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(-) Description

Title :  ROLES OF INDIVIDUAL RESIDUES OF ALPHA-1,3 GALACTOSYLTRANSFERASES IN SUBSTRATE BINDING AND CATALYSIS
 
Authors :  Y. Zhang, G. J. Swaminathan, A. Deshpande, R. Natesh, X. Xie, K. R. Acharya, K. Brew
Date :  26 May 04  (Deposition) - 26 May 05  (Release) - 15 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transferase, Alpha-1, 3-Galactosyltransferase-Udp Complex, Glycosyltransferase, Glycoprotein, Transmembrane, Nucleotide-Binding Protein, Xenotransplantation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Zhang, G. J. Swaminathan, A. Deshpande, E. Boix, R. Natesh, Z. Xie, K. R. Acharya, K. Brew
Roles Of Individual Enzyme-Substrate Interactions By Alpha- 1, 3-Galactosyltransferase In Catalysis And Specificity.
Biochemistry V. 42 13512 2003
PubMed-ID: 14621997  |  Reference-DOI: 10.1021/BI035430R
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - N-ACETYLLACTOSAMINIDE ALPHA-1,3- GALACTOSYLTRANSFERASE
    ChainsA, B
    EC Number2.4.1.151
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPSV-SPORT
    Expression System Taxid562
    Expression System VariantDH5-ALPHA
    Expression System Vector TypePLASMID
    FragmentCATALYTIC DOMAIN, RESIDUES 80-368
    MutationYES
    Organism CommonBOVINE
    Organism ScientificBOS TAURUS
    Organism Taxid9913
    SynonymGALACTOSYLTRANSFERASE, UDP-GALACTOSE, BETA-D-GALACTOSYL-1,4-N-ACETYL-D-GLUCOSAMINIDE ALPHA-1,3-GALACTOSYLTRANSFERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1MN2Ligand/IonMANGANESE (II) ION
2TRS2Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
3UDP2Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
3UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
3UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:225 , ASP A:227 , UDP A:1370 , HOH A:2211BINDING SITE FOR RESIDUE MN A1369
2AC2SOFTWAREASP B:1225 , ASP B:1227 , HOH B:2221 , UDP B:2370BINDING SITE FOR RESIDUE MN B2369
3AC3SOFTWAREPHE A:134 , ALA A:135 , VAL A:136 , TYR A:139 , ILE A:198 , SER A:199 , ARG A:202 , ASP A:225 , VAL A:226 , ASP A:227 , LYS A:359 , TYR A:361 , ARG A:365 , MN A:1369 , TRS A:1371 , HOH A:2110 , HOH A:2211 , HOH A:2212 , HOH A:2213 , HOH A:2214 , HOH A:2215 , HOH A:2216BINDING SITE FOR RESIDUE UDP A1370
4AC4SOFTWARESER A:199 , ALA A:281 , TRP A:314 , HIS A:315 , ASP A:316 , GLU A:317 , UDP A:1370 , HOH A:2214 , HOH A:2215 , HOH A:2217BINDING SITE FOR RESIDUE TRS A1371
5AC5SOFTWAREPHE B:1134 , ALA B:1135 , VAL B:1136 , TYR B:1139 , ILE B:1198 , SER B:1199 , ARG B:1202 , ASP B:1225 , VAL B:1226 , ASP B:1227 , LYS B:1359 , TYR B:1361 , ARG B:1365 , HOH B:2089 , HOH B:2093 , HOH B:2221 , HOH B:2222 , HOH B:2223 , HOH B:2224 , HOH B:2225 , MN B:2369 , TRS B:2371BINDING SITE FOR RESIDUE UDP B2370
6AC6SOFTWAREALA B:1281 , TRP B:1314 , HIS B:1315 , ASP B:1316 , GLU B:1317 , HOH B:2090 , HOH B:2223 , HOH B:2225 , UDP B:2370BINDING SITE FOR RESIDUE TRS B2371

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (3, 6)

Asymmetric Unit (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSBTAT000000160331ENSBTAE00000262074chr11:95459665-95459416250GGTA1_BOVIN-00--
1.2ENSBTAT000000160332ENSBTAE00000262073chr11:95449479-9544938595GGTA1_BOVIN-00--
1.3ENSBTAT000000160333ENSBTAE00000262072chr11:95415347-95415232116GGTA1_BOVIN-00--
1.4ENSBTAT000000160334ENSBTAE00000262071chr11:95404542-9540445489GGTA1_BOVIN1-27270--
1.5ENSBTAT000000160335ENSBTAE00000262069chr11:95397952-9539791736GGTA1_BOVIN27-39130--
1.6ENSBTAT000000160336ENSBTAE00000262068chr11:95396284-9539621966GGTA1_BOVIN39-61230--
1.7ENSBTAT000000160337ENSBTAE00000262067chr11:95395659-9539556793GGTA1_BOVIN61-92322A:82-92
B:1082-1092
11
11
1.8ENSBTAT000000160338ENSBTAE00000004437chr11:95387778-95387641138GGTA1_BOVIN92-138472A:92-138
B:1092-1138
47
47
1.9ENSBTAT000000160339ENSBTAE00000130543chr11:95383311-95382365947GGTA1_BOVIN138-3682312A:138-368
B:1138-1368
231
231

(-) 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:287
 aligned with GGTA1_BOVIN | P14769 from UniProtKB/Swiss-Prot  Length:368

    Alignment length:287
                                    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       
         GGTA1_BOVIN     82 KLKLSDWFNPFKRPEVVTMTKWKAPVVWEGTYNRAVLDNYYAKQKITVGLTVFAVGRYIEHYLEEFLTSANKHFMVGHPVIFYIMVDDVSRMPLIELGPLRSFKVFKIKPEKRWQDISMMRMKTIGEHIVAHIQHEVDFLFCMDVDQVFQDKFGVETLGESVAQLQAWWYKADPNDFTYERRKESAAYIPFGEGDFYYHAAIFGGTPTQVLNITQECFKGILKDKKNDIEAQWHDESHLNKYFLLNKPTKILSPEYCWDYHIGLPADIKLVKMSWQTKEYNVVRNNV  368
               SCOP domains d1vzta_ A: alpha-1,3-galactosyltransferase catalytic domain                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1vztA00 A:82-368 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh.hhhhh.....ee..eeeee.....hhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhh.....eeeeeee.hhhhh........eee..ee.....hhhhhhhhhhhhhhhhhhhhhhhhh.eeeee...eee....hhhhh..eeeee.......hhhhh....................eeeeeeeehhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh...eee.hhhh.hhhhh.........eee...hhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.7   ---------------------------------------------Exon 1.9  PDB: A:138-368 UniProt: 138-368                                                                                                                                                                                               Transcript 1 (1)
           Transcript 1 (2) ----------Exon 1.8  PDB: A:92-138 UniProt: 92-138        -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                1vzt A   82 KLKLSDWFNPFKRPEVVTMTKWKAPVVWEGTYNRAVLDNYYAKQKITVGLTVFAVGRYIEHYLEEFLTSANKHFMVGHPVIFYIMVDDVSRMPLIELGPLRSFKVFKIKPEKRWQDISMMRMKTIGEHIVAHIQHEVDFLFCMDVDQVFQDKFGVETLGESVAQLQAGWYKADPNDFTYERRKESAAYIPFGEGDFYYHAAIFGGTPTQVLNITQECFKGILKDKKNDIEAQWHDESHLNKYFLLNKPTKILSPEYCWDYHIGLPADIKLVKMSWQTKEYNVVRNNV  368
                                    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       

Chain B from PDB  Type:PROTEIN  Length:287
 aligned with GGTA1_BOVIN | P14769 from UniProtKB/Swiss-Prot  Length:368

    Alignment length:287
                                    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       
         GGTA1_BOVIN     82 KLKLSDWFNPFKRPEVVTMTKWKAPVVWEGTYNRAVLDNYYAKQKITVGLTVFAVGRYIEHYLEEFLTSANKHFMVGHPVIFYIMVDDVSRMPLIELGPLRSFKVFKIKPEKRWQDISMMRMKTIGEHIVAHIQHEVDFLFCMDVDQVFQDKFGVETLGESVAQLQAWWYKADPNDFTYERRKESAAYIPFGEGDFYYHAAIFGGTPTQVLNITQECFKGILKDKKNDIEAQWHDESHLNKYFLLNKPTKILSPEYCWDYHIGLPADIKLVKMSWQTKEYNVVRNNV  368
               SCOP domains d1vztb_ B: alpha-1,3-galactosyltransferase catalytic domain                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1vztB00 B:1082-1368 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                                                                CATH domains
           Pfam domains (1) Glyco_transf_6-1vztB01 B:1082-1366                                                                                                                                                                                                                                                           -- Pfam domains (1)
           Pfam domains (2) Glyco_transf_6-1vztB02 B:1082-1366                                                                                                                                                                                                                                                           -- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhh............ee.....hhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhhhhh.....eeeeeee.hhhhh........eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhh.eeeee...eee....hhhhh..eeeee.......hhhhh....................eeeeeeeehhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh...eee.hhhh.hhhhh.........eee...hhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.7   ---------------------------------------------Exon 1.9  PDB: B:1138-1368 UniProt: 138-368                                                                                                                                                                                             Transcript 1 (1)
           Transcript 1 (2) ----------Exon 1.8  PDB: B:1092-1138 UniProt: 92-138     -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                1vzt B 1082 KLKLSDWFNPFKRPEVVTMTKWKAPVVWEGTYNRAVLDNYYAKQKITVGLTVFAVGRYIEHYLEEFLTSANKHFMVGHPVIFYIMVDDVSRMPLIELGPLRSFKVFKIKPEKRWQDISMMRMKTIGEHIVAHIQHEVDFLFCMDVDQVFQDKFGVETLGESVAQLQAGWYKADPNDFTYERRKESAAYIPFGEGDFYYHAAIFGGTPTQVLNITQECFKGILKDKKNDIEAQWHDESHLNKYFLLNKPTKILSPEYCWDYHIGLPADIKLVKMSWQTKEYNVVRNNV 1368
                                  1091      1101      1111      1121      1131      1141      1151      1161      1171      1181      1191      1201      1211      1221      1231      1241      1251      1261      1271      1281      1291      1301      1311      1321      1331      1341      1351      1361       

   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 Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: GT-A (172)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GGTA1_BOVIN | P14769)
molecular function
    GO:0047276    N-acetyllactosaminide 3-alpha-galactosyltransferase activity    Catalysis of the reaction: beta-D-galactosyl-(1,4)-beta-N-acetyl-D-glucosaminyl-R + UDP-galactose = alpha-D-galactosyl-(1,3)-beta-D-galactosyl-(1,4)-beta-N-acetyl-D-glucosaminyl-R + UDP.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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:0033580    protein galactosylation at cell surface    The addition of a galactose unit to a protein amino acid at the surface of a cell.
    GO:0006486    protein glycosylation    A protein modification process that results in the addition of a carbohydrate or carbohydrate derivative unit to a protein amino acid, e.g. the addition of glycan chains to proteins.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0031985    Golgi cisterna    Any of the thin, flattened membrane-bounded compartments that form the central portion of the Golgi complex.
    GO:0032580    Golgi cisterna membrane    The lipid bilayer surrounding any of the thin, flattened compartments that form the central portion of the Golgi complex.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GGTA1_BOVIN | P147691fg5 1g8o 1g93 1gwv 1gww 1gx0 1gx4 1k4v 1o7o 1o7q 1vzu 1vzx 2jcj 2jck 2jcl 2jco 2vfz 2vs3 2vs4 2vs5 2vxl 2vxm 2wgz

(-) Related Entries Specified in the PDB File

1fg5 CRYSTAL STRUCTURE OF BOVINE ALPHA-1,3- GALACTOSYLTRANSFERASECATALYTIC DOMAIN.
1g8o CRYSTALLOGRAPHIC STRUCTURE OF THE NATIVE BOVINE ALPHA-1,3-GALACTOSYLTRANSFERASE CATALYTIC DOMAIN
1g93 CRYSTAL STRUCTURE OF THE BOVINE CATALYTIC DOMAIN OF ALPHA-1,3-GALACTOSYLTRANSFERASE IN THE PRESENCE OF UDP-GALACTOSE
1gwv STRUCTURAL BASIS OF ORDERED BINDING OF DONOR AND ACCEPTOR SUBSTRATES TO THE RETAINING GLYCOSYLTRANSFERASE: ALPHA -1,3 GALACTOSYLTRANSFERASE
1gww STRUCTURAL BASIS OF ORDERED BINDING OF DONOR AND ACCEPTOR SUBSTRATES TO THE RETAINING GLYCOSYLTRANSFERASE: ALPHA -1,3 GALACTOSYLTRANSFERASE
1gx0 STRUCTURAL BASIS OF ORDERED BINDING OF DONOR AND ACCEPTOR SUBSTRATES TO THE RETAINING GLYCOSYLTRANSFERASE: ALPHA -1,3 GALACTOSYLTRANSFERASE
1gx4 STRUCTURAL BASIS OF ORDERED BINDING OF DONOR AND ACCEPTOR SUBSTRATES TO THE RETAINING GLYCOSYLTRANSFERASE: ALPHA -1,3 GALACTOSYLTRANSFERASE
1k4v 1.53 A CRYSTAL STRUCTURE OF THE BETA- GALACTOSIDE-ALPHA-1,3-GALACTOSYLTRANSFERASE IN COMPLEX WITH UDP
1o7o ROLES OF INDIVIDUAL RESIDUES OF ALPHA-1,3 GALACTOSYLTRANSFERASES IN SUBSTRATE BINDING AND CATALYSIS
1o7q ROLES OF INDIVIDUAL RESIDUES OF ALPHA-1,3 GALACTOSYLTRANSFERASES IN SUBSTRATE BINDING AND CATALYSIS