› 4kr7

X-ray diffraction
3.42Å resolution

Crystal structure of a 4-thiouridine synthetase - RNA complex with bound ATP

Released:
DOI: 10.2210/pdb4kr7/pdb
PDB entry 4kr7 coloured by chain, front view.
PDB entry 4kr7 coloured by chain, side view.
PDB entry 4kr7 coloured by chain, top view.
Source organism: Thermotoga maritima MSB8
Primary publication:
Crystal structure of a 4-thiouridine synthetase-RNA complex reveals specificity of tRNA U8 modification.
Neumann P, Lakomek K, Naumann PT, Erwin WM, Lauhon CT, Ficner R
Nucleic Acids Res 42 6673-85 (2014)
PMID: 24705700

Function and Biology Details

Reaction catalysed: 
ATP + [ThiI sulfur-carrier protein]-S-sulfanyl-L-cysteine + uracil in tRNA + 2 reduced ferredoxin [iron-sulfur] cluster = AMP + diphosphate + 4-thiouracil in tRNA + [ThiI sulfur-carrier protein]-L-cysteine + 2 oxidized ferredoxin [iron-sulfur] cluster
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-194858 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Probable tRNA sulfurtransferase Chains: A, B
Molecule details ›
Chains: A, B
Length: 388 amino acids
Theoretical weight: 44.19 KDa
Source organism: Thermotoga maritima MSB8
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9X220 (Residues: 1-388; Coverage: 100%)
Gene names: TM_1694, thiI
Sequence domains:
Structure domains:
RNA (39-MER) Chains: M, X
Molecule details ›
Chains: M, X
Length: 39 nucleotides
Theoretical weight: 12.56 KDa
Source organism: Thermotoga maritima MSB8
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand ATP 2 x ATP
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE X11
Spacegroup: P212121
Unit cell:
a: 103.17Å b: 113.22Å c: 133.18Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.233 0.23 0.274
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

13 review citations

How RNA-Binding Proteins Interact with RNA: Molecules and Mechanisms.
Corley et al. (2020)
12 more

2 mentions without citation

Methionine Sulfoxide Reductases of Archaea.
Maupin-Furlow JA. (2018)
1 more