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(-) Description

Title :  CRYSTAL STRUCTURE OF UDP-GLUCOSYLTRANSFERASE GTFB
 
Authors :  A. M. Mulichak, H. C. Losey, C. T. Walsh, R. M. Garavito
Date :  24 Apr 01  (Deposition) - 18 Jul 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Glycosyltransferase, Rossmann Fold (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. M. Mulichak, H. C. Losey, C. T. Walsh, R. M. Garavito
Structure Of The Udp-Glucosyltransferase Gtfb That Modifies The Heptapeptide Aglycone In The Biosynthesis Of Vancomycin Group Antibiotics.
Structure V. 9 547 2001
PubMed-ID: 11470430  |  Reference-DOI: 10.1016/S0969-2126(01)00616-5
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLYCOSYLTRANSFERASE GTFB
    Chains: A
    EC Number: 2.4.1.-
    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
    Organism Scientific: AMYCOLATOPSIS ORIENTALIS
    Organism Taxid: 31958
    Strain: A82846
    Synonym: UDP-GLYCOSYLTRANSFERASE GTFB

 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
1MG2Ligand/IonMAGNESIUM ION
2SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:310 , GLY A:312 , THR A:313 , HOH A:1497 , HOH A:1635BINDING SITE FOR RESIDUE SO4 A 1403
2AC2SOFTWAREHOH A:1409 , HOH A:1436 , HOH A:1470BINDING SITE FOR RESIDUE MG A 1404
3AC3SOFTWAREASP A:175 , HOH A:1412 , HOH A:1442 , HOH A:1443 , HOH A:1448 , HOH A:1494BINDING SITE FOR RESIDUE MG A 1405

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1IIR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1IIR)

(-) 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 GTFB_AMYOR | P96559 from UniProtKB/Swiss-Prot  Length:407

    Alignment length:401
                                    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       400 
           GTFB_AMYOR     1 MRVLLATCGSRGDTEPLVALAVRVRDLGADVRMCAPPDCAERLAEVGVPHVPVGPSARAPIQRAKPLTAEDVRRFTTEAIATQFDEIPAAAEGCAAVVTTGLLAAAIGVRSVAEKLGIPYFYAFHCPSYVPSPYYPPPPLGEPSTQDTIDIPAQWERNNQSAYQRYGGLLNSHRDAIGLPPVEDIFTFGYTDHPWVAADPVLAPLQPTDLDAVQTGAWILPDERPLSPELAAFLDAGPPPVYLGFGSLGAPADAVRVAIDAIRAHGRRVILSRGWADLVLPDDGADCFAIGEVNHQVLFGRVAAVIHHGGAGTTHVAARAGAPQILLPQMADQPYYAGRVAELGVGVAHDGPIPTFDSLSAALATALTPETHARATAVAGTIRTDGAAVAARLLLDAVSRE 401
               SCOP domains d1iira_ A: UDP-glucosyltransferase GtfB                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1iirA01 A:1-218,A:383-401 Glycogen Phosphorylase B;                                                                                                                                                                       1iirA02 A:219-382 Glycogen    Phosphorylase B;                                                                                                                      1iirA01             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhh...eee...-------.....hhhhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhh..eeeee.hhhhh.........---------hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh...ee................ee............hhhhhhhhhh....eeee.---..hhhhhhhhhhhhhhh...eee...........hhh.eee....hhhhhhhhh.eeee..hhhhhhhhhhhh..eee.....hhhhhhhhhhhh..eee......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iir A   1 MRVLLATCGSRGDTEPLVALAVRVRDLGADVRMCAPPDCAERLAEVGVPHVPVGP-------RAKPLTAEDVRRFTTEAIATQFDEIPAAAEGCAAVVTTGLLAAAIGVRSVAEKLGIPYFYAFHCPSYVPSPYYPPPP---------IDIPAQWERNNQSAYQRYGGLLNSHRDAIGLPPVEDIFTFGYTDHPWVAADPVLAPLQPTDLDAVQTGAWILPDERPLSPELAAFLDAGPPPVYLGF---GAPADAVRVAIDAIRAHGRRVILSRGWADLVLPDDGADCFAIGEVNHQVLFGRVAAVIHHGGAGTTHVAARAGAPQILLPQMADQPYYAGRVAELGVGVAHDGPIPTFDSLSAALATALTPETHARATAVAGTIRTDGAAVAARLLLDAVSRE 401
                                    10        20        30        40        50    |    -  |     70        80        90       100       110       120       130        |-       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       400 
                                                                                 55      63                                                                         139       149                                                                                             245 249
   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  (1, 1)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GTFB_AMYOR | P96559)
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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