› 8b1n

X-ray diffraction
2Å resolution

Crystal structure of TrmD-Tm1570 from Calditerrivibrio nitroreducens in complex with S-adenosyl-L-methionine

Released:
DOI: 10.2210/pdb8b1n/pdb
PDB entry 8b1n coloured by chain, front view.
PDB entry 8b1n coloured by chain, side view.
PDB entry 8b1n coloured by chain, top view.
Source organism: Calditerrivibrio nitroreducens DSM 19672
Primary publication:
Are there double knots in proteins? Prediction and in vitro verification based on TrmD-Tm1570 fusion from C. nitroreducens.
Perlinska AP, Nguyen ML, Pilla SP, Staszor E, Lewandowska I, Bernat A, Purta E, Augustyniak R, Bujnicki JM, Sulkowska JI
OpenAccess logo Front Mol Biosci 10 1223830 (2023)
PMID: 38903539

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + guanine(37) in tRNA = S-adenosyl-L-homocysteine + N(1)-methylguanine(37) in tRNA
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-122950 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
tRNA (guanine-N(1)-)-methyltransferase Chains: A, B
Molecule details ›
Chains: A, B
Length: 436 amino acids
Theoretical weight: 50 KDa
Source organism: Calditerrivibrio nitroreducens DSM 19672
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: E4THH1 (Residues: 1-433; Coverage: 100%)
Gene names: Calni_2012, trmD
Sequence domains:

Ligands and Environments


Cofactor: Ligand SAM 4 x SAM
3 bound ligands:
Ligand MG 2 x MG
Ligand CL 4 x CL
Ligand GOL 8 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.2
Spacegroup: P21212
Unit cell:
a: 96.78Å b: 199.56Å c: 56.7Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.17 0.169 0.209
Expression system: Escherichia coli BL21(DE3)

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