› 4kr6

X-ray diffraction
2.85Å resolution

Crystal structure of a 4-thiouridine synthetase - RNA complex

Released:
DOI: 10.2210/pdb4kr6/pdb
PDB entry 4kr6 coloured by chain, front view.
PDB entry 4kr6 coloured by chain, side view.
PDB entry 4kr6 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
OpenAccess logo 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-578477 (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: C, D
Molecule details ›
Chains: C, D
Length: 39 nucleotides
Theoretical weight: 12.56 KDa
Source organism: Thermotoga maritima MSB8
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand HG 4 x HG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: P212121
Unit cell:
a: 100.652Å b: 110.325Å c: 119.313Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.188 0.186 0.228
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

12 review citations

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

5 mentions without citation

Transfer RNA Modification Enzymes with a Thiouridine Synthetase, Methyltransferase and Pseudouridine Synthase (THUMP) Domain and the Nucleosides They Produce in tRNA.
Hori H. (2023)
4 more