1VZT - JenaLib

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Biological Unit 2 (Jmol Viewer)

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)

Molecule 1 - N-ACETYLLACTOSAMINIDE ALPHA-1,3- GALACTOSYLTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.4.1.151
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PSV-SPORT
	Expression System Taxid	:	562
	Expression System Variant	:	DH5-ALPHA
	Expression System Vector Type	:	PLASMID
	Fragment	:	CATALYTIC DOMAIN, RESIDUES 80-368
	Mutation	:	YES
	Organism Common	:	BOVINE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Synonym	:	GALACTOSYLTRANSFERASE, UDP-GALACTOSE, BETA-D-GALACTOSYL-1,4-N-ACETYL-D-GLUCOSAMINIDE ALPHA-1,3-GALACTOSYLTRANSFERASE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	MN	2	Ligand/Ion	MANGANESE (II) ION
2	TRS	2	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
3	UDP	2	Ligand/Ion	URIDINE-5'-DIPHOSPHATE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION
2	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
3	UDP	1	Ligand/Ion	URIDINE-5'-DIPHOSPHATE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION
2	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
3	UDP	1	Ligand/Ion	URIDINE-5'-DIPHOSPHATE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:225 , ASP A:227 , UDP A:1370 , HOH A:2211	BINDING SITE FOR RESIDUE MN A1369
2	AC2	SOFTWARE	ASP B:1225 , ASP B:1227 , HOH B:2221 , UDP B:2370	BINDING SITE FOR RESIDUE MN B2369
3	AC3	SOFTWARE	PHE 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:2216	BINDING SITE FOR RESIDUE UDP A1370
4	AC4	SOFTWARE	SER 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:2217	BINDING SITE FOR RESIDUE TRS A1371
5	AC5	SOFTWARE	PHE 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:2371	BINDING SITE FOR RESIDUE UDP B2370
6	AC6	SOFTWARE	ALA 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:2370	BINDING SITE FOR RESIDUE TRS B2371

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

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

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

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

Asymmetric Unit (3, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSBTAT00000016033	1	ENSBTAE00000262074	chr11:95459665-95459416	250	GGTA1_BOVIN	-	0	0	-	-
1.2	ENSBTAT00000016033	2	ENSBTAE00000262073	chr11:95449479-95449385	95	GGTA1_BOVIN	-	0	0	-	-
1.3	ENSBTAT00000016033	3	ENSBTAE00000262072	chr11:95415347-95415232	116	GGTA1_BOVIN	-	0	0	-	-
1.4	ENSBTAT00000016033	4	ENSBTAE00000262071	chr11:95404542-95404454	89	GGTA1_BOVIN	1-27	27	0	-	-
1.5	ENSBTAT00000016033	5	ENSBTAE00000262069	chr11:95397952-95397917	36	GGTA1_BOVIN	27-39	13	0	-	-
1.6	ENSBTAT00000016033	6	ENSBTAE00000262068	chr11:95396284-95396219	66	GGTA1_BOVIN	39-61	23	0	-	-
1.7	ENSBTAT00000016033	7	ENSBTAE00000262067	chr11:95395659-95395567	93	GGTA1_BOVIN	61-92	32	2	A:82-92 B:1082-1092	11 11
1.8	ENSBTAT00000016033	8	ENSBTAE00000004437	chr11:95387778-95387641	138	GGTA1_BOVIN	92-138	47	2	A:92-138 B:1092-1138	47 47
1.9	ENSBTAT00000016033	9	ENSBTAE00000130543	chr11:95383311-95382365	947	GGTA1_BOVIN	138-368	231	2	A:138-368 B:1138-1368	231 231

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
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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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Nucleotide-diphospho-sugar transferases (408)

Superfamily: Nucleotide-diphospho-sugar transferases (408)

Family: alpha-1,3-galactosyltransferase-like (125)

Protein domain: alpha-1,3-galactosyltransferase catalytic domain (22)

Cow (Bos taurus) [TaxId: 9913] (22)

1a	d1vzta_	A:
1b	d1vztb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A (231)

Homologous Superfamily: Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A (231)

Bovine (Bos taurus) (20)

1a	1vztA00	A:82-368
1b	1vztB00	B:1082-1368

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GT-A (172)

Family: Glyco_transf_6 (55)

Bos taurus (Bovine) (15)

1a	Glyco_transf_6-1vztB01	B:1082-1366
1b	Glyco_transf_6-1vztB02	B:1082-1366

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.

Asymmetric Unit
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	Cis Peptide Bonds
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	1vzt
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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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (3, 6)

Sequences/Alignments

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SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (13, 13)

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