› 4xfm

X-ray diffraction
1.55Å resolution

Crystal structure of a domain of unknown function (DUF1537) from Pectobacterium atrosepticum (ECA3761), Target EFI-511609, with bound D-threonate, domain swapped dimer

Released:
DOI: 10.2210/pdb4xfm/pdb
PDB entry 4xfm coloured by chain, front view.
PDB entry 4xfm coloured by chain, side view.
PDB entry 4xfm coloured by chain, top view.
Source organism: Pectobacterium atrosepticum SCRI1043
Primary publication:
Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars.
Zhang X, Carter MS, Vetting MW, San Francisco B, Zhao S, Al-Obaidi NF, Solbiati JO, Thiaville JJ, de Crécy-Lagard V, Jacobson MP, Almo SC, Gerlt JA
Proc Natl Acad Sci U S A 113 E4161-9 (2016)
PMID: 27402745

Function and Biology Details

Reaction catalysed: 
ATP + D-threonate = ADP + 4-phospho-D-threonate
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-179478 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
D-threonate kinase Chain: A
Molecule details ›
Chain: A
Length: 464 amino acids
Theoretical weight: 49.28 KDa
Source organism: Pectobacterium atrosepticum SCRI1043
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q6D0N7 (Residues: 1-442; Coverage: 100%)
Gene names: ECA3761, dtnK
Sequence domains:

Ligands and Environments

1 bound ligand:
Ligand THE 1 x THE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 31-ID
Spacegroup: C2
Unit cell:
a: 153.696Å b: 47.611Å c: 64.142Å
α: 90° β: 107.12° γ: 90°
R-values:
R R work R free
0.166 0.164 0.191
Expression system: Escherichia coli BL21(DE3)

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Citations

9 review citations

A short history of RubisCO: the rise and fall (?) of Nature's predominant CO2 fixing enzyme.
Erb et al. (2018)
8 more

2 mentions without citation

Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars.
Zhang et al. (2016)
1 more