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 :  CRYSTAL STRUCTURE OF SAM-DEPENDENT METHYLTRANSFERASE FROM BACTEROIDES VULGATUS ATCC 8482
 
Authors :  V. N. Malashkevich, R. Toro, U. Ramagopal, A. J. Meyer, J. M. Sauder, S. K S. C. Almo, New York Sgx Research Center For Structural Genomi (Nysgxrc)
Date :  07 Jul 08  (Deposition) - 29 Jul 08  (Release) - 11 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.33
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Protein Structure Initiative, New York Structural Genomix Research, Sam-Dependent Methyltransferase =Consortium, Nysgxrc, Methyltransferase, Transferase, Psi-2, New York Sgx Research Center For Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. N. Malashkevich, R. Toro, U. Ramagopal, A. J. Meyer, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of Sam-Dependent Methyltransferase From Bacteroides Vulgatus Atcc 8482
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SAM-DEPENDENT METHYLTRANSFERASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX3(BC)
    Expression System Strain: BL21(DE3)CODON+RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BVU_1015
    Organism Scientific: BACTEROIDES VULGATUS
    Organism Taxid: 435590
    Strain: ATCC 8482

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3DP7)

(-) Sites  (0, 0)

(no "Site" information available for 3DP7)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3DP7)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asn A:316 -Ser A:317

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3DP7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3DP7)

(-) Exons   (0, 0)

(no "Exon" information available for 3DP7)

(-) 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:351
 aligned with A6KZ44_BACV8 | A6KZ44 from UniProtKB/TrEMBL  Length:356

    Alignment length:351
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355 
         A6KZ44_BACV8     6 YTKEQCTAAEAQRLAQEIAFGPVVFQVSRLMLKFGIFQLLSGKREGYTLQEISGRTGLTRYAAQVLLEASLTIGTILLEEDRYVLAKAGWFLLNDKMARVNMEFNHDVNYQGLFHLEEALLNGRPEGLKVFGEWPTIYEGLSQLPEQVQKSWFGFDHFYSDQSFGKALEIVFSHHPKRLLDIGGNTGKWATQCVQYNKEVEVTIVDLPQQLEMMRKQTAGLSGSERIHGHGANLLDRDVPFPTGFDAVWMSQFLDCFSEEEVISILTRVAQSIGKDSKVYIMETLWDRQRYETASYCLTQISLYFTAMANGNSKMFHSDDLIRCIENAGLEVEEIQDNIGLGHSILQCRLK 356
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhhhhhhhhh.eeee..eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh..eeeee....hhhhhhhhhhh...eeeeeehhhhhhhhhhhhh...hhh.eeeee...............eeeee......hhhhhhhhhhhhhhhh....eeeeee.......hhhhhhhhhhhhhhhhhh........hhhhhhhhhhh..eee...........eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dp7 A   5 YTKEQCTAAEAQRLAQEIAFGPVVFQVSRLMLKFGIFQLLSGKREGYTLQEISGRTGLTRYAAQVLLEASLTIGTILLEEDRYVLAKAGWFLLNDKMARVNMEFNHDVNYQGLFHLEEALLNGRPEGLKVFGEWPTIYEGLSQLPEQVQKSWFGFDHFYSDQSFGKALEIVFSHHPKRLLDIGGNTGKWATQCVQYNKEVEVTIVDLPQQLEMMRKQTAGLSGSERIHGHGANLLDRDVPFPTGFDAVWMSQFLDCFSEEEVISILTRVAQSIGKDSKVYIMETLWDRQRYETASYCLTQISLYFTAMANGNSKMFHSDDLIRCIENAGLEVEEIQDNIGLGHSILQCRLK 355
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354 


Chain B from PDB  Type:PROTEIN  Length:350
 aligned with A6KZ44_BACV8 | A6KZ44 from UniProtKB/TrEMBL  Length:356

    Alignment length:350
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356
         A6KZ44_BACV8     7 TKEQCTAAEAQRLAQEIAFGPVVFQVSRLMLKFGIFQLLSGKREGYTLQEISGRTGLTRYAAQVLLEASLTIGTILLEEDRYVLAKAGWFLLNDKMARVNMEFNHDVNYQGLFHLEEALLNGRPEGLKVFGEWPTIYEGLSQLPEQVQKSWFGFDHFYSDQSFGKALEIVFSHHPKRLLDIGGNTGKWATQCVQYNKEVEVTIVDLPQQLEMMRKQTAGLSGSERIHGHGANLLDRDVPFPTGFDAVWMSQFLDCFSEEEVISILTRVAQSIGKDSKVYIMETLWDRQRYETASYCLTQISLYFTAMANGNSKMFHSDDLIRCIENAGLEVEEIQDNIGLGHSILQCRLK 356
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhh..hhhhhhhhhhhhhhh.eeee..eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh........hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh....eeeee....hhhhhhhhhhh...eeeeeehhhhhhhhhhhh....hhh.eeeee...............eeeee......hhhhhhhhhhhhhh......eeeeee.hhhhh.hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh.eeeeeeeeee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dp7 B   6 TKEQCTAAEAQRLAQEIAFGPVVFQVSRLMLKFGIFQLLSGKREGYTLQEISGRTGLTRYAAQVLLEASLTIGTILLEEDRYVLAKAGWFLLNDKMARVNMEFNHDVNYQGLFHLEEALLNGRPEGLKVFGEWPTIYEGLSQLPEQVQKSWFGFDHFYSDQSFGKALEIVFSHHPKRLLDIGGNTGKWATQCVQYNKEVEVTIVDLPQQLEMMRKQTAGLSGSERIHGHGANLLDRDVPFPTGFDAVWMSQFLDCFSEEEVISILTRVAQSIGKDSKVYIMETLWDRQRYETASYCLTQISLYFTAMANGNSKMFHSDDLIRCIENAGLEVEEIQDNIGLGHSILQCRLK 355
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355
   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  (0, 0)

(no "SCOP Domain" information available for 3DP7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3DP7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DP7)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (A6KZ44_BACV8 | A6KZ44)
molecular function
    GO:0008171    O-methyltransferase activity    Catalysis of the transfer of a methyl group to the oxygen atom of an acceptor molecule.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor 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.

 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
(no "Ligands, Modified Residues, Ions" information available for 3dp7)
 
  Sites
(no "Sites" information available for 3dp7)
 
  Cis Peptide Bonds
    Asn A:316 - Ser A:317   [ 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
  3dp7
    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
  A6KZ44_BACV8 | A6KZ44
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  A6KZ44_BACV8 | A6KZ44
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3DP7)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3DP7)