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(-) Description

Title :  SOLUTION STRUCTURE OF AN RRNA METHYLTRANSFERASE (ERMAM) THAT CONFERS MACROLIDE-LINCOSAMIDE-STREPTOGRAMIN ANTIBIOTIC RESISTANCE, NMR, MINIMIZED AVERAGE STRUCTURE
 
Authors :  L. Yu, A. M. Petros, A. Schnuchel, P. Zhong, J. M. Severin, K. Walter, T. F. Holzman, S. W. Fesik
Date :  04 Mar 97  (Deposition) - 04 Mar 98  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A
Keywords :  Methyltransferase, Erm, Ermam, Mls Antibiotics, Nmr, Rrna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Yu, A. M. Petros, A. Schnuchel, P. Zhong, J. M. Severin, K. Walter, T. F. Holzman, S. W. Fesik
Solution Structure Of An Rrna Methyltransferase (Ermam) That Confers Macrolide-Lincosamide-Streptogramin Antibiotic Resistance.
Nat. Struct. Biol. V. 4 483 1997
PubMed-ID: 9187657  |  Reference-DOI: 10.1038/NSB0697-483
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RRNA METHYLTRANSFERASE
    Cell Line: BL21
    Chains: A
    EC Number: 2.1.1.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Gene: ERM
    Expression System Plasmid: PET-24(+)
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Gene: ERM
    Mutation: YES
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 1313
    Strain: 5728, A CLINICAL ISOLATE FROM ABBOTT CULTURE COLLECTION
    Synonym: ERMAM

 Structural Features

(-) Chains, Units

  
NMR Structure : 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1YUB)

(-) Sites  (0, 0)

(no "Site" information available for 1YUB)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

NMR Structure
No.Residues
1His A:163 -Pro A:164

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_RNA_A_N6_MTPS51689 rRNA adenine N(6)-methyltransferase family profile.ERM_STREE3-242  1A:3-242
2RRNA_A_DIMETHPS01131 Ribosomal RNA adenine dimethylases signature.ERM_STREE33-60  1A:33-60

(-) Exons   (0, 0)

(no "Exon" information available for 1YUB)

(-) Sequences/Alignments

NMR Structure
   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:245
 aligned with ERM_STREE | P21236 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:245
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240     
            ERM_STREE     1 MNKNIKYSQNFLTSEKVLNQIIKQLNLKETDTVYEIGTGKGHLTTKLAKISKQVTSIELDSHLFNLSSEKLKLNIRVTLIHQDILQFQFPNKQRYKIVGSIPYHLSTQIIKKVVFESHASDIYLIVEEGFYKRTLDIHRTLGLLLHTQVSIQQLLKLPAECFHPKPKVNSVLIKLTRHTTDVPDKYWKLYTYFVSKWVNREYRQLFTKNQFHQAMKHAKVNNLSTITYEQVLSIFNSYLLFNGRK 245
               SCOP domains d1yuba_ A: rRNA adenine dimethylase                                                                                                                                                                                                                   SCOP domains
               CATH domains 1yubA01 A:1-133,A:148-179 Vaccinia Virus protein VP39                                                                                1yubA02       1yubA01 A:1-133,A:148-179       1yubA02 A:134-147,A:180-245  [code=1.10.8.100, no name defined]    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee..hhhhhhhhhh......eeeee......hhhhhhhh..eeeee....hhhh..........eeeee....hhhh......eeeeee.....hhhhhhhhhhh...eeeeeeee.hhhhhhhh...hhhhhhh..eeeeeeee....eee......eeeeeeee........hhhhhhhhhhhhhh..hhhh....hhhhhhhhh.........hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --SAM_RNA_A_N6_MT  PDB: A:3-242 UniProt: 3-242                                                                                                                                                                                                    --- PROSITE (1)
                PROSITE (2) --------------------------------RRNA_A_DIMETH  PDB: A:33-60 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yub A   1 MNKNIKYSQNFLTSEKVLNQIIKQLNLKETDTVYEIGTGKGHLTTKLAKISKQVTSIELDSHLFNLSSEKLKLNTRVTLIHQDILQFQFPNKQRYKIVGNIPYHLSTQIIKKVVFESRASDIYLIVEEGFYKRTLDIHRTLGLLLHTQVSIQQLLKLPAECFHPKPKVNSVLIKLTRHTTDVPDKYWKLYTYFVSKWVNREYRQLFTKNQFHQAMKHAKVNNLSTITYEQVLSIFNSYLLFNGRK 245
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
   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)

NMR Structure
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

NMR Structure
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

NMR Structure(hide GO term definitions)
Chain A   (ERM_STREE | P21236)
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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    His A:163 - Pro A:164   [ RasMol ]  
 

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