4YVJA

Crystal structure of h. influenzae trmd in complex with sinefungin and trna variant (g36u)
Knot K +31
Knot core range Knot core length Knot tails range Slipknot tails range Slipknot loops range N-end length C-end length Type
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+31 89-132 44 1-88, 133-248 88 116 knot
Chain Sequence
SHMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTLIDAVARFIPGV---------DSFADGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNS
Whole chain analysis
Subchain analysis 

Knotoid cutoff: 0.5


Knotoid matrix content: 1

Knot core range Knot core length Knot tails range Slipknot tails range Slipknot loops range N-end length C-end length Type
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3.1 88-133 46 1-87, 134-239 87 106 knot
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2.1 85-130 46 1-84 136-239 131-135 84 104 slipknot
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2.1 90-200 111 1-87, 209-239 88-89, 201-208 87 31 slipknot
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2.1 90-208 119 1-87, 211-239 88-89, 209-210 87 29 slipknot
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2.1 90-210 121 211-239 1-87 88-89 87 28 slipknot
missing residues 162-170
publication title Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD.
pubmed doi rcsb
structure length 239
molecule tags Transferase/rna
source organism Haemophilus influenzae (strain atcc 51907 / dsm 11121 / kw20 / rd)
sequence length 248
molecule keywords tRNA (guanine-N(1)-)-methyltransferase
ec nomenclature ec 2.1.1.228: tRNA (guanine(37)-N(1))-methyltransferase.
pdb deposition date 2015-03-20
KnotProt deposition date 2015-12-25

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF01746 tRNA_m1G_MT tRNA (Guanine-1)-methyltransferase
Image from the rcsb pdb (www.rcsb.org)
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similar chains in the KnotProt database (?% sequence similarity)
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similar chains in the pdb database (?% sequence similarity)

 
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