Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  RRNA METHYLTRANSFERASE AVIRA FROM STREPTOMYCES VIRIDOCHROMOGENES AT 1.5A
 
Authors :  T. G. Mosbacher, G. E. Schulz
Date :  13 Dec 02  (Deposition) - 16 May 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Transferase, Antibiotic Resistance; Rrna-Methyltransferase, Se-Mad (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. G. Mosbacher, A. Bechthold, G. E. Schulz
Crystal Structure Of The Avilamycin Resistance-Conferring Methyltransferase Avira From Streptomyces Viridochromogenes
J. Mol. Biol. V. 329 147 2003
PubMed-ID: 12742024  |  Reference-DOI: 10.1016/S0022-2836(03)00407-8

(-) Compounds

Molecule 1 - RRNA METHYLTRANSFERASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSETB
    Expression System Strain: B834
    Expression System Taxid: 562
    Expression System Variant: SE-MET
    Mutation: YES
    Organism Scientific: STREPTOMYCES VIRIDOCHROMOGENES
    Organism Taxid: 1938

 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
1MSE2Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1O9G)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1O9G)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:222 -Pro A:223

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1O9G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1O9G)

(-) Exons   (0, 0)

(no "Exon" information available for 1O9G)

(-) 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:249
 aligned with AVRA_STRVR | Q9F5K5 from UniProtKB/Swiss-Prot  Length:250

    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         
           AVRA_STRVR     2 SAYRHAVERIDSSDLACGVVLHSAPGYPAFPVRLATEIFQRALARLPGDGPVTLWDPCCGSGYLLTVLGLLHRRSLRQVIASDVDPAPLELAAKNLALLSPAGLTARELERREQSERFGKPSYLEAAQAARRLRERLTAEGGALPCAIRTADVFDPRALSAVLAGSAPDVVLTDLPYGERTHWEGQVPAQPVAGLLRSLASALPAHAVIAVTDRSRKIPVAPVKALERLKIGTRSAVLVRAADVLEAGP 250
               SCOP domains d1o9ga_ A: rRNA methyltransferase AviRa                                                                                                                                                                                                                   SCOP domains
               CATH domains 1o9gA01 A:2-101,A:145-250 Vaccinia Virus protein VP39                                               1o9gA02 A:102-144 Helix hairpin bin        1o9gA01 A:2-101,A:145-250 Vaccinia Virus protein VP39                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhh..............hhhhhhhhhhhhhhh......eeeee.....hhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhh.....eeeee.hhhhh.......hhhhhhhhhhhhhhhh....eeeeee.............eeeee..eeeeeeehhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o9g A   2 SAYRHAVERmDSSDLACGVVLHSAPGYPAFPVRLATEIFQRALARLPGDGPVTLWDPCCGSGYLLTVLGLLHRRSLRQVIASDVDPAPLELAAKNLALLSPAGLTARELERREQSERFGKPSYLEAAQAARRLRERLTAEGGALPCAIRTADVFDPRALSAVLAGSAPDVVLTDLPYGERTHWEGQVPGQPVAGLLRSLASALPAHAVIAVTDRSRKIPVAPVKALERLKIGTRSAVmVRAADVLEAGP 250
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241         
                                    11-MSE                                                                                                                                                                                                                             239-MSE
   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 1O9G)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (AVRA_STRVR | Q9F5K5)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0008989    rRNA (guanine-N1-)-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing N1-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: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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 1o9g)
 
  Cis Peptide Bonds
    Ala A:222 - Pro A:223   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1o9g
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  AVRA_STRVR | Q9F5K5
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  AVRA_STRVR | Q9F5K5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        AVRA_STRVR | Q9F5K5: 1o9h

(-) Related Entries Specified in the PDB File

1o9g RRNA METHYLTRANSFERASE AVIRA FROM STREPTOMYCES VIRIDOCHROMOGENES AT 1.5A
1qam THE STRUCTURE OF THE RRNA METHYLTRANSFERASE ERMC': IMPLICATIONS FOR THE REACTION MECHANISM
1qan THE STRUCTURE OF THE RRNA METHYLTRANSFERASE ERMC': IMPLICATIONS FOR THE REACTION MECHANISM
1qao THE STRUCTURE OF THE RRNA METHYLTRANSFERASE ERMC': IMPLICATIONS FOR THE REACTION MECHANISM
1qaq THE STRUCTURE OF THE RRNA METHYLTRANSFERASE ERMC': IMPLICATIONS FOR THE REACTION MECHANISM
1yub SOLUTION STRUCTURE OF AN RRNA METHYLTRANSFERASE (ERMAM) THAT CONFERS MACROLIDE -LINCOSAMIDE-STREPTOGRAMIN ANTIBIOTIC RESISTANCE, NMR, MINIMIZED AVERAGE STRUCTURE