4 x RB
Ligand ATP 2 x ATP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Spacegroup: P41212
Unit cell:
a: 95.435Å b: 95.435Å c: 193.318Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.177 0.176 0.196
Expression system: Escherichia coli BL21(DE3)

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Citations

7 citation in other articles

Biosynthesis and characterization of fuscimiditide, an aspartimidylated graspetide.
Elashal et al. (2022)
6 more

1 mention without citation

d-Alanine-d-alanine ligase as a model for the activation of ATP-grasp enzymes by monovalent cations.
Pederick et al. (2020)