› 6pd2

X-ray diffraction
1.95Å resolution

PntC-AEPT: fusion protein of phosphonate-specific cytidylyltransferase and 2-aminoethylphosphonate (AEP) transaminase from Treponema denticola in complex with cytidine monophosphate-AEP

Released:
DOI: 10.2210/pdb6pd2/pdb
PDB entry 6pd2 coloured by chain, front view.
PDB entry 6pd2 coloured by chain, side view.
PDB entry 6pd2 coloured by chain, top view.
Source organism: Treponema denticola ATCC 35405
Primary publication:
The predominance of nucleotidyl activation in bacterial phosphonate biosynthesis.
Rice K, Batul K, Whiteside J, Kelso J, Papinski M, Schmidt E, Pratasouskaya A, Wang D, Sullivan R, Bartlett C, Weadge JT, Van der Kamp MW, Moreno-Hagelsieb G, Suits MD, Horsman GP
OpenAccess logo Nat Commun 10 3698 (2019)
PMID: 31420548

Function and Biology Details

Reaction catalysed: 
(2-aminoethyl)phosphonate + pyruvate = 2-phosphonoacetaldehyde + L-alanine
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-180965 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Bifunctional 2-aminoethylphosphonate cytidylyltransferase/aminotransferase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 624 amino acids
Theoretical weight: 70.15 KDa
Source organism: Treponema denticola ATCC 35405
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q73MU2 (Residues: 1-616; Coverage: 100%)
Gene names: TDE_1415, phnW, pntC
Sequence domains:

Ligands and Environments


Cofactor: Ligand PLP 4 x PLP
6 bound ligands:
Ligand MG 8 x MG
Ligand PO4 11 x PO4
Ligand 0RC 4 x 0RC
Ligand EDO 27 x EDO
Ligand ACT 3 x ACT
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CLSI BEAMLINE 08ID-1
Spacegroup: P21
Unit cell:
a: 76.45Å b: 154.05Å c: 134.58Å
α: 90° β: 90.9° γ: 90°
R-values:
R R work R free
0.222 0.22 0.254
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Boosting the Full Potential of PyMOL with Structural Biology Plugins.
Rosignoli et al. (2022)
8 other articles

1 mention without citation

The predominance of nucleotidyl activation in bacterial phosphonate biosynthesis.
Rice et al. (2019)