› 5nfj

X-ray diffraction
1.96Å resolution

Crystal structure of the methyltransferase subunit of human mitochondrial Ribonuclease P (MRPP1) bound to S-adenosyl-methionine (SAM)

Released:
DOI: 10.2210/pdb5nfj/pdb
PDB entry 5nfj coloured by chain, front view.
PDB entry 5nfj coloured by chain, side view.
PDB entry 5nfj coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Oerum S, Kopec J, Fitzpatrick F, Newman JA, Chalk R, Shrestha L, Fairhead M, Talon R, Burgess-Brown N, von Delft F, Arrowsmith C, Edwards C, Bountra C, Oppermann U, Yue WW, Structural Genomics Consortium (SGC)

Function and Biology Details

Reactions catalysed: 
S-adenosyl-L-methionine + adenine(9) in tRNA = S-adenosyl-L-homocysteine + N(1)-methyladenine(9) in tRNA
S-adenosyl-L-methionine + guanine(9) in tRNA = S-adenosyl-L-homocysteine + N(1)-methylguanine(9) in tRNA
Biochemical function:
  • not assigned
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-181620 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
tRNA methyltransferase 10 homolog C Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 202 amino acids
Theoretical weight: 23.8 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q7L0Y3 (Residues: 203-403; Coverage: 50%)
Gene names: MRPP1, RG9MTD1, TRMT10C
Sequence domains: tRNA (Guanine-1)-methyltransferase

Ligands and Environments


Cofactor: Ligand SAM 3 x SAM
2 bound ligands:
Ligand GOL 7 x GOL
Ligand EDO 4 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P43
Unit cell:
a: 82.64Å b: 82.64Å c: 148.62Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.186 0.185 0.206
Expression system: Escherichia coli

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