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


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