5GM8A

Methylation at position 32 of trna catalyzed by trmj alters oxidative stress response in pseudomonas aeruiginosa
Total Genus 60
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The genus trace: a function that shows values of genus (vertical axis) for subchains spanned between the first residue, and all other residues (shown on horizontal axis). The number of the latter residue and the genus of a given subchain are shown interactively.

Total Genus
60
Knots found
sequence length
170
structure length
170
Chain Sequence
QSMMLDRIRVVLVNTSHPGNIGGAARAMKNMGLSQLVLVQPESFPHGDAVARASGATDILDAARVVDTLEEALSGCSVVLGTSARDRRIPWPLLDPRECATTCLEHLEANGEVALVFGREYAGLTNEELQRCQFHVHIPSDPEFGSLNLAAAVQVLTYEVRMAWLAAQGK
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The genus matrix. At position (x,y) a genus value for a subchain spanned between x’th and y’th residue is shown. Values of the genus are represented by color, according to the scale given on the right.

Structure visualization

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Chord Diagram
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molecule keywords tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ
publication title Methylation at position 32 of tRNA catalyzed by TrmJ alters oxidative stress response in Pseudomonas aeruginosa.
pubmed doi rcsb
source organism Pseudomonas aeruginosa
molecule tags Transferase
total genus 60
structure length 170
sequence length 170
chains with identical sequence B, C, D
other databases KnotProt 2.0: K +31
ec nomenclature ec 2.1.1.200: tRNA (cytidine(32)/uridine(32)-2'-O)-methyltransferase.
pdb deposition date 2016-07-13

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF00588 SpoU_methylase SpoU rRNA Methylase family
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.40.1280.10 Alpha Beta 3-Layer(aba) Sandwich Alpha/beta knot Alpha/beta knot 5gm8A01
4J3CA 1GZ0A 1MXIA 4YQDA 1VHKA 2HA8A 1UALA 4MCCA 1ZJRA 3AXZA 1V6ZA 4YQ3A 4CNDA 4YPXA 4MCDA 4YQ8A 5GM8A 1UAKA 4H3ZA 4YVIA 4YQ1A 3ONPA 1NXZA 4YQJA 3N4JA 4CNGA 4YQOA 4YPYA 3OIIA 1J85A 1VH0A 4JALA 2Z0YA 4YQLA 4YVKA 4YQIA 4KDZA 3OINA 1O6DA 3E5YA 1VHYA 2EGWA 2V3JA 4E8BA 1NS5A 4YQSA 3L8UA 4L69A 5GMBA 4YQ7A 1V2XA 4YPZA 1UAJA 2EGVA 2CX8A 4YQNA 3KW2A 3NK6A 4XBOA 4YQPA 3DCMX 4YQKA 4RG1A 4YQ9A 3BBDA 1Z85A 4FAKA 1K3RA 4YQ4A 4YVGA 4YQCA 4YVJA 3AIAA 3GYQA 3KNUA 4IG6A 3QUVA 2QWVA 3KY7A 4H3YA 5FAIA 3ILKA 1P9PA 3BBHA 5CO4A 4YQQA 2YY8A 4YQ0A 4YQ5A 4YQBA 4MCBA 3OIJA 3IEFA 3AI9X 1OY5A 3IC6A 4PZKA 2O3AA 5GMCA 4YQGA 1UAMA 3KTYA 4JAKA 1X7PA 4CNFA 4YQAA 4YVHA 4X3LA 2I6DA 4YQ2A 4CNEA 1X7OA 2V3KA 3O7BA 4YQ6A 4X3MA 1IPAA 4KGNA 2QMMA 3NK7A 3BBEA 4YPWA 5D9FA 4YQTA 3N4KA 1TO0A 4YQRA
chains in the Genus database with same CATH superfamily
4J3CA 1GZ0A 1MXIA 4YQDA 1VHKA 2HA8A 1UALA 4MCCA 1ZJRA 3AXZA 1V6ZA 4YQ3A 4CNDA 4YPXA 4MCDA 4YQ8A 5GM8A 1UAKA 4JWHA 4H3ZA 4YVIA 4YQ1A 3ONPA 1NXZA 4YQJA 3N4JA 4JWJA 4JWGA 4CNGA 4YQOA 4YPYA 3OIIA 1J85A 1VH0A 4JALA 2Z0YA 4YQLA 4YVKA 4YQIA 4KDZA 3OINA 1O6DA 3E5YA 4FMWA 1VHYA 2EGWA 2V3JA 4E8BA 1NS5A 4YQSA 3L8UA 4L69A 5GMBA 4YQ7A 1V2XA 4YPZA 1UAJA 2EGVA 2CX8A 4YQNA 3KW2A 3NK6A 4XBOA 4YQPA 3DCMX 4YQKA 4RG1A 4YQ9A 3BBDA 1Z85A 4FAKA 1K3RA 4YQ4A 4YVGA 4YQCA 4YVJA 3AIAA 3GYQA 3KNUA 4IG6A 3QUVA 2QWVA 3KY7A 4H3YA 5FAIA 3ILKA 1P9PA 3BBHA 5CO4A 4YQQA 2YY8A 4YQ0A 4YQ5A 4YQBA 4MCBA 3OIJA 3IEFA 3AI9X 1OY5A 3IC6A 4PZKA 2O3AA 5GMCA 4YQGA 1UAMA 3KTYA 4JAKA 1X7PA 4CNFA 4YQAA 4YVHA 4X3LA 2I6DA 4YQ2A 4CNEA 1X7OA 2V3KA 3O7BA 4YQ6A 4X3MA 1IPAA 4KGNA 2QMMA 3NK7A 3BBEA 4YPWA 4JWFA 5D9FA 4YQTA 3N4KA 1TO0A 4YQRA
chains in the Genus database with same CATH topology
4J3CA 1GZ0A 1MXIA 4YQDA 1VHKA 2HA8A 1UALA 4MCCA 1ZJRA 3AXZA 1V6ZA 4YQ3A 4CNDA 4YPXA 4MCDA 4YQ8A 5GM8A 1UAKA 4JWHA 4H3ZA 4YVIA 4YQ1A 3ONPA 1NXZA 4YQJA 3N4JA 4JWJA 4JWGA 4CNGA 4YQOA 4YPYA 3OIIA 1J85A 1VH0A 4JALA 2Z0YA 4YQLA 4YVKA 4YQIA 4KDZA 3OINA 1O6DA 3E5YA 4FMWA 1VHYA 2EGWA 2V3JA 4E8BA 1NS5A 4YQSA 3L8UA 4L69A 5GMBA 4YQ7A 1V2XA 4YPZA 1UAJA 2EGVA 2CX8A 4YQNA 3KW2A 3NK6A 4XBOA 4YQPA 3DCMX 4YQKA 4RG1A 4YQ9A 3BBDA 1Z85A 4FAKA 1K3RA 4YQ4A 4YVGA 4YQCA 4YVJA 3AIAA 3GYQA 3KNUA 4IG6A 3QUVA 2QWVA 3KY7A 4H3YA 5FAIA 3ILKA 1P9PA 3BBHA 5CO4A 4YQQA 2YY8A 4YQ0A 4YQ5A 4YQBA 4MCBA 3OIJA 3IEFA 3AI9X 1OY5A 3IC6A 4PZKA 2O3AA 5GMCA 4YQGA 1UAMA 3KTYA 4JAKA 1X7PA 4CNFA 4YQAA 4YVHA 4X3LA 2I6DA 4YQ2A 4CNEA 1X7OA 2V3KA 3O7BA 4YQ6A 4X3MA 1IPAA 4KGNA 2QMMA 3NK7A 3BBEA 4YPWA 4JWFA 5D9FA 4YQTA 3N4KA 1TO0A 4YQRA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 4J3C A;  1GZ0 A;  1MXI A;  4YQD A;  1VHK A;  2HA8 A;  1UAL A;  4MCC A;  1ZJR A;  3AXZ A;  1V6Z A;  4YQ3 A;  4CND A;  4YPX A;  4MCD A;  4YQ8 A;  5GM8 A;  1UAK A;  4H3Z A;  4YVI A;  4YQ1 A;  3ONP A;  1NXZ A;  4YQJ A;  3N4J A;  4CNG A;  4YQO A;  4YPY A;  3OII A;  1J85 A;  1VH0 A;  4JAL A;  2Z0Y A;  4YQL A;  4YVK A;  4YQI A;  4KDZ A;  3OIN A;  1O6D A;  3E5Y A;  1VHY A;  2EGW A;  2V3J A;  4E8B A;  1NS5 A;  4YQS A;  3L8U A;  4L69 A;  5GMB A;  4YQ7 A;  1V2X A;  4YPZ A;  1UAJ A;  2EGV A;  2CX8 A;  4YQN A;  3KW2 A;  3NK6 A;  4XBO A;  4YQP A;  3DCM X;  4YQK A;  4RG1 A;  4YQ9 A;  3BBD A;  1Z85 A;  4FAK A;  1K3R A;  4YQ4 A;  4YVG A;  4YQC A;  4YVJ A;  3AIA A;  3GYQ A;  3KNU A;  4IG6 A;  3QUV A;  2QWV A;  3KY7 A;  4H3Y A;  5FAI A;  3ILK A;  1P9P A;  3BBH A;  5CO4 A;  4YQQ A;  2YY8 A;  4YQ0 A;  4YQ5 A;  4YQB A;  4MCB A;  3OIJ A;  3IEF A;  3AI9 X;  1OY5 A;  3IC6 A;  4PZK A;  2O3A A;  5GMC A;  4YQG A;  1UAM A;  3KTY A;  4JAK A;  1X7P A;  4CNF A;  4YQA A;  4YVH A;  4X3L A;  2I6D A;  4YQ2 A;  4CNE A;  1X7O A;  2V3K A;  3O7B A;  4YQ6 A;  4X3M A;  1IPA A;  4KGN A;  2QMM A;  3NK7 A;  3BBE A;  4YPW A;  5D9F A;  4YQT A;  3N4K A;  1TO0 A;  4YQR A; 
#chains in the Genus database with same CATH topology
 4J3C A;  1GZ0 A;  1MXI A;  4YQD A;  1VHK A;  2HA8 A;  1UAL A;  4MCC A;  1ZJR A;  3AXZ A;  1V6Z A;  4YQ3 A;  4CND A;  4YPX A;  4MCD A;  4YQ8 A;  5GM8 A;  1UAK A;  4JWH A;  4H3Z A;  4YVI A;  4YQ1 A;  3ONP A;  1NXZ A;  4YQJ A;  3N4J A;  4JWJ A;  4JWG A;  4CNG A;  4YQO A;  4YPY A;  3OII A;  1J85 A;  1VH0 A;  4JAL A;  2Z0Y A;  4YQL A;  4YVK A;  4YQI A;  4KDZ A;  3OIN A;  1O6D A;  3E5Y A;  4FMW A;  1VHY A;  2EGW A;  2V3J A;  4E8B A;  1NS5 A;  4YQS A;  3L8U A;  4L69 A;  5GMB A;  4YQ7 A;  1V2X A;  4YPZ A;  1UAJ A;  2EGV A;  2CX8 A;  4YQN A;  3KW2 A;  3NK6 A;  4XBO A;  4YQP A;  3DCM X;  4YQK A;  4RG1 A;  4YQ9 A;  3BBD A;  1Z85 A;  4FAK A;  1K3R A;  4YQ4 A;  4YVG A;  4YQC A;  4YVJ A;  3AIA A;  3GYQ A;  3KNU A;  4IG6 A;  3QUV A;  2QWV A;  3KY7 A;  4H3Y A;  5FAI A;  3ILK A;  1P9P A;  3BBH A;  5CO4 A;  4YQQ A;  2YY8 A;  4YQ0 A;  4YQ5 A;  4YQB A;  4MCB A;  3OIJ A;  3IEF A;  3AI9 X;  1OY5 A;  3IC6 A;  4PZK A;  2O3A A;  5GMC A;  4YQG A;  1UAM A;  3KTY A;  4JAK A;  1X7P A;  4CNF A;  4YQA A;  4YVH A;  4X3L A;  2I6D A;  4YQ2 A;  4CNE A;  1X7O A;  2V3K A;  3O7B A;  4YQ6 A;  4X3M A;  1IPA A;  4KGN A;  2QMM A;  3NK7 A;  3BBE A;  4YPW A;  4JWF A;  5D9F A;  4YQT A;  3N4K A;  1TO0 A;  4YQR A; 
#chains in the Genus database with same CATH homology
 4J3C A;  1GZ0 A;  1MXI A;  4YQD A;  1VHK A;  2HA8 A;  1UAL A;  4MCC A;  1ZJR A;  3AXZ A;  1V6Z A;  4YQ3 A;  4CND A;  4YPX A;  4MCD A;  4YQ8 A;  5GM8 A;  1UAK A;  4JWH A;  4H3Z A;  4YVI A;  4YQ1 A;  3ONP A;  1NXZ A;  4YQJ A;  3N4J A;  4JWJ A;  4JWG A;  4CNG A;  4YQO A;  4YPY A;  3OII A;  1J85 A;  1VH0 A;  4JAL A;  2Z0Y A;  4YQL A;  4YVK A;  4YQI A;  4KDZ A;  3OIN A;  1O6D A;  3E5Y A;  4FMW A;  1VHY A;  2EGW A;  2V3J A;  4E8B A;  1NS5 A;  4YQS A;  3L8U A;  4L69 A;  5GMB A;  4YQ7 A;  1V2X A;  4YPZ A;  1UAJ A;  2EGV A;  2CX8 A;  4YQN A;  3KW2 A;  3NK6 A;  4XBO A;  4YQP A;  3DCM X;  4YQK A;  4RG1 A;  4YQ9 A;  3BBD A;  1Z85 A;  4FAK A;  1K3R A;  4YQ4 A;  4YVG A;  4YQC A;  4YVJ A;  3AIA A;  3GYQ A;  3KNU A;  4IG6 A;  3QUV A;  2QWV A;  3KY7 A;  4H3Y A;  5FAI A;  3ILK A;  1P9P A;  3BBH A;  5CO4 A;  4YQQ A;  2YY8 A;  4YQ0 A;  4YQ5 A;  4YQB A;  4MCB A;  3OIJ A;  3IEF A;  3AI9 X;  1OY5 A;  3IC6 A;  4PZK A;  2O3A A;  5GMC A;  4YQG A;  1UAM A;  3KTY A;  4JAK A;  1X7P A;  4CNF A;  4YQA A;  4YVH A;  4X3L A;  2I6D A;  4YQ2 A;  4CNE A;  1X7O A;  2V3K A;  3O7B A;  4YQ6 A;  4X3M A;  1IPA A;  4KGN A;  2QMM A;  3NK7 A;  3BBE A;  4YPW A;  4JWF A;  5D9F A;  4YQT A;  3N4K A;  1TO0 A;  4YQR A; 
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similar chains in the Genus database (?% sequence similarity)
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similar chains in the pdb database (?% sequence similarity)

 
#similar chains in the Genus database (?% sequence similarity)
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#similar chains, but unknotted
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