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(-) Description

Title :  CRYSTAL STRUCTURE OF RRNA METHYLASE FROM ESCHERICHIA COLI
 
Authors :  S. Eswaramoorthy, S. K. Burley, S. Swaminathan, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  31 Oct 07  (Deposition) - 27 Nov 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A
Keywords :  10094B, Nysgxrc, Rmtb, Structural Genomics, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Methyltransferase, Plasmid (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Eswaramoorthy, S. K. Burley, S. Swaminathan
Crystal Structure Of Rrna Methylase From Escherichia Coli.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 16S RRNA METHYLASE
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneRMTB
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    Synonym16S RIBOSOMAL RNA METHYLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
15GP1Ligand/IonGUANOSINE-5'-MONOPHOSPHATE
2MSE2Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:53 , HIS A:81 , SER A:83 , ALA A:111 , ASP A:131 , ILE A:132 , GLN A:156 , ASP A:157 , VAL A:158 , PHE A:173 , LYS A:174 , HOH A:522BINDING SITE FOR RESIDUE 5GP A 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3B89)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3B89)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3B89)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3B89)

(-) Exons   (0, 0)

(no "Exon" information available for 3B89)

(-) 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:240
 aligned with Q763K9_ECOLX | Q763K9 from UniProtKB/TrEMBL  Length:251

    Alignment length:249
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241         
         Q763K9_ECOLX     2 NINDALTSILASKKYRALCPDTVRRILTEEWGRHKSPKQTVEAARTRLHGICGAYVTPESLKAAAAALSAGDVKKALSLHASTKERLAELDTLYDFIFSAETPRRVLDIACGLNPLALYERGIASVWGCDIHQGLGDVITPFAREKDWDFTFALQDVLCAPPAEAGDLALIFKLLPLLEREQAGSAMALLQSLNTPRMAVSFPTRSLGGRGKGMEANYAAWFEGGLPAEFEIEDKKTIGTELIYLIKKN 250
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3b89A01 A:2-55                                         3b89A02 A:57-250 Vaccinia Virus protein VP39                                                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh........hhhhhhhhhhhhhhh......hhhhhhhhhhh....-.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhh.....eeeee....hhhhhhh....eeeeee.hhhhhhhhhhhhhh...eeeeee.............eeee..hhhhhhhhh.hhhhhhhhh....eeeeeee...--------..hhhhhhhhhh...eeeeeeeee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b89 A   2 NINDALTSILASKKYRALCPDTVRRILTEEWGRHKSPKQTVEAARTRLHGICGA-VTPESLKAAAAALSAGDVKKALSLHASTKERLAELDTLYDFIFSAETPRRVLDIACGLNPLALYERGIASVWGCDIHQGLGDVITPFAREKDWDFTFALQDVLCAPPAEAGDLALIFKLLPLLEREQAGSAmALLQSLNTPRmAVSFPTRS--------EANYAAWFEGGLPAEFEIEDKKTIGTELIYLIKKN 250
                                    11        21        31        41        51   | |  61        71        81        91       101       111       121       131       141       151       161       171       181      |191       201     |   -    |  221       231       241         
                                                                                55 |                                                                                                                                188-MSE    199-MSE 207      216                                  
                                                                                  57                                                                                                                                                                                                 

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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  (0, 0)

(no "SCOP Domain" information available for 3B89)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3B89)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q763K9_ECOLX | Q763K9)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0008649    rRNA methyltransferase activity    Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a nucleoside residue in an rRNA molecule.
    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:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0031167    rRNA methylation    The posttranscriptional addition of methyl groups to specific residues in an rRNA molecule.
    GO:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.

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 Related Entries

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UniProtKB/TrEMBL
        Q763K9_ECOLX | Q763K93frh 3fri

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