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(-) Description

Title :  CRYSTAL STRUCTURE OF THE GLYCOSYLTRANSFERASE SNOGD FROM STREPTOMYCES NOGALATER
 
Authors :  M. Claesson, V. Siitonen, D. Dobritzsch, M. Metsa-Ketela, G. Schneide
Date :  09 Mar 12  (Deposition) - 05 Sep 12  (Release) - 05 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.59
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase, Polyketide Biosynthesis, Gt1 Family, Nogalamycin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Claesson, V. Siitonen, D. Dobritzsch, M. Metsa-Ketela, G. Schneider
Crystal Structure Of The Glycosyltransferase Snogd From The Biosynthetic Pathway Of The Nogalamycin In Streptomyces Nogalater.
Febs J. V. 279 3251 2012
PubMed-ID: 22804797  |  Reference-DOI: 10.1111/J.1742-4658.2012.08711.X

(-) Compounds

Molecule 1 - SNOGD
    Atcc: 27451
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC-BSAI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: STREPTOMYCES NOGALATER
    Organism Taxid: 38314
    Other Details: THE PROTEIN WAS SUBJECTED TO METHYLATION. MOST LYSINE RESIDUES AND THE N-TERMINAL AMINO GROUP SHOULD BE DIMETHYLATED. ONLY FOR K384 DIMETHYLATION WAS VISIBLE IN THE ELECTRON DENSITY MAP AND THUS MODELED.

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1MLY2Mod. Amino AcidN-DIMETHYL-LYSINE

(-) Sites  (0, 0)

(no "Site" information available for 4AMG)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4AMG)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asp B:83 -Pro B:84
2Ala B:239 -Leu B:240

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4AMG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4AMG)

(-) Exons   (0, 0)

(no "Exon" information available for 4AMG)

(-) 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:362
 aligned with Q9RN61_STRNO | Q9RN61 from UniProtKB/TrEMBL  Length:390

    Alignment length:382
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387  
         Q9RN61_STRNO     8 RTGGIMRALFITSPGLSHILPTVPLAQALRALGHEVRYATGGDIRAVAEAGLCAVDVSPGVNYAKLFVPDDTDVTDPMHSEGLGEGFFAEMFARVSAVAVDGALRTARSWRPDLVVHTPTQGAGPLTAAALQLPCVELPLGPADSEPGLGALIRRAMSKDYERHGVTGEPTGSVRLTTTPPSVEALLPEDRRSPGAWPMRYVPYNGGAVLPDWLPPAAGRRRIAVTLGSIDALSGGIAKLAPLFSEVADVDAEFVLTLGGGDLALLGELPANVRVVEWIPLGALLETCDAIIHHGGSGTLLTALAAGVPQCVIPHGSYQDTNRDVLTGLGIGFDAEAGSLGAEQCRRLLDDAGLREAALRVRQEMSEMPPPAETAAKLVALA 389
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..---.eeeee...hhhhhh.hhhhhhhhhhh..eeeeee...hhhhhh...eeee......hhhhhh...------------hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhh...eee........hhhhhhhhhhhhhhhhhhh........eeeee..hhhhhhh.hhhhh....ee.........ee............eeee......--......hhhhhhhhhhh..eeeee...............eeee...hhhhhhh...eeee..hhhhhhhhhhhh..eee...---hhhhhhhhhhh..eee......hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4amg A  11 QS---MRALFITSPGLSHILPTVPLAQALRALGHEVRYATGGDIRAVAEAGLCAVDVSPGVNYAKLFVPDD------------GEGFFAEMFARVSAVAVDGALRTARSWRPDLVVHTPTQGAGPLTAAALQLPCVELPLGPADSEPGLGALIRRAMSKDYERHGVTGEPTGSVRLTTTPPSVEALLPEDRRSPGAWPMRYVPYNGGAVLPDWLPPAAGRRRIAVTLGSID--SGGIAKLAPLFSEVADVDAEFVLTLGGGDLALLGELPANVRVVEWIPLGALLETCDAIIHHGGSGTLLTALAAGVPQCVIPH---QDTNRDVLTGLGIGFDAEAGSLGAEQCRRLLDDAGLREAALRVRQEMSEMPPPAETAAkLVALA 389
                             |   |  17        27        37        47        57        67        77|        -   |    97       107       117       127       137       147       157       167       177       187       197       207       217       227       237|  |   247       257       267       277       287       297       307       317    |  327       337       347       357       367       377      |387  
                             |  13                                                               78           91                                                                                                                                                238  |                                                                              322 326                                                       384-MLY 
                            12                                                                                                                                                                                                                                     241                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:370
 aligned with Q9RN61_STRNO | Q9RN61 from UniProtKB/TrEMBL  Length:390

    Alignment length:382
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387  
         Q9RN61_STRNO     8 RTGGIMRALFITSPGLSHILPTVPLAQALRALGHEVRYATGGDIRAVAEAGLCAVDVSPGVNYAKLFVPDDTDVTDPMHSEGLGEGFFAEMFARVSAVAVDGALRTARSWRPDLVVHTPTQGAGPLTAAALQLPCVELPLGPADSEPGLGALIRRAMSKDYERHGVTGEPTGSVRLTTTPPSVEALLPEDRRSPGAWPMRYVPYNGGAVLPDWLPPAAGRRRIAVTLGSIDALSGGIAKLAPLFSEVADVDAEFVLTLGGGDLALLGELPANVRVVEWIPLGALLETCDAIIHHGGSGTLLTALAAGVPQCVIPHGSYQDTNRDVLTGLGIGFDAEAGSLGAEQCRRLLDDAGLREAALRVRQEMSEMPPPAETAAKLVALA 389
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..---.eeeee...hhhhhh.hhhhhhhhhhh..eeeeee...hhhhhh...eeee......hhhhhh..-----........hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhh...eee..........hhhhhhhhhhhhhhhhh........eeeee..hhhhhhh..........ee.........ee............eeeee........hhhhhhhhhhhhhhhh..eeeee...............eeee...hhhhhhh...eeee....hhhhhhhhhh..eee....----..hhhhhhh..eee......hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4amg B  11 QS---MRALFITSPGLSHILPTVPLAQALRALGHEVRYATGGDIRAVAEAGLCAVDVSPGVNYAKLFVPD-----DPMHSEGLGEGFFAEMFARVSAVAVDGALRTARSWRPDLVVHTPTQGAGPLTAAALQLPCVELPLGPADSEPGLGALIRRAMSKDYERHGVTGEPTGSVRLTTTPPSVEALLPEDRRSPGAWPMRYVPYNGGAVLPDWLPPAAGRRRIAVTLGSIDALSGGIAKLAPLFSEVADVDAEFVLTLGGGDLALLGELPANVRVVEWIPLGALLETCDAIIHHGGSGTLLTALAAGVPQCVIPHG----TNRDVLTGLGIGFDAEAGSLGAEQCRRLLDDAGLREAALRVRQEMSEMPPPAETAAkLVALA 389
                             |   |  17        27        37        47        57        67        77     |  87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317     |   -|      337       347       357       367       377      |387  
                            12  13                                                              77    83                                                                                                                                                                                                                                             323  328                                                     384-MLY
   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 4AMG)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4AMG)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AMG)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9RN61_STRNO | Q9RN61)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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.
    GO:0016758    transferase activity, transferring hexosyl groups    Catalysis of the transfer of a hexosyl group from one compound (donor) to another (acceptor).
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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  Cis Peptide Bonds
    Ala B:239 - Leu B:240   [ RasMol ]  
    Asp B:83 - Pro B:84   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/TrEMBL
        Q9RN61_STRNO | Q9RN61: 4amb 4an4

(-) Related Entries Specified in the PDB File

4amb CRYSTAL STRUCTURE OF THE GLYCOSYLTRANSFERASE SNOGD FROM STREPTOMYCES NOGALATER
4an4 CRYSTAL STRUCTURE OF THE GLYCOSYLTRANSFERASE SNOGD FROM STREPTOMYCES NOGALATER