› 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 4xfm coloured by chain and viewed from the front.
PDB 4xfm coloured by chain and viewed from the side.
PDB 4xfm coloured by chain and viewed from the top.
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 Cr��cy-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:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
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

7 review citations

Underground metabolism facilitates the evolution of novel pathways for vitamin B6 biosynthesis.
Richts et al. (2021)
6 more

1 mention 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)