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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 :  08 Mar 12  (Deposition) - 05 Sep 12  (Release) - 05 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.62
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
    Fragment: RESIDUES 13-390
    Organism Scientific: STREPTOMYCES NOGALATER
    Organism Taxid: 38314

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1DUD1Ligand/IonDEOXYURIDINE-5'-DIPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:86 , GLU A:88 , SER B:24 , ASN B:212 , SER B:236 , ILE B:237 , THR B:264 , TRP B:285 , ILE B:286 , PRO B:287 , LEU B:288 , HIS B:301 , GLY B:303 , SER B:304 , GLY B:305 , THR B:306BINDING SITE FOR RESIDUE DUD B1391

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4AMB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4AMB)

(-) 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:370
 aligned with Q9RN61_STRNO | Q9RN61 from UniProtKB/TrEMBL  Length:390

    Alignment length:378
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381        
         Q9RN61_STRNO    12 IMRALFITSPGLSHILPTVPLAQALRALGHEVRYATGGDIRAVAEAGLCAVDVSPGVNYAKLFVPDDTDVTDPMHSEGLGEGFFAEMFARVSAVAVDGALRTARSWRPDLVVHTPTQGAGPLTAAALQLPCVELPLGPADSEPGLGALIRRAMSKDYERHGVTGEPTGSVRLTTTPPSVEALLPEDRRSPGAWPMRYVPYNGGAVLPDWLPPAAGRRRIAVTLGSIDALSGGIAKLAPLFSEVADVDAEFVLTLGGGDLALLGELPANVRVVEWIPLGALLETCDAIIHHGGSGTLLTALAAGVPQCVIPHGSYQDTNRDVLTGLGIGFDAEAGSLGAEQCRRLLDDAGLREAALRVRQEMSEMPPPAETAAKLVALA 389
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...hhhhhh.hhhhhhhhhhh..eeeeee...hhhhhh...eeee.....hhhhhhh.-------.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhh...eee...hhhhh..hhhhhhhhhhhhhhhhh........eeeee..hhhhhhh.hhhhh....ee.........ee............eeeee........hhhhhhhhhhhhhhhh..eeeee....hhhhh......eeee...hhhhhhh...eeee..hhhhhhhhhhhh..eee......-..hhhhhhhh..eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4amb A  12 SMRALFITSPGLSHILPTVPLAQALRALGHEVRYATGGDIRAVAEAGLCAVDVSPGVNYAKLFVP-------PMHSEGLGEGFFAEMFARVSAVAVDGALRTARSWRPDLVVHTPTQGAGPLTAAALQLPCVELPLGPADSEPGLGALIRRAMSKDYERHGVTGEPTGSVRLTTTPPSVEALLPEDRRSPGAWPMRYVPYNGGAVLPDWLPPAAGRRRIAVTLGSIDALSGGIAKLAPLFSEVADVDAEFVLTLGGGDLALLGELPANVRVVEWIPLGALLETCDAIIHHGGSGTLLTALAAGVPQCVIPHGSY-DTNRDVLTGLGIGFDAEAGSLGAEQCRRLLDDAGLREAALRVRQEMSEMPPPAETAAKLVALA 389
                                    21        31        41        51        61        71    |    -  |     91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321   | | 331       341       351       361       371       381        
                                                                                           76      84                                                                                                                                                                                                                                              325 |                                                              
                                                                                                                                                                                                                                                                                                                                                     327                                                              


Chain B from PDB  Type:PROTEIN  Length:373
 aligned with Q9RN61_STRNO | Q9RN61 from UniProtKB/TrEMBL  Length:390

    Alignment length:383
                                    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 RTGGIMRALFITSPGLSHILPTVPLAQALRALGHEVRYATGGDIRAVAEAGLCAVDVSPGVNYAKLFVPDDTDVTDPMHSEGLGEGFFAEMFARVSAVAVDGALRTARSWRPDLVVHTPTQGAGPLTAAALQLPCVELPLGPADSEPGLGALIRRAMSKDYERHGVTGEPTGSVRLTTTPPSVEALLPEDRRSPGAWPMRYVPYNGGAVLPDWLPPAAGRRRIAVTLGSIDALSGGIAKLAPLFSEVADVDAEFVLTLGGGDLALLGELPANVRVVEWIPLGALLETCDAIIHHGGSGTLLTALAAGVPQCVIPHGSYQDTNRDVLTGLGIGFDAEAGSLGAEQCRRLLDDAGLREAALRVRQEMSEMPPPAETAAKLVALAG 390
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..---.eeeee...hhhhhh.hhhhhhhhhhh..eeeeee...hhhhhh...eeee.....hhhhhhh.-------.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhh...eee...hhhhh..hhhhhhhhhhhhhhhhh........eeeee..hhhhhhh.hhhhh....ee.........eee...........eeeee..........hhhhhhhhhhhhhh..eeeee....hhhhh......eeee...hhhhhhh...eeee..hhhhhhhhhhhh..eee........hhhhhhhhh..eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4amb B  11 QS---MRALFITSPGLSHILPTVPLAQALRALGHEVRYATGGDIRAVAEAGLCAVDVSPGVNYAKLFVP-------PMHSEGLGEGFFAEMFARVSAVAVDGALRTARSWRPDLVVHTPTQGAGPLTAAALQLPCVELPLGPADSEPGLGALIRRAMSKDYERHGVTGEPTGSVRLTTTPPSVEALLPEDRRSPGAWPMRYVPYNGGAVLPDWLPPAAGRRRIAVTLGSIDALSGGIAKLAPLFSEVADVDAEFVLTLGGGDLALLGELPANVRVVEWIPLGALLETCDAIIHHGGSGTLLTALAAGVPQCVIPHGSYQDTNRDVLTGLGIGFDAEAGSLGAEQCRRLLDDAGLREAALRVRQEMSEMPPPAETAAKLVALAG 390
                             |   |  17        27        37        47        57        67        |-      | 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   
                            12  13                                                             76      84
   Legend:   → Mismatch (orange background)
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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 4AMB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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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 Related Entries

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

UniProtKB/TrEMBL
        Q9RN61_STRNO | Q9RN61: 4amg 4an4

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