5GMCA

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
174
structure length
174
Chain Sequence
NLYFQSMMLDRIRVVLVNTSHPGNIGGAARAMKNMGLSQLVLVQPESFPHGDAVARASGATDILDAARVVDTLEEALSGCSVVLGTSARDRRIPWPLLDPRECATTCLEHLEANGEVALVFGREYAGLTNEELQRCQFHVHIPSDPEFGSLNLAAAVQVLTYEVRMAWLAAQGK
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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 174
sequence length 174
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 5gmcA01
4YVKA 4YQJA 4YQLA 4E8BA 2O3AA 3BBDA 5GM8A 3DCMX 4CNDA 3AIAA 3KW2A 4JALA 4YQ7A 4YQ0A 1P9PA 4YQ4A 3ILKA 4YQSA 1X7OA 1VH0A 4FAKA 3NK7A 4YQNA 4YQAA 4PZKA 2QMMA 1Z85A 3ONPA 1V2XA 3QUVA 3E5YA 3IC6A 3BBHA 1NXZA 1IPAA 4RG1A 2I6DA 4YQ9A 3KTYA 1MXIA 3KNUA 4IG6A 4CNFA 3IEFA 2CX8A 1UAMA 4X3MA 1V6ZA 4YQOA 2Z0YA 4YQTA 5D9FA 1X7PA 5CO4A 4YQRA 4YQKA 4YQ1A 4CNGA 1K3RA 3L8UA 1VHKA 2EGWA 3N4JA 4J3CA 3OIIA 1J85A 2V3KA 1UAKA 4MCBA 4YQBA 4YQ2A 3O7BA 4XBOA 4YPWA 1UALA 3OINA 4YPZA 4YQIA 4CNEA 1OY5A 2HA8A 4YVGA 2QWVA 4YQ3A 4YQCA 4L69A 5FAIA 1VHYA 5GMCA 3AXZA 4H3YA 3N4KA 4H3ZA 2V3JA 4YVIA 4JAKA 4KDZA 2YY8A 3OIJA 3GYQA 1GZ0A 4YPXA 1TO0A 4YVJA 1O6DA 1UAJA 1NS5A 4YQQA 5GMBA 4YVHA 3NK6A 1ZJRA 4MCDA 4X3LA 4MCCA 4YPYA 4YQGA 4YQPA 4YQ6A 4KGNA 4YQ5A 2EGVA 3AI9X 3BBEA 4YQ8A 3KY7A 4YQDA
chains in the Genus database with same CATH superfamily
4YVKA 4YQJA 4YQLA 4E8BA 2O3AA 3BBDA 5GM8A 3DCMX 4CNDA 3AIAA 3KW2A 4JALA 4YQ7A 4YQ0A 1P9PA 4JWGA 4YQ4A 3ILKA 4YQSA 1X7OA 1VH0A 4FAKA 3NK7A 4YQNA 4YQAA 4PZKA 2QMMA 1Z85A 3ONPA 1V2XA 3QUVA 3E5YA 3IC6A 3BBHA 1NXZA 1IPAA 4RG1A 2I6DA 4YQ9A 3KTYA 1MXIA 3KNUA 4IG6A 4CNFA 3IEFA 2CX8A 1UAMA 4X3MA 1V6ZA 4YQOA 2Z0YA 4YQTA 4JWJA 5D9FA 1X7PA 5CO4A 4YQRA 4YQKA 4YQ1A 4CNGA 1K3RA 3L8UA 1VHKA 2EGWA 3N4JA 4J3CA 3OIIA 1J85A 2V3KA 1UAKA 4MCBA 4FMWA 4YQBA 4YQ2A 3O7BA 4XBOA 4YPWA 1UALA 3OINA 4YPZA 4YQIA 4CNEA 1OY5A 4JWFA 2HA8A 4YVGA 2QWVA 4YQ3A 4YQCA 4L69A 5FAIA 1VHYA 5GMCA 3AXZA 4H3YA 3N4KA 4H3ZA 2V3JA 4YVIA 4JAKA 4KDZA 2YY8A 3OIJA 3GYQA 1GZ0A 4YPXA 1TO0A 4YVJA 1O6DA 1UAJA 1NS5A 4YQQA 5GMBA 4YVHA 3NK6A 4JWHA 1ZJRA 4MCDA 4X3LA 4MCCA 4YPYA 4YQGA 4YQPA 4YQ6A 4KGNA 4YQ5A 2EGVA 3AI9X 3BBEA 4YQ8A 3KY7A 4YQDA
chains in the Genus database with same CATH topology
4YVKA 4YQJA 4YQLA 4E8BA 2O3AA 3BBDA 5GM8A 3DCMX 4CNDA 3AIAA 3KW2A 4JALA 4YQ7A 4YQ0A 1P9PA 4JWGA 4YQ4A 3ILKA 4YQSA 1X7OA 1VH0A 4FAKA 3NK7A 4YQNA 4YQAA 4PZKA 2QMMA 1Z85A 3ONPA 1V2XA 3QUVA 3E5YA 3IC6A 3BBHA 1NXZA 1IPAA 4RG1A 2I6DA 4YQ9A 3KTYA 1MXIA 3KNUA 4IG6A 4CNFA 3IEFA 2CX8A 1UAMA 4X3MA 1V6ZA 4YQOA 2Z0YA 4YQTA 4JWJA 5D9FA 1X7PA 5CO4A 4YQRA 4YQKA 4YQ1A 4CNGA 1K3RA 3L8UA 1VHKA 2EGWA 3N4JA 4J3CA 3OIIA 1J85A 2V3KA 1UAKA 4MCBA 4FMWA 4YQBA 4YQ2A 3O7BA 4XBOA 4YPWA 1UALA 3OINA 4YPZA 4YQIA 4CNEA 1OY5A 4JWFA 2HA8A 4YVGA 2QWVA 4YQ3A 4YQCA 4L69A 5FAIA 1VHYA 5GMCA 3AXZA 4H3YA 3N4KA 4H3ZA 2V3JA 4YVIA 4JAKA 4KDZA 2YY8A 3OIJA 3GYQA 1GZ0A 4YPXA 1TO0A 4YVJA 1O6DA 1UAJA 1NS5A 4YQQA 5GMBA 4YVHA 3NK6A 4JWHA 1ZJRA 4MCDA 4X3LA 4MCCA 4YPYA 4YQGA 4YQPA 4YQ6A 4KGNA 4YQ5A 2EGVA 3AI9X 3BBEA 4YQ8A 3KY7A 4YQDA
chains in the Genus database with same CATH homology


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