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(-) Description

Title :  CHIMERIC GLYCOSYLTRANSFERASE FOR THE GENERATION OF NOVEL NATURAL PRODUCTS
 
Authors :  M. V. B. Dias, A. W. Truman, S. Wu, T. L. Blundell, F. Huang, J. B. Spencer
Date :  20 Apr 09  (Deposition) - 28 Jul 09  (Release) - 28 Jul 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Glycosyltransferase, Gtfa, Chimeric Protein, Vancomycin, Teicoplanin, Antibiotic (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. W. Truman, M. V. B. Dias, S. Wu, T. L. Blundell, F. Huang, J. B. Spencer
Chimeric Glycosyltransferases For The Generation Of Hybrid Glycopeptides
Chem. Biol. V. 16 676 2009
PubMed-ID: 19549605  |  Reference-DOI: 10.1016/J.CHEMBIOL.2009.04.013
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLYCOSYLTRANSFERASE GTFA, GLYCOSYLTRANSFERASE
    ChainsA
    EC Number2.4.-.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET 28A(+)
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 1-214, UNP RESIDUES 218-393
    GeneGTFA
    Organism ScientificAMYCOLATOPSIS ORIENTALIS, ACTINOPLANES TEICHOMYCETICUS
    Organism Taxid31958, 1867
    SynonymGTFA, ORF1, PCZA361.19, GTFA PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
2U2F1Ligand/IonURIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:10 , ARG A:11 , GLY A:12 , ASP A:13 , ARG A:207 , GLY A:229 , SER A:230 , GLU A:275 , VAL A:276 , HIS A:278 , HIS A:291 , GLY A:293 , ALA A:294 , GLY A:295 , THR A:296 , ASP A:315 , GLN A:316 , HOH A:512 , HOH A:522 , HOH A:553 , HOH A:562 , HOH A:635 , HOH A:637 , HOH A:645 , HOH A:670 , HOH A:690 , HOH A:737 , HOH A:1029BINDING SITE FOR RESIDUE U2F A 547
2AC2SOFTWAREVAL A:57 , ARG A:62 , HOH A:672 , HOH A:804BINDING SITE FOR RESIDUE SO4 A 600
3AC3SOFTWAREARG A:120 , HOH A:780 , HOH A:999BINDING SITE FOR RESIDUE SO4 A 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3H4I)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3H4I)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3H4I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3H4I)

(-) Exons   (0, 0)

(no "Exon" information available for 3H4I)

(-) 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:392
 aligned with GTFA_AMYOR | P96558 from UniProtKB/Swiss-Prot  Length:396

    Alignment length:399
                                                                                                                                                                                                                                                                                                                                                                                                                                    396    
                                    11        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       391    |    
           GTFA_AMYOR     2 RVLITGCGSRGDTEPLVALAARLRELGADARMCLPPDYVERCAEVGVPMVPVGRAVRAGAREPGELPPGAAEVVTEVVAEWFDKVPAAIEGCDAVVTTGLLPAAVAVRSMAEKLGIPYRYTVLSPDHLPSEQSQAERDMYNQGADRLFGDAVNSHRASIGLPPVEHLYDYGYTDQPWLAADPVLSPLRPTDLGTVQTGAWILPDERPLSAELEAFLAAGSTPVYVGFGSSSRPATADAAKMAIKAVRASGRRIVLSRGWADLVLPDDGADCFVVGEVNLQELFGRVAAAIHHDSAGTTLLAMRAGIPQIVVRRVVDNVVEQAYHADRVAELGVGVAVDGPVPTIDSLSAALDTALAPEIRARATTVADTIRADGTTVAAQLLFDAVSLEKPTVPA----   -
               SCOP domains d3h4ia_ A: TDP-epi-vancosaminyltransferase GtfA                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.hhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhh...eee.....hhhhh........hhhhhhhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh...ee..............................hhhhhhhhhh....eeee....--....hhhhhhhhhhhhh...eeee..............eeee...hhhhhhhhh.eeee..hhhhhhhhhhhh..eee.....h----hhhhhhhhhhhh.eee......hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh-hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h4i A   2 GVLITGCGSRGDTEPLVALAARLRELGADARMCLPPDYVERCAEVGVPMVPVGRAVRAGAREPGELPPGAAEVVTEVVAEWFDKVPAAIEGCDAVVTTGLLPAAVAVRSMAEKLGIPYRYTVLSPDHLPSEQSQAERDMYNQGADRLFGDAVNSHRASIGLPPVEHLYDYGYTDQPWLAADPVLSPLRPTDLGTVQTGAWILPDQRPLSAELEGFLRAGSPPVYVGFGSG--PAPAEAARVAIEAVRAQGRRVVLSSGWAGLGRIDEGDDCLVVGEVNHQVLFGRVAAVVHHGGAGTTTAVTRAGAPQVVVPQKAD----QPYYAGRVADLGVGVAHDGPTPTVESLSAALATALTPGIRARAAAVAGTIRTDGTTVAAKLLLEAISR-AKLAAALEHH 542
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231  |    239       249       259       269       279       289       299       309     |   -|      325       335       345       355       365       375       533         
                                                                                                                                                                                                                                                               231  |                                                                                315  316                                                                383 |         
                                                                                                                                                                                                                                                                  232                                                                                                                                                          533         

Chain A from PDB  Type:PROTEIN  Length:392
 aligned with Q6ZZJ7_ACTTI | Q6ZZJ7 from UniProtKB/TrEMBL  Length:393

    Alignment length:396
                                                                                          64                                                                                                                                                                                                                                                                                                                                 387        
                                                                                        63 |                                                                                                                                                                                                                                                                                                                               386 |   393  
                                    11        21        31        41        51        61 | |    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380     | 389   |  
         Q6ZZJ7_ACTTI     2 RVLFSSYGTRGDVEPLVALAVRLRELGAEVRMCASPDYVERLAEVEVPMVPIGQPVRAGARK-GAAPPGAPEAVAEVIAEQFDRVPPFAEGCDAVVASGLVSTAVAVRSVAEKLGIHHYAYAVLSPSFLRAPGVTDSRDLRARANQGAYRQFGGPLNSHRAAVGLPPVEKVIDYAFTERPWLAADPVLDPLRPTDPDVVQTGAWILPDQRPLSAELEGFLRAGSPPVYVGFGSGPAPAEAARVAIEAVRAQGRRVVLSSGWAGLGRIDEGDDCLVVGEVNHQVLFGRVAAVVHHGGAGTTTAVTRAGAPQVVVPQKADQPYYAGRVADLGVGVAHDGPTPTVESLSAALATALTPGIRARAAAVAGTIRTDGTTVAAKLLLEAISR-QRSSVPA--   -
               SCOP domains d3h4ia_ A: TDP-epi-vancosaminyltransferase GtfA                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee.hhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhh...eee.....hhhhh........hhhhhhhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhh..-eeeee.hhhhhhhh---hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh...ee..............................hhhhhhhhhh....eeee........hhhhhhhhhhhhh...eeee..............eeee...hhhhhhhhh.eeee..hhhhhhhhhhhh..eee.....hhhhhhhhhhhhh.eee......hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3h4i A   2 GVLITGCGSRGDTEPLVALAARLRELGADARMCLPPDYVERCAEVGVPMVPVGRAVRAGAREPGELPPGAAEVVTEVVAEWFDKVPAAIEGCDAVVTTGLLPAAVAVRSMAEKLGIP-YRYTVLSPDHLPSE---QSQAERDMYNQGADRLFGDAVNSHRASIGLPPVEHLYDYGYTDQPWLAADPVLSPLRPTDLGTVQTGAWILPDQRPLSAELEGFLRAGSPPVYVGFGSGPAPAEAARVAIEAVRAQGRRVVLSSGWAGLGRIDEGDDCLVVGEVNHQVLFGRVAAVVHHGGAGTTTAVTRAGAPQVVVPQKADQPYYAGRVADLGVGVAHDGPTPTVESLSAALATALTPGIRARAAAVAGTIRTDGTTVAAKLLLEAISRAKLAAALEHH 542
                                    11        21        31        41        51        61        71        81        91       101       111      |120       130 |   | 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     ||536      
                                                                                                                                              118 |          132 133                                                                                                                                                                                                                                                       383|         
                                                                                                                                                119                                                                                                                                                                                                                                                                         533         

   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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3H4I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3H4I)

(-) Gene Ontology  (11, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GTFA_AMYOR | P96558)
molecular function
    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:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
    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: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:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0030259    lipid glycosylation    Covalent attachment of a glycosyl residue to a lipid molecule.
    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.
    GO:0033072    vancomycin biosynthetic process    The chemical reactions and pathways leading to the formation of vancomycin, (3S,6R,7R,11R,23S,26S,30aS,36R,38aR)-44-[2-O-(3-amino-2,3,6-trideoxy-3-C-methyl-alpha-L-lyxo-hexopyranosyl)-beta-D-glucopyranosyloxy]-3-(carbamoylmethyl)-10,19-dichloro-2,3,4,5,6,7,23,25,26,36,37,38,38a-tetradecahydro-7,22,28,30,32-pentahydroxy-6-(N-methyl-D-leucyl)-2,5,24,38,39-pentaoxo-1H,22H-23,36-(epiminomethano)-8,11:18,21-dietheno-13,16:31,35-di(metheno)[1,6,9]oxadiazacyclohexadecino[4,5-m][10,2,16]benzoxadiazacyclotetracosine-26-carboxylic acid, a complex glycopeptide from Streptomyces orientalis that inhibits a specific step in the synthesis of the peptidoglycan layer in Gram-positive bacteria.

Chain A   (Q6ZZJ7_ACTTI | Q6ZZJ7)
molecular function
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
    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:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0030259    lipid glycosylation    Covalent attachment of a glycosyl residue to a lipid molecule.
    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/Swiss-Prot
        GTFA_AMYOR | P965581pn3 1pnv 3h4t
        Q6ZZJ7_ACTTI | Q6ZZJ73h4t

(-) Related Entries Specified in the PDB File

3h4t THE SAME PROTEIN COMPLEXED WITH UDP