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(-) Description

Title :  CRYSTAL STRUCTURE OF STREPTOMYCES VENEZUELAE DESVI
 
Authors :  H. M. Holden, E. S. Burgie
Date :  14 Jan 08  (Deposition) - 25 Mar 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Methyltransferase, Desosamine, Sugar, Carbohydrate, Antibiotic, Sam, Adomet (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. S. Burgie, H. M. Holden
Three-Dimensional Structure Of Desvi From Streptomyces Venezuelae: A Sugar N, N-Dimethyltransferase Required For Dtdp-Desosamine Biosynthesis.
Biochemistry V. 47 3982 2008
PubMed-ID: 18327916  |  Reference-DOI: 10.1021/BI800063J
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - N,N-DIMETHYLTRANSFERASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B(+)
    Expression System Strain: ROSETTA (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DESVI
    Organism Scientific: STREPTOMYCES VENEZUELAE
    Organism Taxid: 54571
    Strain: ATCC NO. 15,439

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2SAM2Ligand/IonS-ADENOSYLMETHIONINE
3UPP2Ligand/IonPHENYL-URIDINE-5'-DIPHOSPHATE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:21 , ALA A:46 , CYS A:47 , HIS A:52 , GLU A:67 , LEU A:68 , SER A:69 , MET A:72 , GLY A:88 , ASP A:89 , MET A:90 , ARG A:91 , MET A:105 , PHE A:106 , SER A:108 , HOH A:269 , HOH A:291 , HOH A:341 , HOH A:362 , HOH A:402BINDING SITE FOR RESIDUE SAM A 238
2AC2SOFTWARETYR B:21 , ALA B:46 , HIS B:52 , GLU B:67 , LEU B:68 , SER B:69 , MET B:72 , GLY B:88 , ASP B:89 , MET B:90 , MET B:105 , PHE B:106 , SER B:108 , HOH B:300 , HOH B:301 , HOH B:321 , HOH B:414 , HOH B:498 , HOH B:523BINDING SITE FOR RESIDUE SAM B 238
3AC3SOFTWARETYR A:14 , ARG A:17 , PHE A:106 , TRP A:140 , TRP A:141 , THR A:145 , PHE A:146 , ALA A:147 , TRP A:150 , SER A:152 , ARG A:165 , SER A:167 , SER A:169 , MET A:178 , ILE A:200 , ARG A:229 , HOH A:356 , HOH A:413BINDING SITE FOR RESIDUE UPP A 239
4AC4SOFTWARETYR B:14 , ARG B:17 , PHE B:106 , TRP B:140 , TRP B:141 , THR B:145 , PHE B:146 , ALA B:147 , TRP B:150 , SER B:152 , ARG B:165 , SER B:167 , SER B:169 , MET B:178 , ARG B:229 , HOH B:446 , HOH B:478BINDING SITE FOR RESIDUE UPP B 239
5AC5SOFTWAREPRO B:81 , ARG B:171 , GLY B:173 , HOH B:265 , HOH B:308BINDING SITE FOR RESIDUE EDO B 240

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3BXO)

(-) 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:236
 aligned with DESVI_STRVZ | Q9ZGH6 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:236
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231      
          DESVI_STRVZ     2 YEVDHADVYDLFYLGRGKDYAAEASDIADLVRSRTPEASSLLDVACGTGTHLEHFTKEFGDTAGLELSEDMLTHARKRLPDATLHQGDMRDFRLGRKFSAVVSMFSSVGYLKTTEELGAAVASFAEHLEPGGVVVVEPWWFPETFADGWVSADVVRRDGRTVARVSHSVREGNATRMEVHFTVADPGKGVRHFSDVHLITLFHQAEYEAAFTAAGLRVEYLEGGPSGRGLFVGVPA 237
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3bxoA01 A:2-143,A:203-237 Vaccinia Virus protein VP39                                                                                         3bxoA02 A:144-202 CAC2371-like domains                     3bxoA01 A:2-143,A:203-237           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhheeeeee.hhhhhhhhhhhh...eeee...........eeeeee..hhhhhh.hhhhhhhhhhhhhhheeeeeeeee.............eeeeeeee..eeeeeeeeeeee..eeeeeeeeeeee...eeeeeeeeeeee..hhhhhhhhhhhh.eeeeee........eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bxo A   2 YEVDHADVYDLFYLGRGKDYAAEASDIADLVRSRTPEASSLLDVACGTGTHLEHFTKEFGDTAGLELSEDMLTHARKRLPDATLHQGDMRDFRLGRKFSAVVSMFSSVGYLKTTEELGAAVASFAEHLEPGGVVVVEPWWFPETFADGWVSADVVRRDGRTVARVSHSVREGNATRMEVHFTVADPGKGVRHFSDVHLITLFHQAEYEAAFTAAGLRVEYLEGGPSGRGLFVGVPA 237
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231      


Chain B from PDB  Type:PROTEIN  Length:236
 aligned with DESVI_STRVZ | Q9ZGH6 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:236
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231      
          DESVI_STRVZ     2 YEVDHADVYDLFYLGRGKDYAAEASDIADLVRSRTPEASSLLDVACGTGTHLEHFTKEFGDTAGLELSEDMLTHARKRLPDATLHQGDMRDFRLGRKFSAVVSMFSSVGYLKTTEELGAAVASFAEHLEPGGVVVVEPWWFPETFADGWVSADVVRRDGRTVARVSHSVREGNATRMEVHFTVADPGKGVRHFSDVHLITLFHQAEYEAAFTAAGLRVEYLEGGPSGRGLFVGVPA 237
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3bxoB01 B:2-143,B:203-237 Vaccinia Virus protein VP39                                                                                         3bxoB02 B:144-202 CAC2371-like domains                     3bxoB01 B:2-143,B:203-237           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhheeeeee.hhhhhhhhhhhh...eeee...........eeeeee..hhhhhh.hhhhhhhhhhhhhhheeeeeeeee.............eeeeeeee..eeeeeeeeeeee..eeeeeeeeeeee...eeeeeeeeeeee..hhhhhhhhhhhh.eeeeee........eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bxo B   2 YEVDHADVYDLFYLGRGKDYAAEASDIADLVRSRTPEASSLLDVACGTGTHLEHFTKEFGDTAGLELSEDMLTHARKRLPDATLHQGDMRDFRLGRKFSAVVSMFSSVGYLKTTEELGAAVASFAEHLEPGGVVVVEPWWFPETFADGWVSADVVRRDGRTVARVSHSVREGNATRMEVHFTVADPGKGVRHFSDVHLITLFHQAEYEAAFTAAGLRVEYLEGGPSGRGLFVGVPA 237
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 3BXO)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DESVI_STRVZ | Q9ZGH6)
molecular function
    GO:0008757    S-adenosylmethionine-dependent methyltransferase activity    Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a substrate.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    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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