› 4nhk

X-ray diffraction
1.9Å resolution

Crystal structure of Tpa1p from Saccharomyces cerevisiae, termination and polyadenylation protein 1, in complex with pyridine-2,4-dicarboxylic acid (2,4-PDCA)

Released:
DOI: 10.2210/pdb4nhk/pdb
PDB entry 4nhk coloured by chain, front view.
PDB entry 4nhk coloured by chain, side view.
PDB entry 4nhk coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Structure of the ribosomal oxygenase OGFOD1 provides insights into the regio- and stereoselectivity of prolyl hydroxylases.
Horita S, Scotti JS, Thinnes C, Mottaghi-Taromsari YS, Thalhammer A, Ge W, Aik W, Loenarz C, Schofield CJ, McDonough MA
OpenAccess logo Structure 23 639-52 (2015)
PMID: 25728928

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-154006 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Prolyl 3,4-dihydroxylase TPA1 Chain: A
Molecule details ›
Chain: A
Length: 647 amino acids
Theoretical weight: 74.49 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P40032 (Residues: 21-644; Coverage: 97%)
Gene names: TPA1, YER049W
Sequence domains: Oxoglutarate and iron-dependent oxygenase degradation C-term
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand MN 1 x MN
Ligand PD2 1 x PD2
Ligand GOL 4 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: C2
Unit cell:
a: 168.044Å b: 67.716Å c: 70.871Å
α: 90° β: 104.93° γ: 90°
R-values:
R R work R free
0.155 0.155 0.176
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

5 review citations

2-Oxoglutarate-Dependent Oxygenases.
Islam et al. (2018)
4 more

2 mentions without citation

Pro-metastatic collagen lysyl hydroxylase dimer assemblies stabilized by Fe2+-binding.
Guo et al. (2018)
1 more