› 4h3z

X-ray diffraction
2.15Å resolution

Crystal structure of a symmetric dimer of a tRNA (guanine-(N(1)-)-methyltransferase from Burkholderia phymatum bound to S-adenosyl homocystein in both half-sites

Released:
DOI: 10.2210/pdb4h3z/pdb
PDB entry 4h3z coloured by chain, front view.
PDB entry 4h3z coloured by chain, side view.
PDB entry 4h3z coloured by chain, top view.
Source organism: Paraburkholderia phymatum STM815
Primary publication:
Combining functional and structural genomics to sample the essential Burkholderia structome.
Baugh L, Gallagher LA, Patrapuvich R, Clifton MC, Gardberg AS, Edwards TE, Armour B, Begley DW, Dieterich SH, Dranow DM, Abendroth J, Fairman JW, Fox D, Staker BL, Phan I, Gillespie A, Choi R, Nakazawa-Hewitt S, Nguyen MT, Napuli A, Barrett L, Buchko GW, Stacy R, Myler PJ, Stewart LJ, Manoil C, Van Voorhis WC
PLoS One 8 e53851 (2013)
PMID: 23382856

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-109655 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
tRNA (guanine-N(1)-)-methyltransferase Chains: A, B
Molecule details ›
Chains: A, B
Length: 276 amino acids
Theoretical weight: 30.79 KDa
Source organism: Paraburkholderia phymatum STM815
Expression system: Escherichia coli
UniProt:
  • Canonical: B2JF31 (Residues: 1-255; Coverage: 100%)
Gene names: Bphy_0771, trmD
Sequence domains: tRNA (Guanine-1)-methyltransferase
Structure domains:

Ligands and Environments


Cofactor: Ligand SAH 2 x SAH
1 bound ligand:
Ligand CL 2 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E+ SUPERBRIGHT
Spacegroup: C2221
Unit cell:
a: 58.85Å b: 188.09Å c: 127.68Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.189 0.186 0.228
Expression system: Escherichia coli

Quick links

Citations

11 review citations

Prokaryotic Heme Biosynthesis: Multiple Pathways to a Common Essential Product.
Dailey et al. (2017)
10 more

1 mention without citation

Combining functional and structural genomics to sample the essential Burkholderia structome.
Baugh et al. (2013)