› 3thp

X-ray diffraction
3.2Å resolution

Crystal structure and RNA binding properties of the RRM/AlkB domains in human ABH8, an enzyme catalyzing tRNA hypermodification, Northeast Structural Genomics Consortium Target HR5601B

Released:
DOI: 10.2210/pdb3thp/pdb
PDB entry 3thp coloured by chain, front view.
PDB entry 3thp coloured by chain, side view.
PDB entry 3thp coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structure and RNA binding properties of the RNA recognition motif (RRM) and AlkB domains in human AlkB homolog 8 (ABH8), an enzyme catalyzing tRNA hypermodification.
Pastore C, Topalidou I, Forouhar F, Yan AC, Levy M, Hunt JF
J Biol Chem 287 2130-43 (2012)
PMID: 22065580

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + carboxymethyluridine(34) in tRNA = S-adenosyl-L-homocysteine + 5-(2-methoxy-2-oxoethyl)uridine(34) in tRNA
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo tetramer
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-188384 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Alkylated DNA repair protein alkB homolog 8 Chain: A
Molecule details ›
Chain: A
Length: 345 amino acids
Theoretical weight: 39.69 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q96BT7 (Residues: 25-355; Coverage: 50%)
Gene names: ABH8, ALKBH8
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand ZN 1 x ZN
Ligand MN 1 x MN
Ligand AKG 1 x AKG
1 modified residue:
Ligand MSE 7 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X4C
Spacegroup: I222
Unit cell:
a: 68.276Å b: 81.675Å c: 144.72Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.22 0.217 0.283
Expression system: Escherichia coli

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Citations

20 review citations

The AlkB Family of Fe(II)/α-Ketoglutarate-dependent Dioxygenases: Repairing Nucleic Acid Alkylation Damage and Beyond.
Fedeles et al. (2015)
19 more

4 mentions without citation

Crystal structure and RNA binding properties of the RNA recognition motif (RRM) and AlkB domains in human AlkB homolog 8 (ABH8), an enzyme catalyzing tRNA hypermodification.
Pastore et al. (2012)
3 more