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(-) Description

Title :  CRYSTAL STRUCTURE OF AN O-METHYLTRANSFERASE (NCSB1) FROM NEOCARZINOSTATIN BIOSYNTHESIS IN COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEINE (SAH)
 
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 :  2.08
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Co-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
    Atcc: 15944
    Chains: A, B
    EC Number: 2.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBS5002
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector: PET-30XA/LIC
    Expression System Vector Type: PLASMID
    Gene: NCSB1
    Organism Scientific: STREPTOMYCES CARZINOSTATICUS SUBSP. NEOCARZINOSTATICUS
    Organism Taxid: 167636

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:133 , PHE A:146 , HIS A:153 , GLY A:177 , GLY A:179 , ASP A:200 , LEU A:201 , GLY A:226 , SER A:227 , PHE A:228 , SER A:242 , ASP A:247 , TRP A:248 , HOH A:537 , HOH A:540 , HOH A:556 , HOH A:609 , HOH A:692 , HOH A:709 , HOH A:769BINDING SITE FOR RESIDUE SAH A 401
2AC2SOFTWARETRP B:133 , ASP B:175 , GLY B:177 , GLY B:178 , GLY B:179 , ASP B:200 , LEU B:201 , PRO B:204 , GLY B:226 , SER B:227 , PHE B:228 , SER B:242 , ALA B:243 , ASP B:247 , TRP B:248 , HOH B:575 , HOH B:659 , HOH B:754BINDING SITE FOR RESIDUE SAH B 401
3AC3SOFTWAREMET B:150 , HOH B:753BINDING SITE FOR RESIDUE GOL B 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3I53)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3I53)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3I53)

(-) 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:10-330

(-) Exons   (0, 0)

(no "Exon" information available for 3I53)

(-) 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:325
 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 3i53A01 A:5-99 'winged helix' repressor DNA binding domain                                     ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh.hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh..eee.....eee..hhhhhh......hhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhh.eeeee....hhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhh.....eeeee............eeeee.hhhhhhhhhhhhhhhhhhhhhh...eeeeee....---.hhhhhhhhhhhhh....hhhhhhhhhhhh.eeeeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----SAM_OMT_II  PDB: A:10-332 UniProt: 10-332                                                                                                                                                                                                                                                                                           PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i53 A   5 AAHIGLRALADLATPMAVRVAATLRVADHIAAGHRTAAEIASAAGAHADSLDRLLRHLVAVGLFTRDGQGVYGLTEFGEQLRDDHAAGKRKWLDMNSAVGRGDLGFVELAHSIRTGQPAYPVRYGTSFWEDLGSDPVLSASFDTLMSHHLELDYTGIAAKYDWAALGHVVDVGGGSGGLLSALLTAHEDLSGTVLDLQGPASAAHRRFLDTGLSGRAQVVVGSFFDPLPAGAGGYVLSAVLHDWDDLSAVAILRRCAEAAGSGGVVLVIEAVAG---AGTGMDLRMLTYFGGKERSLAELGELAAQAGLAVRAAHPISYVSIVEMTAL 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        
                                                                                                                                                                                                                                                                                                           278 282                                                  


Chain B from PDB  Type:PROTEIN  Length:303
 aligned with NCSB1_STRCZ | Q84HC8 from UniProtKB/Swiss-Prot  Length:332

    Alignment length:322
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328  
          NCSB1_STRCZ     9 GLRALADLATPMAVRVAATLRVADHIAAGHRTAAEIASAAGAHADSLDRLLRHLVAVGLFTRDGQGVYGLTEFGEQLRDDHAAGKRKWLDMNSAVGRGDLGFVELAHSIRTGQPAYPVRYGTSFWEDLGSDPVLSASFDTLMSHHLELDYTGIAAKYDWAALGHVVDVGGGSGGLLSALLTAHEDLSGTVLDLQGPASAAHRRFLDTGLSGRAQVVVGSFFDPLPAGAGGYVLSAVLHDWDDLSAVAILRRCAEAAGSGGVVLVIEAVAGDEHAGTGMDLRMLTYFGGKERSLAELGELAAQAGLAVRAAHPISYVSIVEMT 330
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3i53B01 B:9-99 'winged helix' repressor DNA binding domain                                 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhh.eee.....eee.hhhhhhh......hhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhhhhhhhhh.--------..hhhhh.hhhh.eeeee....hhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhh.....eeeee............eeeee......hhhhhhhhhhhhhhhhh...eeeeee-------.hhhhhhhhhhhhh..----hhhhhhhhhh..ee...eee..eeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -SAM_OMT_II  PDB: B:10-330 UniProt: 10-332                                                                                                                                                                                                                                                                                         PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i53 B   9 GLRALADLATPMAVRVAATLRVADHIAAGHRTAAEIASAAGAHADSLDRLLRHLVAVGLFTRDGQGVYGLTEFGEQLRDDHAAGKRKWLDMNSAVGRGDLGFVELAHSIRTGQPAYPVRYGTSFWEDLGSDPVLSASFDTLM--------TGIAAKYDWAALGHVVDVGGGSGGLLSALLTAHEDLSGTVLDLQGPASAAHRRFLDTGLSGRAQVVVGSFFDPLPAGAGGYVLSAVLHDWDDLSAVAILRRCAEAAGSGGVVLVIE-------AGTGMDLRMLTYFGGK----AELGELAAQAGLAVRAAHPISYVSIVEMT 330
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148 |       -|      168       178       188       198       208       218       228       238       248       258       268     |   -   |   288        |-   |   308       318       328  
                                                                                                                                                                       150      159                                                                                                                274     282            297  302
   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 3I53)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3I53)

(-) 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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NCSB1_STRCZ | Q84HC8: 3i58 3i5u 3i64

(-) Related Entries Specified in the PDB File

3i58 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
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)