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(-) Description

Title :  THE STRUCTURE OF THE RRNA METHYLTRANSFERASE ERMC': IMPLICATIONS FOR THE REACTION MECHANISM
 
Authors :  G. Schluckebier, P. Zhong, K. D. Stewart, T. J. Kavanaugh, C. Abad- Zapatero
Date :  25 Mar 99  (Deposition) - 29 Mar 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Rrna Methyltransferase Ermc', Cofactor Analogs (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Schluckebier, P. Zhong, K. D. Stewart, T. J. Kavanaugh, C. Abad-Zapatero
The 2. 2 A Structure Of The Rrna Methyltransferase Ermc' And Its Complexes With Cofactor And Cofactor Analogs: Implications For The Reaction Mechanism.
J. Mol. Biol. V. 289 277 1999
PubMed-ID: 10366505  |  Reference-DOI: 10.1006/JMBI.1999.2788
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ERMC' METHYLTRANSFERASE
    Chains: A
    EC Number: 2.1.1.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:131 , ARG A:134 , ARG A:140 , HOH A:943BINDING SITE FOR RESIDUE ACT A 901
2AC2SOFTWARESER A:15 , LYS A:16 , HIS A:17 , ASN A:33 , PHE A:54 , GLN A:79 , HOH A:907 , HOH A:1019 , HOH A:1092BINDING SITE FOR RESIDUE ACT A 902

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1QAM)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1His A:164 -Pro A:165

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QAM)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRNA_A_DIMETHPS01131 Ribosomal RNA adenine dimethylases signature.ERM_BACIU34-61  1A:34-61

(-) Exons   (0, 0)

(no "Exon" information available for 1QAM)

(-) 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:235
 aligned with ERM_BACIU | P13956 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:235
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239     
            ERM_BACIU    10 QNFITSKHNIDKIMTNIRLNEHDNIFEIGSGKGHFTLELVQRCNFVTAIEIDHKLCKTTENKLVDHDNFQVLNKDILQFKFPKNQSYKIFGNIPYNISTDIIRKIVFDSIADEIYLIVEYGFAKRLLNTKRSLALFLMAEVDISILSMVPREYFHPKPKVNSSLIRLNRKKSRISHKDKQKYNYFVMKWVNKEYKKIFTKNQFNNSLKHAGIDDLNNISFEQFLSLFNSYKLFNK 244
               SCOP domains d1qama_ A: rRNA adenine dimethylase                                                                                                                                                                                                         SCOP domains
               CATH domains 1qamA01 A:10-134,A:149-180 Vaccinia Virus protein VP39                                                                       1qamA02       1qamA01 A:10-134,A:149-180      1qamA02 A:135-148,A:181-244  [code=1.10.8.100, no name defined]  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhh........eeeee....hhhhhhhhhhh.eeeee..hhhhhhhhhhhh.....eeee..hhhhh........eeeee.hhhhhhhhhhhhhhh....eeeeeeehhhhhhhh...hhhhhhhh..eeeeeeeeehhhhh.......eeeeeeee.....hhhhhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------RRNA_A_DIMETH  PDB: A:34-61 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qam A  10 QNFITSKHNIDKIMTNIRLNEHDNIFEIGSGKGHFTLELVQRCNFVTAIEIDHKLCKTTENKLVDHDNFQVLNKDILQFKFPKNQSYKIFGNIPYNISTDIIRKIVFDSIADEIYLIVEYGFAKRLLNTKRSLALFLMAEVDISILSMVPREYFHPKPKVNSSLIRLNRKKSRISHKDKQKYNYFVMKWVNKEYKKIFTKNQFNNSLKHAGIDDLNNISFEQFLSLFNSYKLFNK 244
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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, 1)

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

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1QAM)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ERM_BACIU | P13956)
molecular function
    GO:0052910    23S rRNA (adenine(2085)-N(6))-dimethyltransferase activity    Catalysis of the reaction: 2 S-adenosyl-L-methionine + adenine(2085) in 23S rRNA = 2 S-adenosyl-L-homocysteine + N(6)-dimethyladenine(2085) in 23S rRNA.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0000179    rRNA (adenine-N6,N6-)-dimethyltransferase activity    Catalysis of the dimethylation two adjacent A residues in the loop closing the 3'-terminal stem of the 18S rRNA, using S-adenosyl-L-methionine as a methyl donor.
    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:0000154    rRNA modification    The covalent alteration of one or more nucleotides within an rRNA molecule to produce an rRNA molecule with a sequence that differs from that coded genetically.
    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

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ERM_BACIU | P13956: 1qan 1qao 1qaq 2erc

(-) Related Entries Specified in the PDB File

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