2VFZ - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF ALPHA-1,3 GALACTOSYLTRANSFERASE (R365K) IN COMPLEX WITH UDP-2F-GALACTOSE

Authors :   H. Jamaluddin, P. Tumbale, S. G. Withers, K. R. Acharya, K. Brew

Date :   06 Nov 07 (Deposition) - 13 Nov 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym./Biol. Unit : A,B

Keywords :   3 Galactosyltransferase, Manganese, Transferase, Glycoprotein, Metal-Binding, Gt, R365K, Alpha-1, Membrane, Alpha Gt, Galactose, Enzyme Mechanism, Glycosyltransferase, Galactosyltransferase, Substrate Specificity, Signal-Anchor, Transmembrane, Golgi Apparatus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Jamaluddin, P. Tumbale, S. G. Withers, K. R. Acharya, K. Brew
Conformational Changes Induced By Binding Udp-2F- Galactose To Alpha-1, 3 Galactosyltransferase- Implications For Catalysis
J. Mol. Biol. V. 369 1270 2007
PubMed-ID: 17493636 | Reference-DOI: 10.1016/J.JMB.2007.04.012

Molecule 1 - N-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYL TRANSFERASE
	Chains	:	A, B
	EC Number	:	2.4.1.151, 2.4.1.87
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Fragment	:	CATALYTIC DOMAIN, RESIDUES 80-368
	Mutation	:	YES
	Organism Common	:	BOVINE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Other Details	:	URIDINE-5'-DIPHOSPHATE-2-DEOXY-2- FLUOROGALACTOSE MANGANESE ION
	Synonym	:	GALACTOSYLTRANSFERASE, UDP-GALACTOSE BETA-D-GALACTOSYL-1,4-N-ACETYL- D-GLUCOSAMINIDE ALPHA-1,3-GALACTOSYLTRANSFERASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	MN	2	Ligand/Ion	MANGANESE (II) ION
2	UPF	2	Ligand/Ion	URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUOROGALACTOSE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:134 , VAL A:136 , TYR A:139 , ILE A:198 , SER A:199 , ARG A:202 , ASP A:225 , VAL A:226 , ASP A:227 , HIS A:280 , ALA A:281 , ALA A:282 , HIS A:315 , ASP A:316 , GLU A:317 , LYS A:359 , MN A:1361	BINDING SITE FOR RESIDUE UPF A1360
2	AC2	SOFTWARE	ASP A:225 , ASP A:227 , UPF A:1360	BINDING SITE FOR RESIDUE MN A1361
3	AC3	SOFTWARE	PHE A:92 , PHE B:1134 , ALA B:1135 , VAL B:1136 , TYR B:1139 , TRP B:1195 , ILE B:1198 , SER B:1199 , ARG B:1202 , ASP B:1225 , VAL B:1226 , ASP B:1227 , HIS B:1280 , ALA B:1281 , ALA B:1282 , HIS B:1315 , ASP B:1316 , GLU B:1317 , LYS B:1359 , HOH B:2246 , MN B:2365	BINDING SITE FOR RESIDUE UPF B2364
4	AC4	SOFTWARE	ASP B:1225 , ASP B:1227 , HOH B:2247 , UPF B:2364	BINDING SITE FOR RESIDUE MN B2365

(no "SS Bond" information available for 2VFZ)

(no "Cis Peptide Bond" information available for 2VFZ)

(no "SAP(SNP)/Variant" information available for 2VFZ)

(no "PROSITE Motif" information available for 2VFZ)

Asymmetric/Biological 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:1083-1092	11 10
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:138-359 B:1138-1363	222 226

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:278
 aligned with GGTA1_BOVIN | P14769 from UniProtKB/Swiss-Prot  Length:368

    Alignment length:278
                                    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        
         GGTA1_BOVIN     82 KLKLSDWFNPFKRPEVVTMTKWKAPVVWEGTYNRAVLDNYYAKQKITVGLTVFAVGRYIEHYLEEFLTSANKHFMVGHPVIFYIMVDDVSRMPLIELGPLRSFKVFKIKPEKRWQDISMMRMKTIGEHIVAHIQHEVDFLFCMDVDQVFQDKFGVETLGESVAQLQAWWYKADPNDFTYERRKESAAYIPFGEGDFYYHAAIFGGTPTQVLNITQECFKGILKDKKNDIEAQWHDESHLNKYFLLNKPTKILSPEYCWDYHIGLPADIKLVKMSWQTK  359
               SCOP domains d2vfza_ A: alpha-1,3-galactosyltransferase catalytic domain                                                                                                                                                                                                                            SCOP domains
               CATH domains 2vfzA00 A:82-359 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.....hhhhhhhhhhhhhhhhhhhhhhhh..eeeee...eee....hhhhh..eeeee.......hhhhh....................eeeeeeeehhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh...eee.hhhh.hhhhh.........eee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.7   ---------------------------------------------Exon 1.9  PDB: A:138-359 UniProt: 138-368 [INCOMPLETE]                                                                                                                                                                         Transcript 1 (1)
           Transcript 1 (2) ----------Exon 1.8  PDB: A:92-138 UniProt: 92-138        ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                2vfz A   82 KLKLSDWFNPFKRPEVVTMTKWKAPVVWEGTYNRAVLDNYYAKQKITVGLTVFAVGRYIEHYLEEFLTSANKHFMVGHPVIFYIMVDDVSRMPLIELGPLRSFKVFKIKPEKRWQDISMMRMKTIGEHIVAHIQHEVDFLFCMDVDQVFQDKFGVETLGESVAQLQAWWYKADPNDFTYERRKESAAYIPFGEGDFYYHAAIFGGTPTQVLNITQECFKGILKDKKNDIEAQWHDESHLNKYFLLNKPTKILSPEYCWDYHIGLPADIKLVKMSWQTK  359
                                    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

Chain B from PDB  Type:PROTEIN  Length:281
 aligned with GGTA1_BOVIN | P14769 from UniProtKB/Swiss-Prot  Length:368

    Alignment length:281
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362 
         GGTA1_BOVIN     83 LKLSDWFNPFKRPEVVTMTKWKAPVVWEGTYNRAVLDNYYAKQKITVGLTVFAVGRYIEHYLEEFLTSANKHFMVGHPVIFYIMVDDVSRMPLIELGPLRSFKVFKIKPEKRWQDISMMRMKTIGEHIVAHIQHEVDFLFCMDVDQVFQDKFGVETLGESVAQLQAWWYKADPNDFTYERRKESAAYIPFGEGDFYYHAAIFGGTPTQVLNITQECFKGILKDKKNDIEAQWHDESHLNKYFLLNKPTKILSPEYCWDYHIGLPADIKLVKMSWQTKEYNV  363
               SCOP domains d2vfzb_ B: alpha-1,3-galactosyltransferase catalytic domain                                                                                                                                                                                                                               SCOP domains
               CATH domains 2vfzB00 B:1083-1363 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                                                          CATH domains
           Pfam domains (1) Glyco_transf_6-2vfzB01 B:1083-1363                                                                                                                                                                                                                                                        Pfam domains (1)
           Pfam domains (2) Glyco_transf_6-2vfzB02 B:1083-1363                                                                                                                                                                                                                                                        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....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.7  ---------------------------------------------Exon 1.9  PDB: B:1138-1363 UniProt: 138-368 [INCOMPLETE]                                                                                                                                                                           Transcript 1 (1)
           Transcript 1 (2) ---------Exon 1.8  PDB: B:1092-1138 UniProt: 92-138     --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                2vfz B 1083 LKLSDWFNPFKRPEVVTMTKWKAPVVWEGTYNRAVLDNYYAKQKITVGLTVFAVGRYIEHYLEEFLTSANKHFMVGHPVIFYIMVDDVSRMPLIELGPLRSFKVFKIKPEKRWQDISMMRMKTIGEHIVAHIQHEVDFLFCMDVDQVFQDKFGVETLGESVAQLQAWWYKADPNDFTYERRKESAAYIPFGEGDFYYHAAIFGGTPTQVLNITQECFKGILKDKKNDIEAQWHDESHLNKYFLLNKPTKILSPEYCWDYHIGLPADIKLVKMSWQTKEYNV 1363
                                  1092      1102      1112      1122      1132      1142      1152      1162      1172      1182      1192      1202      1212      1222      1232      1242      1252      1262      1272      1282      1292      1302      1312      1322      1332      1342      1352      1362

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/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

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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	d2vfza_	A:
1b	d2vfzb_	B:

Asymmetric/Biological 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	2vfzA00	A:82-359
1b	2vfzB00	B:1083-1363

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GT-A (172)

Family: Glyco_transf_6 (55)

Bos taurus (Bovine) (15)

1a	Glyco_transf_6-2vfzB01	B:1083-1363
1b	Glyco_transf_6-2vfzB02	B:1083-1363

Asymmetric/Biological 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/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2vfz)

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	2vfz
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	GGTA1_BOVIN \| P14769
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	2.4.1.151
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	2.4.1.87
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	GGTA1_BOVIN \| P14769
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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
1vzt	ROLES ON INDIVIDUAL RESIDUES OF ALPHA-1,3 GALACTOSYLTRANSFERASES IN SUBSTRATE BINDING AND CATALYSIS
1vzu	ROLES OF ACTIVE SITE TRYPTOPHANS IN SUBSTRATE BINDING AND CATALYSIS BY ALPHA-1, 3 GALACTOSYLTRANSFERASE
1vzx	ROLES OF ACTIVE SITE TRYPTOPHANS IN SUBSTRATE BINDING AND CATALYSIS BY ALPHA-1, 3 GALACTOSYLTRANSFERASE
2jcj	CRYSTAL STRUCTURE OF ALPHA-1,3 GALACTOSYLTRANSFERASE (C-TERMINUS TRUNCATED MUTANT-C3) IN COMPLEX WITH UDP AND TRIS
2jck	CRYSTAL STRUCTURE OF ALPHA-1,3 GALACTOSYLTRANSFERASE (R365K) IN COMPLEX WITH UDP AND 2 MANGANESE ION
2jcl	CRYSTAL STRUCTURE OF ALPHA-1,3 GALACTOSYLTRANSFERASE (R365K) IN THE ABSENCE OF LIGANDS
2jco	CRYSTAL STRUCTURE OF WILD TYPE ALPHA-1,3 GALACTOSYLTRANSFERASE IN THE ABSENCE OF LIGANDS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

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

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (13, 13)

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Related Entries Specified in the PDB File