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(-) Description

Title :  CRYSTAL STRUCTURE OF TDP-EPI-VANCOSAMINYLTRANSFERASE GTFA IN COMPLEXES WITH TDP AND VANCOMYCIN
 
Authors :  A. M. Mulichak, H. C. Losey, W. Lu, Z. Wawrzak, C. T. Walsh, R. M. Garavito
Date :  13 Jun 03  (Deposition) - 12 Aug 03  (Release) - 27 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Gt-B Glycosyltransferase, Rossmann Fold, Glycopeptide, Antibiotic, Transferase-Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. M. Mulichak, H. C. Losey, W. Lu, Z. Wawrzak, C. T. Walsh, R. M. Garavit
Structure Of The Tdp-Epi-Vancosaminyltransferase Gtfa From The Chloroeremomycin Biosynthetic Pathway.
Proc. Natl. Acad. Sci. Usa V. 100 9238 2003
PubMed-ID: 12874381  |  Reference-DOI: 10.1073/PNAS.1233577100

(-) Compounds

Molecule 1 - GLYCOSYLTRANSFERASE GTFA
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET22B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: GTFA
    Organism Scientific: AMYCOLATOPSIS ORIENTALIS
    Organism Taxid: 31958
 
Molecule 2 - VANCOMYCIN
    Chains: C
    Organism Scientific: AMYCOLATOPSIS ORIENTALIS
    Organism Taxid: 31958

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 9)

Asymmetric/Biological Unit (8, 9)
No.NameCountTypeFull Name
13FG1Mod. Amino Acid(2S)-AMINO(3,5-DIHYDROXYPHENYL)ETHANOIC ACID
2BGC1Ligand/IonBETA-D-GLUCOSE
3GHP2Mod. Amino Acid(2R)-AMINO(4-HYDROXYPHENYL)ETHANOIC ACID
4MLU1Mod. Amino AcidN-METHYLLEUCINE
5OMY1Mod. Amino Acid(BETAR)-3-CHLORO-BETA-HYDROXY-L-TYROSINE
6OMZ1Mod. Amino Acid(BETAR)-3-CHLORO-BETA-HYDROXY-D-TYROSINE
7RER1Ligand/Ion(1R,3S,4S,5S)-3-AMINO-2,3,6-TRIDEOXY-3-METHYL-ALPHA-L-ARABINO-HEXOPYRANOSE
8TYD1Ligand/IonTHYMIDINE-5'-DIPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:10 , ARG A:11 , GLY A:12 , GLU A:15 , GLY A:229 , SER A:230 , GLY A:276 , GLU A:277 , VAL A:278 , HIS A:293 , SER A:295 , GLY A:297 , THR A:298 , LEU A:301 , HOH A:2035 , HOH A:2036BINDING SITE FOR RESIDUE TYD A 405
2AC2SOFTWARESER B:10 , ASP B:13 , PRO B:68 , PRO B:69 , GLY B:70 , ALA B:72 , LEU B:101 , LEU B:102 , PRO B:103 , ASP B:127 , HIS B:128 , GLN B:133 , TYR B:141 , GLY B:144 , ALA B:145 , LEU B:148 , PHE B:149 , TYR B:169 , TYR B:173 , LEU B:332 , PRO B:358 , GLU B:359 , ALA B:362 , ARG B:363 , THR B:366 , HOH C:2003 , HOH C:2004 , HOH C:2005BINDING SITE FOR LINKED RESIDUES C 1 to 9

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1PNV)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:340 -Pro A:341
2Ghp C:5 -Omy C:6

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PNV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1PNV)

(-) Exons   (0, 0)

(no "Exon" information available for 1PNV)

(-) 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:382
 aligned with GTFA_AMYOR | P96558 from UniProtKB/Swiss-Prot  Length:396

    Alignment length:390
                                    10        20        30        40        50        60        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       390
           GTFA_AMYOR     1 MRVLITGCGSRGDTEPLVALAARLRELGADARMCLPPDYVERCAEVGVPMVPVGRAVRAGAREPGELPPGAAEVVTEVVAEWFDKVPAAIEGCDAVVTTGLLPAAVAVRSMAEKLGIPYRYTVLSPDHLPSEQSQAERDMYNQGADRLFGDAVNSHRASIGLPPVEHLYDYGYTDQPWLAADPVLSPLRPTDLGTVQTGAWILPDERPLSAELEAFLAAGSTPVYVGFGSSSRPATADAAKMAIKAVRASGRRIVLSRGWADLVLPDDGADCFVVGEVNLQELFGRVAAAIHHDSAGTTLLAMRAGIPQIVVRRVVDNVVEQAYHADRVAELGVGVAVDGPVPTIDSLSAALDTALAPEIRARATTVADTIRADGTTVAAQLLFDAVSLE 390
               SCOP domains d1pnva_ A: TDP-epi-vancosaminyltransferase GtfA                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1pnvA01 A:1-201,A:372-387 Glycogen Phosphorylase B;                                                                                                                                                      1pnvA02 A:202-371 Glycogen Phosphorylase B;                                                                                                                               1pnvA01         --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee.hhhhhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhhhh..eee.....hhhhh...........hhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhh..eeeee.hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh...ee................ee............hhhhhhhhhh....eeee......hhhhhhhhhhhhhhhhh...eeee................ee...hhhhhhhhh.eeee..hhhhhhhhhh....eeee...--------hhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1pnv A   1 MRVLITGCGSRGDTEPLVALAARLRELGADARMCLPPDYVERCAEVGVPMVPVGRAVRAGAREPGELPPGAAEVVTEVVAEWFDKVPAAIEGCDAVVTTGLLPAAVAVRSMAEKLGIPYRYTVLSPDHLPSEQSQAERDMYNQGADRLFGDAVNSHRASIGLPPVEHLYDYGYTDQPWLAADPVLSPLRPTDLGTVQTGAWILPDERPLSAELEAFLAAGSTPVYVGFGSSSRPATADAAKMAIKAVRASGRRIVLSRGWADLVLPDDGADCFVVGEVNLQELFGRVAAAIHHDSAGTTLLAMRAGIPQIVVRRV--------YHADRVAELGVGVAVDGPVPTIDSLSAALDTALAPEIRARATTVADTIRADGTTVAAQLLFDAVSLE 390
                                    10        20        30        40        50        60        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    |    -   |   330       340       350       360       370       380       390
                                                                                                                                                                                                                                                                                                                                                    315      324                                                                  


Chain B from PDB  Type:PROTEIN  Length:384
 aligned with GTFA_AMYOR | P96558 from UniProtKB/Swiss-Prot  Length:396

    Alignment length:391
                                    10        20        30        40        50        60        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       390 
           GTFA_AMYOR     1 MRVLITGCGSRGDTEPLVALAARLRELGADARMCLPPDYVERCAEVGVPMVPVGRAVRAGAREPGELPPGAAEVVTEVVAEWFDKVPAAIEGCDAVVTTGLLPAAVAVRSMAEKLGIPYRYTVLSPDHLPSEQSQAERDMYNQGADRLFGDAVNSHRASIGLPPVEHLYDYGYTDQPWLAADPVLSPLRPTDLGTVQTGAWILPDERPLSAELEAFLAAGSTPVYVGFGSSSRPATADAAKMAIKAVRASGRRIVLSRGWADLVLPDDGADCFVVGEVNLQELFGRVAAAIHHDSAGTTLLAMRAGIPQIVVRRVVDNVVEQAYHADRVAELGVGVAVDGPVPTIDSLSAALDTALAPEIRARATTVADTIRADGTTVAAQLLFDAVSLEK 391
               SCOP domains d1pnvb_ B: TDP-epi-vancosaminyltransferase GtfA                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1pnvB01 B:1-201,B:372-387 Glycogen Phosphorylase B;                                                                                                                                                      1pnvB02 B:202-371 Glycogen Phosphorylase B;                                                                                                                               1pnvB01         ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.hhhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhh....eee..................hhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhh...ee..............................hhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhhh...eeee..............eeee...hhhhhhh....eeee.hhhhhhhhhhhh..eeee...-------hhhhhhhhhh..ee.......hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pnv B   1 MRVLITGCGSRGDTEPLVALAARLRELGADARMCLPPDYVERCAEVGVPMVPVGRAVRAGAREPGELPPGAAEVVTEVVAEWFDKVPAAIEGCDAVVTTGLLPAAVAVRSMAEKLGIPYRYTVLSPDHLPSEQSQAERDMYNQGADRLFGDAVNSHRASIGLPPVEHLYDYGYTDQPWLAADPVLSPLRPTDLGTVQTGAWILPDERPLSAELEAFLAAGSTPVYVGFGSSSRPATADAAKMAIKAVRASGRRIVLSRGWADLVLPDDGADCFVVGEVNLQELFGRVAAAIHHDSAGTTLLAMRAGIPQIVVRRV-------AYHADRVAELGVGVAVDGPVPTIDSLSAALDTALAPEIRARATTVADTIRADGTTVAAQLLFDAVSLEK 391
                                    10        20        30        40        50        60        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    |    -  |    330       340       350       360       370       380       390 
                                                                                                                                                                                                                                                                                                                                                    315     323                                                                    


Chain C from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 1pnv C   1 xxNxxxx   7
                            || ||||
                            1-MLU||
                             2-OMZ|
                               4-GHP
                                5-GHP
                                 6-OMY
                                  7-3FG
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1PNV)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GTFA_AMYOR | P96558: 1pn3 3h4i 3h4t

(-) Related Entries Specified in the PDB File

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1gac SOLUTION STRUCTURE OF A82846B COMPLEXED WITH ITS CELL WALL PENTAPEPTIDE FRAGMENT
1ghg CRYSTAL STRUCTURE OF VANCOMYCIN AGLYCON
1pn3 CRYSTAL STRUCTURE OF TDP-EPI-VANCOSAMINYLTRANSFERASE GTFA COMPLEXD WITH TDP AND DESVANCOSAMINYL VANCOMYCIN
1qd8 CRYSTAL STRUCTURE OF VANCOMYCIN COMPLEXED WITH N-ACETYL GLYCIN
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1sho CRYSTAL STRUCTURE OF VANCOMYCIN