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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 :  15 Mar 12  (Deposition) - 05 Sep 12  (Release) - 05 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Transferase, Glycosyltransferase, 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 - GLYCOSYL TRANSFERASE
    Atcc: 27451
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC-BSAI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 13-390
    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.
    Synonym: SNOGD

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1DUD2Ligand/IonDEOXYURIDINE-5'-DIPHOSPHATE
2MLY4Mod. Amino AcidN-DIMETHYL-LYSINE
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1DUD1Ligand/IonDEOXYURIDINE-5'-DIPHOSPHATE
2MLY2Mod. Amino AcidN-DIMETHYL-LYSINE
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1DUD1Ligand/IonDEOXYURIDINE-5'-DIPHOSPHATE
2MLY2Mod. Amino AcidN-DIMETHYL-LYSINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER 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 B 401
2AC2SOFTWARESER D:24 , ASN D:212 , SER D:236 , THR D:264 , TRP D:285 , ILE D:286 , LEU D:288 , HIS D:301 , GLY D:303 , SER D:304 , GLY D:305 , THR D:306BINDING SITE FOR RESIDUE DUD D 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4AN4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4AN4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4AN4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4AN4)

(-) Exons   (0, 0)

(no "Exon" information available for 4AN4)

(-) Sequences/Alignments

Asymmetric 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:358
 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....hhhhhhhhhhh..eee.........hhhhhhhhhhhhhhhhhh........eeeee..hhhhhhh.hhhhh....ee.........ee............eeeee..---------...hhhhhhhh....eeeee......eee......eeee...hhhhhhh...eeee..hhhhhhhhhhhh..eee.....--hhhhhhhhhh..eee......hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4an4 A  11 QS---MRALFITSPGLSHILPTVPLAQALRALGHEVRYATGGDIRAVAEAGLCAVDVSPGVNYAKLFVPDDT-----------GEGFFAEMFARVSAVAVDGALRTARSWRPDLVVHTPTQGAGPLTAAALQLPCVELPLGPADSEPGLGALIRRAMSKDYERHGVTGEPTGSVRLTTTPPSVEALLPEDRRSPGAWPMRYVPYNGGAVLPDWLPPAAGRRRIAVTLG---------AKLAPLFSEVADVDAEFVLTLGGGDLALLGELPANVRVVEWIPLGALLETCDAIIHHGGSGTLLTALAAGVPQCVIPHGS--DTNRDVLTGLGIGFDAEAGSLGAEQCRRLLDDAGLREAALRVRQEMSEMPPPAETAAkLVALAG 390
                             |   |  17        27        37        47        57        67        77 |       -   |    97       107       117       127       137       147       157       167       177       187       197       207       217       227       | -       247       257       267       277       287       297       307       317      |327       337       347       357       367       377      |387   
                             |  13                                                                79          91                                                                                                                                             235       245                                                                            324  |                                                      384-MLY  
                            12                                                                                                                                                                                                                                                                                                                           327                                                               


Chain B from PDB  Type:PROTEIN  Length:359
 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.....hhhhh.-----------------hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhh..eee..........hhhhhhhhhhhhhhhhh........eeeee..hhhhhhh.hhhhh....ee.........eee...........eeeee.........hhhhhhhhhhhhhhh..eeeee...............eeee...hhhhhhh...eeee..hhhhhhhhhhhh..eee...----hhhhhhhhhh..eee......hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4an4 B  11 QS---MRALFITSPGLSHILPTVPLAQALRALGHEVRYATGGDIRAVAEAGLCAVDVSPGVNYAKLF-----------------EGFFAEMFARVSAVAVDGALRTARSWRPDLVVHTPTQGAGPLTAAALQLPCVELPLGPADSEPGLGALIRRAMSKDYERHGVTGEPTGSVRLTTTPPSVEALLPEDRRSPGAWPMRYVPYNGGAVLPDWLPPAAGRRRIAVTLGSIDALSGGIAKLAPLFSEVADVDAEFVLTLGGGDLALLGELPANVRVVEWIPLGALLETCDAIIHHGGSGTLLTALAAGVPQCVIPH----DTNRDVLTGLGIGFDAEAGSLGAEQCRRLLDDAGLREAALRVRQEMSEMPPPAETAAkLVALAG 390
                             |   |  17        27        37        47        57        67      |  -         -    |   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                                                           74                92                                                                                                                                                                                                                                   322  327                                                      384-MLY  


Chain C from PDB  Type:PROTEIN  Length:328
 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.....hhhhhhh.-----------------hhhhhhhhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhh..eee.......-----hhhhhhhhhhhhhhh........eeeee..hhhhhhh..----....ee.........eee...........eeee..--------.eee......hhhhh..eeeee......eee......eeee...hhhhhhh...eeee..hhhhhhhhhhhh..eee...-----hhhhhhhhhh.------------hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4an4 C  11 QS---MRALFITSPGLSHILPTVPLAQALRALGHEVRYATGGDIRAVAEAGLCAVDVSPGVNYAKLFVP-----------------FFAEMFARVSAVAVDGALRTARSWRPDLVVHTPTQGAGPLTAAALQLPCVELPLGPAD-----GALIRRAMSKDYERHGVTGEPTGSVRLTTTPPSVEALLP----SPGAWPMRYVPYNGGAVLPDWLPPAAGRRRIAVTL--------GIAKLAPLFSEVADVDAEFVLTLGGGDLALLGELPANVRVVEWIPLGALLETCDAIIHHGGSGTLLTALAAGVPQCVIPH-----TNRDVLTGLGI------------QCRRLLDDAGLREAALRVRQEMSEMPPPAETAAkLVALA 389
                             |   |  17        27        37        47        57        67        |-         -      | 97       107       117       127       137       147   |   157       167       177       187       | -  |    207       217       227      |  -     | 247       257       267       277       287       297       307       317    |    -|      337|        -   |   357       367       377      |387  
                            12  13                                                             76                94                                                      151   157                                   195  200                               234      243                                                                            322   328       338          351                              384-MLY 


Chain D from PDB  Type:PROTEIN  Length:348
 aligned with Q9RN61_STRNO | Q9RN61 from UniProtKB/TrEMBL  Length:390

    Alignment length:379
                                    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 IMRALFITSPGLSHILPTVPLAQALRALGHEVRYATGGDIRAVAEAGLCAVDVSPGVNYAKLFVPDDTDVTDPMHSEGLGEGFFAEMFARVSAVAVDGALRTARSWRPDLVVHTPTQGAGPLTAAALQLPCVELPLGPADSEPGLGALIRRAMSKDYERHGVTGEPTGSVRLTTTPPSVEALLPEDRRSPGAWPMRYVPYNGGAVLPDWLPPAAGRRRIAVTLGSIDALSGGIAKLAPLFSEVADVDAEFVLTLGGGDLALLGELPANVRVVEWIPLGALLETCDAIIHHGGSGTLLTALAAGVPQCVIPHGSYQDTNRDVLTGLGIGFDAEAGSLGAEQCRRLLDDAGLREAALRVRQEMSEMPPPAETAAKLVALAG 390
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhh.hhhhhhhhhhh..eeeeee...hhhhhh...eeee..........------------------hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhh..eee.......-----hhhhhhhhhhhhhhh........eeeee..hhhhhhh.hhhhh....ee.........eee...........eeeee.......---hhhhhhhhhh......eeeee....hhhhhh--...eeee...hhhhhhh...eeee..hhhhhhhhhhhh..eee....---hhhhhhhhhh..eee......hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4an4 D  12 SMRALFITSPGLSHILPTVPLAQALRALGHEVRYATGGDIRAVAEAGLCAVDVSPGVNYAKL------------------EGFFAEMFARVSAVAVDGALRTARSWRPDLVVHTPTQGAGPLTAAALQLPCVELPLGPAD-----GALIRRAMSKDYERHGVTGEPTGSVRLTTTPPSVEALLPEDRRSPGAWPMRYVPYNGGAVLPDWLPPAAGRRRIAVTLGSIDAL---IAKLAPLFSEVADVDAEFVLTLGGGDLALLG--PANVRVVEWIPLGALLETCDAIIHHGGSGTLLTALAAGVPQCVIPHG---DTNRDVLTGLGIGFDAEAGSLGAEQCRRLLDDAGLREAALRVRQEMSEMPPPAETAAkLVALAG 390
                                    21        31        41        51        61        71 |       -         -|      101       111       121       131       141       151     | 161       171       181       191       201       211       221       231        |-  |    251       261       271  |  | 281       291       301       311       321 |   | 331       341       351       361       371       381  |      
                                                                                        73                 92                                                        151   157                                                                                240 244                           274  |                                           323 327                                                      384-MLY  
                                                                                                                                                                                                                                                                                                   277
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  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 4AN4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4AN4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AN4)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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: 4amb 4amg

(-) Related Entries Specified in the PDB File

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