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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publication title Methylation at position 32 of tRNA catalyzed by TrmJ alters oxidative stress response in Pseudomonas aeruginosa.
pubmed doi rcsb
molecule keywords tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ
molecule tags Transferase
source organism Pseudomonas aeruginosa
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
4H3ZA 4YQ1A 4H3YA 1OY5A 3OIIA 1UALA 3AI9X 1Z85A 4YQIA 4YQ7A 2EGWA 4YQBA 1V6ZA 3OINA 3NK7A 4KGNA 4YPWA 1MXIA 3DCMX 5D9FA 4CNFA 4YQ5A 4YVIA 4MCBA 2QWVA 1ZJRA 4YVGA 1X7OA 3KTYA 4XBOA 4RG1A 1VHKA 4YVHA 1VHYA 4FAKA 2QMMA 3GYQA 4YPZA 1UAKA 4YQRA 1NS5A 3OIJA 3AIAA 5CO4A 4CNDA 3BBDA 3QUVA 4YQDA 4L69A 4CNGA 1UAMA 4IG6A 4J3CA 4YQSA 4MCCA 4YQKA 4YQ4A 4YQ6A 1K3RA 1TO0A 1O6DA 3KNUA 4YQ0A 3IC6A 1X7PA 5GMCA 4YQ9A 4PZKA 2Z0YA 2HA8A 3O7BA 3KW2A 1IPAA 4E8BA 1J85A 3L8UA 3AXZA 3BBHA 2YY8A 1VH0A 4YPYA 4X3LA 3KY7A 5GM8A 2O3AA 4MCDA 3E5YA 4YQCA 4YQLA 4YQNA 4YQAA 4YVKA 1P9PA 4YQOA 5GMBA 2V3JA 4JALA 2I6DA 3ILKA 1UAJA 3NK6A 3ONPA 4KDZA 2V3KA 4YQTA 1NXZA 4YPXA 2EGVA 4YQQA 1GZ0A 4YQ8A 4JAKA 2CX8A 3BBEA 4X3MA 4YVJA 3IEFA 4YQ2A 4YQ3A 1V2XA 3N4KA 4YQPA 4CNEA 4YQGA 3N4JA 4YQJA 5FAIA
chains in the Genus database with same CATH superfamily
4H3ZA 4YQ1A 4H3YA 1OY5A 3OIIA 1UALA 3AI9X 1Z85A 4YQIA 4YQ7A 2EGWA 4YQBA 1V6ZA 3OINA 3NK7A 4JWJA 4KGNA 4YPWA 1MXIA 3DCMX 5D9FA 4CNFA 4YQ5A 4YVIA 4MCBA 2QWVA 1ZJRA 4YVGA 1X7OA 3KTYA 4XBOA 4RG1A 1VHKA 4YVHA 1VHYA 4FAKA 2QMMA 3GYQA 4YPZA 1UAKA 4YQRA 1NS5A 3OIJA 3AIAA 5CO4A 4JWGA 3BBDA 4CNDA 3QUVA 4YQDA 4L69A 4CNGA 1UAMA 4IG6A 4J3CA 4YQSA 4MCCA 4YQKA 4YQ4A 4YQ6A 4FMWA 1K3RA 1TO0A 1O6DA 3KNUA 4YQ0A 3IC6A 1X7PA 5GMCA 4YQ9A 4PZKA 2Z0YA 2HA8A 3O7BA 3KW2A 1IPAA 4E8BA 1J85A 3L8UA 3AXZA 3BBHA 2YY8A 1VH0A 4YPYA 4X3LA 3KY7A 5GM8A 2O3AA 4MCDA 3E5YA 4YQCA 4YQLA 4YQNA 4YQAA 4YVKA 1P9PA 4YQOA 4JWHA 5GMBA 2V3JA 4JALA 2I6DA 3ILKA 1UAJA 3NK6A 3ONPA 4KDZA 2V3KA 4YQTA 1NXZA 4YPXA 2EGVA 4YQQA 1GZ0A 4YQ8A 4JAKA 2CX8A 3BBEA 4X3MA 4YVJA 3IEFA 4JWFA 4YQ2A 4YQ3A 1V2XA 3N4KA 4YQPA 4CNEA 4YQGA 3N4JA 4YQJA 5FAIA
chains in the Genus database with same CATH topology
4H3ZA 4YQ1A 4H3YA 1OY5A 3OIIA 1UALA 3AI9X 1Z85A 4YQIA 4YQ7A 2EGWA 4YQBA 1V6ZA 3OINA 3NK7A 4JWJA 4KGNA 4YPWA 1MXIA 3DCMX 5D9FA 4CNFA 4YQ5A 4YVIA 4MCBA 2QWVA 1ZJRA 4YVGA 1X7OA 3KTYA 4XBOA 4RG1A 1VHKA 4YVHA 1VHYA 4FAKA 2QMMA 3GYQA 4YPZA 1UAKA 4YQRA 1NS5A 3OIJA 3AIAA 5CO4A 4JWGA 3BBDA 4CNDA 3QUVA 4YQDA 4L69A 4CNGA 1UAMA 4IG6A 4J3CA 4YQSA 4MCCA 4YQKA 4YQ4A 4YQ6A 4FMWA 1K3RA 1TO0A 1O6DA 3KNUA 4YQ0A 3IC6A 1X7PA 5GMCA 4YQ9A 4PZKA 2Z0YA 2HA8A 3O7BA 3KW2A 1IPAA 4E8BA 1J85A 3L8UA 3AXZA 3BBHA 2YY8A 1VH0A 4YPYA 4X3LA 3KY7A 5GM8A 2O3AA 4MCDA 3E5YA 4YQCA 4YQLA 4YQNA 4YQAA 4YVKA 1P9PA 4YQOA 4JWHA 5GMBA 2V3JA 4JALA 2I6DA 3ILKA 1UAJA 3NK6A 3ONPA 4KDZA 2V3KA 4YQTA 1NXZA 4YPXA 2EGVA 4YQQA 1GZ0A 4YQ8A 4JAKA 2CX8A 3BBEA 4X3MA 4YVJA 3IEFA 4JWFA 4YQ2A 4YQ3A 1V2XA 3N4KA 4YQPA 4CNEA 4YQGA 3N4JA 4YQJA 5FAIA
chains in the Genus database with same CATH homology


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