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


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