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

(-) Description

Title :  CRYSTAL STRUCTURE OF AN O-METHYLTRANSFERASE (NCSB1) FROM NEOCARZINOSTATIN BIOSYNTHESIS IN COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEINE (SAH) AND 2-HYDROXY-7-METHOXY-5-METHYL NAPHTHOIC ACID (NA)
 
Authors :  H. A. Cooke, S. D. Bruner
Date :  03 Jul 09  (Deposition) - 01 Sep 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.69
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ternary Complex, Rossmann-Like Fold, Methyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. A. Cooke, E. L. Guenther, Y. Luo, B. Shen, S. D. Bruner
Molecular Basis Of Substrate Promiscuity For The Sam-Dependent O-Methyltransferase Ncsb1, Involved In The Biosynthesis Of The Enediyne Antitumor Antibiotic Neocarzinostatin.
Biochemistry V. 48 9590 2009
PubMed-ID: 19702337  |  Reference-DOI: 10.1021/BI901257Q

(-) Compounds

Molecule 1 - O-METHYLTRANSFERASE
    Atcc15944
    ChainsA, B
    EC Number2.1.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPBS5002
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System VectorPET-30XA/LIC
    Expression System Vector TypePLASMID
    GeneNCSB1
    Organism ScientificSTREPTOMYCES CARZINOSTATICUS SUBSP. NEOCARZINOSTATICUS
    Organism Taxid167636

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
17NA2Ligand/Ion2-HYDROXY-7-METHOXY-5-METHYL NAPHTHOIC ACID
2GOL2Ligand/IonGLYCEROL
3SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:133 , MET A:150 , HIS A:153 , GLY A:177 , GLY A:178 , GLY A:179 , ASP A:200 , LEU A:201 , GLY A:226 , SER A:227 , PHE A:228 , SER A:242 , ASP A:247 , HOH A:533 , HOH A:546 , HOH A:576BINDING SITE FOR RESIDUE SAH A 401
2AC2SOFTWARETRP A:96 , VAL A:103 , MET A:150 , HIS A:246 , MET A:286 , ARG A:289 , MET A:290 , HOH A:577 , ARG B:11BINDING SITE FOR RESIDUE 7NA A 402
3AC3SOFTWAREGLY A:219 , HOH A:630 , ASP B:32 , HIS B:33 , HIS B:38BINDING SITE FOR RESIDUE GOL A 403
4AC4SOFTWARETRP B:133 , MET B:150 , HIS B:153 , GLY B:177 , GLY B:179 , ASP B:200 , LEU B:201 , GLY B:226 , SER B:227 , PHE B:228 , SER B:242 , ASP B:247 , HOH B:518 , HOH B:536 , HOH B:542BINDING SITE FOR RESIDUE SAH B 401
5AC5SOFTWAREARG A:11 , TRP B:96 , VAL B:103 , MET B:150 , ALA B:243 , HIS B:246 , ARG B:289 , MET B:290 , HOH B:554 , HOH B:599BINDING SITE FOR RESIDUE 7NA B 402
6AC6SOFTWAREHIS A:33 , GLY B:219BINDING SITE FOR RESIDUE GOL B 404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3I58)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3I58)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3I58)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_OMT_IIPS51683 SAM-dependent O-methyltransferase class II-type profile.NCSB1_STRCZ10-332
 
  2A:10-332
B:10-332

(-) Exons   (0, 0)

(no "Exon" information available for 3I58)

(-) 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:328
 aligned with NCSB1_STRCZ | Q84HC8 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:328
                                    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        
          NCSB1_STRCZ     5 AAHIGLRALADLATPMAVRVAATLRVADHIAAGHRTAAEIASAAGAHADSLDRLLRHLVAVGLFTRDGQGVYGLTEFGEQLRDDHAAGKRKWLDMNSAVGRGDLGFVELAHSIRTGQPAYPVRYGTSFWEDLGSDPVLSASFDTLMSHHLELDYTGIAAKYDWAALGHVVDVGGGSGGLLSALLTAHEDLSGTVLDLQGPASAAHRRFLDTGLSGRAQVVVGSFFDPLPAGAGGYVLSAVLHDWDDLSAVAILRRCAEAAGSGGVVLVIEAVAGDEHAGTGMDLRMLTYFGGKERSLAELGELAAQAGLAVRAAHPISYVSIVEMTAL 332
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3i58A01 A:5-99 'winged helix' repressor DNA binding domain                                     ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh.hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhh.eee.....eee..hhhhhh......hhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.hhhh.eeeee....hhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhh....eeeee............eeeee.hhhhhhhhhhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhh....hhhhhhhhhhh..eeeeeeeee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----SAM_OMT_II  PDB: A:10-332 UniProt: 10-332                                                                                                                                                                                                                                                                                           PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i58 A   5 AAHIGLRALADLATPMAVRVAATLRVADHIAAGHRTAAEIASAAGAHADSLDRLLRHLVAVGLFTRDGQGVYGLTEFGEQLRDDHAAGKRKWLDMNSAVGRGDLGFVELAHSIRTGQPAYPVRYGTSFWEDLGSDPVLSASFDTLMSHHLELDYTGIAAKYDWAALGHVVDVGGGSGGLLSALLTAHEDLSGTVLDLQGPASAAHRRFLDTGLSGRAQVVVGSFFDPLPAGAGGYVLSAVLHDWDDLSAVAILRRCAEAAGSGGVVLVIEAVAGDEHAGTGMDLRMLTYFGGKERSLAELGELAAQAGLAVRAAHPISYVSIVEMTAL 332
                                    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        

Chain B from PDB  Type:PROTEIN  Length:328
 aligned with NCSB1_STRCZ | Q84HC8 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:328
                                    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        
          NCSB1_STRCZ     5 AAHIGLRALADLATPMAVRVAATLRVADHIAAGHRTAAEIASAAGAHADSLDRLLRHLVAVGLFTRDGQGVYGLTEFGEQLRDDHAAGKRKWLDMNSAVGRGDLGFVELAHSIRTGQPAYPVRYGTSFWEDLGSDPVLSASFDTLMSHHLELDYTGIAAKYDWAALGHVVDVGGGSGGLLSALLTAHEDLSGTVLDLQGPASAAHRRFLDTGLSGRAQVVVGSFFDPLPAGAGGYVLSAVLHDWDDLSAVAILRRCAEAAGSGGVVLVIEAVAGDEHAGTGMDLRMLTYFGGKERSLAELGELAAQAGLAVRAAHPISYVSIVEMTAL 332
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3i58B01 B:5-99 'winged helix' repressor DNA binding domain                                     ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh.hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhh.eee.....eee..hhhhhh......hhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhh.eeeee....hhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhh.....eeeee............eeeee.hhhhhhhhhhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhh....hhhhhhhhhhh..eeeeeeeee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----SAM_OMT_II  PDB: B:10-332 UniProt: 10-332                                                                                                                                                                                                                                                                                           PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i58 B   5 AAHIGLRALADLATPMAVRVAATLRVADHIAAGHRTAAEIASAAGAHADSLDRLLRHLVAVGLFTRDGQGVYGLTEFGEQLRDDHAAGKRKWLDMNSAVGRGDLGFVELAHSIRTGQPAYPVRYGTSFWEDLGSDPVLSASFDTLMSHHLELDYTGIAAKYDWAALGHVVDVGGGSGGLLSALLTAHEDLSGTVLDLQGPASAAHRRFLDTGLSGRAQVVVGSFFDPLPAGAGGYVLSAVLHDWDDLSAVAILRRCAEAAGSGGVVLVIEAVAGDEHAGTGMDLRMLTYFGGKERSLAELGELAAQAGLAVRAAHPISYVSIVEMTAL 332
                                    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        

   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 3I58)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3I58)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (NCSB1_STRCZ | Q84HC8)
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:0017000    antibiotic biosynthetic process    The chemical reactions and pathways resulting in the formation of an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
    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
    7NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SAH  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3i58)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3i58
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  NCSB1_STRCZ | Q84HC8
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.1.1.-
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  NCSB1_STRCZ | Q84HC8
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        NCSB1_STRCZ | Q84HC83i53 3i5u 3i64

(-) Related Entries Specified in the PDB File

3i53 CRYSTAL STRUCTURE OF AN O-METHYLTRANSFERASE (NCSB1) FROM NEOCARZINOSTATIN BIOSYNTHESIS IN COMPLEX WITH S-ADENOSYL-L- HOMOCYSTEINE (SAH)
3i5u CRYSTAL STRUCTURE OF AN O-METHYLTRANSFERASE (NCSB1) FROM NEOCARZINOSTATIN BIOSYNTHESIS IN COMPLEX WITH S- ADENOSYLMETHIONINE (SAM) AND 2-HYDROXY-5-METHYL NAPHTHOIC ACID
3i64 CRYSTAL STRUCTURE OF AN O-METHYLTRANSFERASE (NCSB1) FROM NEOCARZINOSTATIN BIOSYNTHESIS IN COMPLEX WITH S-ADENOSYL-L- HOMOCYSTEINE (SAH) AND 1,4-DIHYDROXY-2-NAPHTHOIC ACID (DHN)