4H3ZA

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
Genus: 81
Knot K +31

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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 92-135 44 1-91, 136-255 91 120 knot
Chain Sequence
SMQFDIVTLFPDMFRALTDWGITSRAAKQERYGLRTWNPRDFTTDNYRTIDDRPYGGGPGMVMLARPLEDAINAAKAAQAEQGIGGARVVMMSPQGATLNHDKVMRFAAEPGLILLCGRYEAIDQRLIDRVVDEEVSLGDFVLSGGELPAMALIDAVVRHLPGVLN------QDSFVDGLLDCPHYTRPEEYDGVRVPDVLLGGHHAEIEQWRRREALRNTWLKRPDLIVQARKNKLLSRADEAWLASLAKDASK
Whole chain analysis

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Subchain analysis 

Knotoid cutoff: 0.5


Knotoid matrix content: 1


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Knot core range Knot core length Knot tails range Slipknot tails range Slipknot loops range N-end length C-end length Type
view details
3.1 91-136 46 1-90, 137-249 90 113 knot
sequence length 255
structure length 249
publication title Combining functional and structural genomics to sample the essential Burkholderia structome.
pubmed doi rcsb
molecule tags Transferase
molecule keywords tRNA (guanine-N(1)-)-methyltransferase
source organism Burkholderia phymatum
missing residues 167-172
total genus Genus: 81
ec nomenclature ec 2.1.1.228: tRNA (guanine(37)-N(1))-methyltransferase.
pdb deposition date 2012-09-14
KnotProt deposition date 2014-07-31

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)
cath code
ClassArchitectureTopologyHomologyDomain
1.10.1270.20 Mainly Alpha Orthogonal Bundle Trp Operon Repressor; Chain A tRNA(m1g37)methyltransferase, domain 2 4h3zA02
3.40.1280.10 Alpha Beta 3-Layer(aba) Sandwich Alpha/beta knot Alpha/beta knot 4h3zA01
3NK7A 3KTYA 3AIAA 1VHYA 2I6DA 3DCMX 3N4JA 4IG6A 3ILKA 3ONPA 1X7OA 1UAJA 3N4KA 3AXZA 3L8UA 2QWVA 4E8BA 2CX8A 3E5YA 1NXZA 1ZJRA 4H3YA 1TO0A 1VHKA 1VH0A 1V6ZA 4FAKA 1GZ0A 2Z0YA 4CNGB 3QUVA 1K3RA 3NK6A 1UAKA 1UALA 3AI9X 3GYQA 4H3ZA 3IC6A 2QMMA 4CNFB 1NS5A 1V2XA 2HA8A 2YY8A 3IEFA 3KY7A 1O6DA 1X7PA 2O3AA 3KNUA 1J85A 1P9PA 4CNEB 1UAMA 1MXIA
chains in the KnotProt database with same CATH superfamily
3NK7A 3KTYA 3AIAA 1VHYA 2I6DA 3DCMX 3N4JA 4IG6A 3ILKA 3ONPA 1X7OA 1UAJA 3N4KA 3AXZA 3L8UA 2QWVA 4E8BA 2CX8A 3E5YA 1NXZA 1ZJRA 4H3YA 1TO0A 1VHKA 1VH0A 1V6ZA 4FAKA 1GZ0A 2Z0YA 4CNGB 3QUVA 1K3RA 3NK6A 1UAKA 1UALA 3AI9X 3GYQA 4H3ZA 3IC6A 2QMMA 4CNFB 1NS5A 1V2XA 2HA8A 2YY8A 3IEFA 3KY7A 1O6DA 1X7PA 2O3AA 3KNUA 1J85A 1P9PA 4CNEB 1UAMA 1MXIA
chains in the KnotProt database with same CATH topology
3NK7A 3KTYA 3AIAA 1VHYA 2I6DA 3DCMX 3N4JA 4IG6A 3ILKA 3ONPA 1X7OA 1UAJA 3N4KA 3AXZA 3L8UA 2QWVA 4E8BA 2CX8A 3E5YA 1NXZA 1ZJRA 4H3YA 1TO0A 1VHKA 1VH0A 1V6ZA 4FAKA 1GZ0A 2Z0YA 4CNGB 3QUVA 1K3RA 3NK6A 1UAKA 1UALA 3AI9X 3GYQA 4H3ZA 3IC6A 2QMMA 4CNFB 1NS5A 1V2XA 2HA8A 2YY8A 3IEFA 3KY7A 1O6DA 1X7PA 2O3AA 3KNUA 1J85A 1P9PA 4CNEB 1UAMA 1MXIA
chains in the KnotProt database with same CATH homology

  
#chains in the KnotProt database with same CATH superfamily
 3NK7 A;  3KTY A;  3AIA A;  1VHY A;  2I6D A;  3DCM X;  3N4J A;  4IG6 A;  3ILK A;  3ONP A;  1X7O A;  1UAJ A;  3N4K A;  3AXZ A;  3L8U A;  2QWV A;  4E8B A;  2CX8 A;  3E5Y A;  1NXZ A;  1ZJR A;  4H3Y A;  1TO0 A;  1VHK A;  1VH0 A;  1V6Z A;  4FAK A;  1GZ0 A;  2Z0Y A;  4CNG B;  3QUV A;  1K3R A;  3NK6 A;  1UAK A;  1UAL A;  3AI9 X;  3GYQ A;  4H3Z A;  3IC6 A;  2QMM A;  4CNF B;  1NS5 A;  1V2X A;  2HA8 A;  2YY8 A;  3IEF A;  3KY7 A;  1O6D A;  1X7P A;  2O3A A;  3KNU A;  1J85 A;  1P9P A;  4CNE B;  1UAM A;  1MXI A; 
#chains in the KnotProt database with same CATH topology
 3NK7 A;  3KTY A;  3AIA A;  1VHY A;  2I6D A;  3DCM X;  3N4J A;  4IG6 A;  3ILK A;  3ONP A;  1X7O A;  1UAJ A;  3N4K A;  3AXZ A;  3L8U A;  2QWV A;  4E8B A;  2CX8 A;  3E5Y A;  1NXZ A;  1ZJR A;  4H3Y A;  1TO0 A;  1VHK A;  1VH0 A;  1V6Z A;  4FAK A;  1GZ0 A;  2Z0Y A;  4CNG B;  3QUV A;  1K3R A;  3NK6 A;  1UAK A;  1UAL A;  3AI9 X;  3GYQ A;  4H3Z A;  3IC6 A;  2QMM A;  4CNF B;  1NS5 A;  1V2X A;  2HA8 A;  2YY8 A;  3IEF A;  3KY7 A;  1O6D A;  1X7P A;  2O3A A;  3KNU A;  1J85 A;  1P9P A;  4CNE B;  1UAM A;  1MXI A; 
#chains in the KnotProt database with same CATH homology
 3NK7 A;  3KTY A;  3AIA A;  1VHY A;  2I6D A;  3DCM X;  3N4J A;  4IG6 A;  3ILK A;  3ONP A;  1X7O A;  1UAJ A;  3N4K A;  3AXZ A;  3L8U A;  2QWV A;  4E8B A;  2CX8 A;  3E5Y A;  1NXZ A;  1ZJR A;  4H3Y A;  1TO0 A;  1VHK A;  1VH0 A;  1V6Z A;  4FAK A;  1GZ0 A;  2Z0Y A;  4CNG B;  3QUV A;  1K3R A;  3NK6 A;  1UAK A;  1UAL A;  3AI9 X;  3GYQ A;  4H3Z A;  3IC6 A;  2QMM A;  4CNF B;  1NS5 A;  1V2X A;  2HA8 A;  2YY8 A;  3IEF A;  3KY7 A;  1O6D A;  1X7P A;  2O3A A;  3KNU A;  1J85 A;  1P9P A;  4CNE B;  1UAM A;  1MXI A;
1UAJA 1UAKA 1UALA 1UAMA 3AXZA 4H3ZA 4YQDA 4YVGA 4YVHA
similar chains in the KnotProt database (40% sequence similarity)
None
similar chains in the pdb database (40% sequence similarity)

  
#similar chains in the KnotProt database (40% sequence similarity)
1UAJ A; 1UAK A; 1UAL A; 1UAM A; 3AXZ A; 4H3Z A; 4YQD A; 4YVG A; 4YVH A; 
#similar chains, but unknotted

#similar chains in the pdb database (40% sequence similarity)
How to cite
KnotProt | Interdisciplinary Laboratory of Biological Systems Modelling
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