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(-) Description

Title :  THE STRUCTURE OF BSTRMB
 
Authors :  I. Zegers, F. Van Vliet, J. Bujnicki, J. Kosinski, D. Gigot, L. Droogmans
Date :  12 Dec 05  (Deposition) - 15 Aug 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Methyltransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Zegers, D. Gigot, F. Van Vliet, C. Tricot, S. Aymerich, J. M. Bujnicki, J. Kosinski, L. Droogmans
Crystal Structure Of Bacillus Subtilis Trmb, The Trna (M7G46) Methyltransferase.
Nucleic Acids Res. V. 34 1925 2006
PubMed-ID: 16600901  |  Reference-DOI: 10.1093/NAR/GKL116
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRNA (GUANINE-N(7)-)-METHYLTRANSFERASE
    Chains: A, B
    EC Number: 2.1.1.33
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: TRMB
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: TRNAM7G46, - METHYLTRANSFERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1K3Ligand/IonPOTASSIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:46 , ASN A:115 , HOH A:257 , HOH A:578BINDING SITE FOR RESIDUE K A 250
2AC2SOFTWAREGLY B:46 , ASN B:115 , HOH B:261 , HOH B:315 , HOH B:423 , HOH B:469BINDING SITE FOR RESIDUE K B 251
3AC3SOFTWARESER A:167 , LEU A:171 , SER B:167 , LEU B:171BINDING SITE FOR RESIDUE K A 252

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2FCA)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2FCA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2FCA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2FCA)

(-) Exons   (0, 0)

(no "Exon" information available for 2FCA)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:205
 aligned with TRMB_BACSU | O34522 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:206
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207      
           TRMB_BACSU     8 WADDFLAENADIAISNPADYKGKWNTVFGNDNPIHIEVGTGKGQFISGMAKQNPDINYIGIELFKSVIVTAVQKVKDSEAQNVKLLNIDADTLTDVFEPGEVKRVYLNFSDPWPKKRHEKRRLTYSHFLKKYEEVMGKGGSIHFKTDNRGLFEYSLKSFSEYGLLLTYVSLDLHNSNLEGNIMTEYEEKFSALGQPIYRAEVEWRT 213
               SCOP domains --d2fcaa1 A:10-213 tRNA (guanine-N(7)-)-methyltransferase TrmB                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author h-hhhhhhh......hhhhhh.hhhhhhh....eeeee....hhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhh....eeee..hhhhhhhhh......eeeee......hhhhhhhh..hhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh.eeeeee.hhhhh.........hhhhh.......eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fca A   9 W-DDFLAENADIAISNPADYKGKWNTVFGNDNPIHIEVGTGKGQFISGMAKQNPDINYIGIELFKSVIVTAVQKVKDSEAQNVKLLNIDADTLTDVFEPGEVKRVYLNFSDPWPKKRHEKRRLTYSHFLKKYEEVMGKGGSIHFKTDNRGLFEYSLKSFSEYGLLLTYVSLDLHNSNLEGNIMTEYEEKFSALGQPIYRAEVEWRT 213
                            | |     17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207      
                            | |                                                                                                                                                                                                           
                            9 |                                                                                                                                                                                                           
                             10                                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:203
 aligned with TRMB_BACSU | O34522 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:203
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   
           TRMB_BACSU    11 DFLAENADIAISNPADYKGKWNTVFGNDNPIHIEVGTGKGQFISGMAKQNPDINYIGIELFKSVIVTAVQKVKDSEAQNVKLLNIDADTLTDVFEPGEVKRVYLNFSDPWPKKRHEKRRLTYSHFLKKYEEVMGKGGSIHFKTDNRGLFEYSLKSFSEYGLLLTYVSLDLHNSNLEGNIMTEYEEKFSALGQPIYRAEVEWRT 213
               SCOP domains d2fcab_ B: tRNA (guanine-N(7)-)-methyltransferase TrmB                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhh.hhhhhhh....eeeee....hhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhh....eeee..hhhhhhhh.......eeeee......hhhhhhhh..hhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh.eeeeee.hhhhh.....................eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fca B  11 DFLAENADIAISNPADYKGKWNTVFGNDNPIHIEVGTGKGQFISGMAKQNPDINYIGIELFKSVIVTAVQKVKDSEAQNVKLLNIDADTLTDVFEPGEVKRVYLNFSDPWPKKRHEKRRLTYSHFLKKYEEVMGKGGSIHFKTDNRGLFEYSLKSFSEYGLLLTYVSLDLHNSNLEGNIMTEYEEKFSALGQPIYRAEVEWRT 213
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2FCA)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2FCA)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TRMB_BACSU | O34522)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0008176    tRNA (guanine-N7-)-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing N7-methylguanine.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0036265    RNA (guanine-N7)-methylation    The addition of a methyl group to the N7 atom in the base portion of a guanine nucleotide residue in an RNA molecule.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0006400    tRNA modification    The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.
    GO:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
cellular component
    GO:0043527    tRNA methyltransferase complex    A multimeric protein complex involved in the methylation of specific nucleotides in tRNA.

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