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Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds

X-ray diffraction
1.94Å resolution
PDB entry 4yqj coloured by chain, front view.
PDB entry 4yqj coloured by chain, side view.
PDB entry 4yqj coloured by chain, top view.
Source organism: Haemophilus influenzae Rd KW20
Assembly composition:
homo dimer (preferred)
Entry contents: 1 distinct polypeptide molecule

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Assemblies

Assembly 1 (preferred)
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Assembly Name: tRNA (guanine-N(1)-)-methyltransferase
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Multimeric state: homo dimer
Accessible surface area: 21219.07 Å2
Buried surface area: 6808.43 Å2
Dissociation area: 3,404.21 Å2
Dissociation energy (ΔGdiss): 39.39 kcal/mol
Dissociation entropy (TΔSdiss): 14.18 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-155154

Macromolecules

tRNA (guanine-N(1)-)-methyltransferase
Chain: A
Length: 254 amino acids
Theoretical weight: 28.38 KDa
Source organism: Haemophilus influenzae Rd KW20
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P43912 (Residues: 1-246; Coverage: 100%)
Gene names: HI_0202, trmD
Pfam: tRNA (Guanine-1)-methyltransferase
InterPro:
CATH:
tRNA (guanine-N(1)-)-methyltransferase in PDB entry 4yqj, assembly 1, front view.
tRNA (guanine-N(1)-)-methyltransferase in PDB entry 4yqj, assembly 1, side view.
tRNA (guanine-N(1)-)-methyltransferase in PDB entry 4yqj, assembly 1, top view.
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