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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, Z. Xie, K. R. Acharya, K. Brew
Date :  12 Nov 02  (Deposition) - 06 Nov 03  (Release) - 15 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
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
    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  (5, 15)

Asymmetric Unit (5, 15)
No.NameCountTypeFull Name
1GAL2Ligand/IonBETA-D-GALACTOSE
2GOL5Ligand/IonGLYCEROL
3MN2Ligand/IonMANGANESE (II) ION
4NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
5UDP4Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 1 (4, 6)
No.NameCountTypeFull Name
1GAL1Ligand/IonBETA-D-GALACTOSE
2GOL2Ligand/IonGLYCEROL
3MN-1Ligand/IonMANGANESE (II) ION
4NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
5UDP2Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 2 (4, 7)
No.NameCountTypeFull Name
1GAL1Ligand/IonBETA-D-GALACTOSE
2GOL3Ligand/IonGLYCEROL
3MN-1Ligand/IonMANGANESE (II) ION
4NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
5UDP2Ligand/IonURIDINE-5'-DIPHOSPHATE

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:247 , THR A:259 , TYR A:278 , TRP A:314 , GLU A:317 , TRP A:356 , LYS A:359 , NAG A:1373 , UDP A:1374 , HOH A:2454 , HOH A:2455 , HOH A:2456 , HOH A:2464BINDING SITE FOR RESIDUE GAL A1372
02AC2SOFTWAREGLN A:247 , TRP A:249 , TRP A:250 , TRP A:356 , GAL A:1372 , HOH A:2454 , HOH A:2457 , HOH A:2459 , HOH A:2460 , HOH A:2461 , HOH A:2462BINDING SITE FOR RESIDUE NAG A1373
03AC3SOFTWAREGLN B:247 , THR B:259 , TYR B:278 , TRP B:314 , GLU B:317 , TRP B:356 , LYS B:359 , NAG B:1374 , UDP B:1376 , HOH B:2445 , HOH B:2466 , HOH B:2467 , HOH B:2468 , HOH B:2477BINDING SITE FOR RESIDUE GAL B1373
04AC4SOFTWAREGLN B:247 , TRP B:249 , TRP B:250 , TRP B:356 , GAL B:1373 , GOL B:1379 , HOH B:2468 , HOH B:2469 , HOH B:2470 , HOH B:2471 , HOH B:2472 , HOH B:2473BINDING SITE FOR RESIDUE NAG B1374
05AC5SOFTWAREASP B:225 , ASP B:227 , UDP B:1376 , HOH B:2464BINDING SITE FOR RESIDUE MN B1369
06AC6SOFTWAREASP A:225 , ASP A:227 , UDP A:1374 , HOH A:2453BINDING SITE FOR RESIDUE MN A1371
07AC7SOFTWAREPHE 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:1371 , GAL A:1372 , HOH A:2226 , HOH A:2263 , HOH A:2265 , HOH A:2453 , HOH A:2463 , HOH A:2464 , HOH A:2465BINDING SITE FOR RESIDUE UDP A1374
08AC8SOFTWAREARG A:194 , ASP A:197 , LYS A:306 , HOH A:2467BINDING SITE FOR RESIDUE UDP A1375
09AC9SOFTWAREPHE B:134 , ALA B:135 , VAL B:136 , TYR B:139 , ILE B:198 , SER B:199 , ARG B:202 , ASP B:225 , VAL B:226 , ASP B:227 , LYS B:359 , TYR B:361 , ARG B:365 , MN B:1369 , GAL B:1373 , HOH B:2232 , HOH B:2268 , HOH B:2270 , HOH B:2464 , HOH B:2475 , HOH B:2476 , HOH B:2477BINDING SITE FOR RESIDUE UDP B1376
10BC1SOFTWAREARG B:194 , ASP B:197 , LYS B:306 , HOH B:2221 , HOH B:2478BINDING SITE FOR RESIDUE UDP B1377
11BC2SOFTWAREHIS A:142 , GLU A:146 , GLN A:357 , GLU A:360 , HOH A:2450 , HOH A:2451BINDING SITE FOR RESIDUE GOL A1369
12BC3SOFTWAREARG A:262 , ARG A:263 , LYS A:264 , HOH A:2307 , HOH A:2309 , HOH A:2317 , ASP B:254 , ASP B:257BINDING SITE FOR RESIDUE GOL A1370
13BC4SOFTWAREHIS B:142 , GLU B:146 , GLN B:357 , GLU B:360BINDING SITE FOR RESIDUE GOL B1372
14BC5SOFTWARESER B:86 , HOH B:2002 , HOH B:2009 , HOH B:2479 , HOH B:2480BINDING SITE FOR RESIDUE GOL B1378
15BC6SOFTWARELYS B:359 , TYR B:361 , NAG B:1374 , HOH B:2481 , HOH B:2482 , HOH B:2483 , HOH B:2484BINDING SITE FOR RESIDUE GOL B1379

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1O7Q)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1O7Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1O7Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1O7Q)

(-) 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:82-92
11
11
1.8ENSBTAT000000160338ENSBTAE00000004437chr11:95387778-95387641138GGTA1_BOVIN92-138472A:92-138
B:92-138
47
47
1.9ENSBTAT000000160339ENSBTAE00000130543chr11:95383311-95382365947GGTA1_BOVIN138-3682312A:138-368
B:138-368
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 d1o7qa_ A: alpha-1,3-galactosyltransferase catalytic domain                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1o7qA00 A:82-368 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh............ee.....hhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhhhhh.....eeeeeee.hhhhh........eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhh.eeeee...eee....hhhhh..eeeee.......hhhhh....................eeeeeeeehhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh...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)
                 1o7q A  82 KLKLSDWFNPFKRPEVVTMTKWKAPVVWEGTYNRAVLDNYYAKQKITVGLTVFAVGRYIEHYLEEFLTSANKHFMVGHPVIFYIMVDDVSRMPLIELGPLRSFKVFKIKPEKRWQDISMMRMKTIGEHIVAHIQHEVDFLFCMDVDQVFQDKFGVETLGESVAQLQAWWYKADPNDFTYERRKESAAYIPFGEGDFYYHAAIFGGTPTQVLNITQECFKGILKDKKNDIEAQWHDESHLNKYFLLNKPTKILSPEYCWDYHIGLPADIKLVKMSWQTKEYNVVRNNV 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 d1o7qb_ B: alpha-1,3-galactosyltransferase catalytic domain                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1o7qB00 B:82-368 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                                                                   CATH domains
           Pfam domains (1) Glyco_transf_6-1o7qB01 B:82-366                                                                                                                                                                                                                                                              -- Pfam domains (1)
           Pfam domains (2) Glyco_transf_6-1o7qB02 B:82-366                                                                                                                                                                                                                                                              -- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhh............ee.....hhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhhhhh.....eeeeeee.hhhhh........eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhh.eeeee...eee....hhhhh..eeeee.......hhhhh....................eeeeeeeehhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh...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:138-368 UniProt: 138-368                                                                                                                                                                                               Transcript 1 (1)
           Transcript 1 (2) ----------Exon 1.8  PDB: B:92-138 UniProt: 92-138        -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1o7q B  82 KLKLSDWFNPFKRPEVVTMTKWKAPVVWEGTYNRAVLDNYYAKQKITVGLTVFAVGRYIEHYLEEFLTSANKHFMVGHPVIFYIMVDDVSRMPLIELGPLRSFKVFKIKPEKRWQDISMMRMKTIGEHIVAHIQHEVDFLFCMDVDQVFQDKFGVETLGESVAQLQAWWYKADPNDFTYERRKESAAYIPFGEGDFYYHAAIFGGTPTQVLNITQECFKGILKDKKNDIEAQWHDESHLNKYFLLNKPTKILSPEYCWDYHIGLPADIKLVKMSWQTKEYNVVRNNV 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       

   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 1vzt 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
1o7r ROLES OF INDIVIDUAL RESIDUES OF ALPHA-1,3 GALACTOSYLTRANSFERASES IN SUBSTRATE BINDING AND CATALYSIS