› 4ntm

X-ray diffraction
2.05Å resolution

QueD soaked with sepiapterin (selenomethionine substituted protein)

Released:
DOI: 10.2210/pdb4ntm/pdb
PDB entry 4ntm coloured by chain, front view.
PDB entry 4ntm coloured by chain, side view.
PDB entry 4ntm coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Biochemical and structural studies of 6-carboxy-5,6,7,8-tetrahydropterin synthase reveal the molecular basis of catalytic promiscuity within the tunnel-fold superfamily.
Miles ZD, Roberts SA, McCarty RM, Bandarian V
J Biol Chem 289 23641-52 (2014)
PMID: 24990950

Function and Biology Details

Reaction catalysed: 
7,8-dihydroneopterin 3'-triphosphate + H(2)O = 6-carboxy-5,6,7,8-tetrahydropterin + acetaldehyde + triphosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-159177 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
6-carboxy-5,6,7,8-tetrahydropterin synthase Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 121 amino acids
Theoretical weight: 13.98 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P65870 (Residues: 1-121; Coverage: 100%)
Gene names: JW2735, b2765, queD, ygcM
Sequence domains: 6-pyruvoyl tetrahydropterin synthase
Structure domains: 6-pyruvoyl tetrahydropterin synthase/QueD

Ligands and Environments

2 bound ligands:
Ligand ZN 6 x ZN
Ligand 2K8 6 x 2K8
1 modified residue:
Ligand MSE 24 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-2
Spacegroup: P41212
Unit cell:
a: 111.297Å b: 111.297Å c: 126.047Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.226 0.224 0.255
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 review citations

Deazaguanine derivatives, examples of crosstalk between RNA and DNA modification pathways.
Hutinet et al. (2017)
3 more

1 mention without citation

Biochemical and structural studies of 6-carboxy-5,6,7,8-tetrahydropterin synthase reveal the molecular basis of catalytic promiscuity within the tunnel-fold superfamily.
Miles et al. (2014)