2JCJ - JenaLib

Title :   CRYSTAL STRUCTURE OF ALPHA-1,3 GALACTOSYLTRANSFERASE (C-TERMINUS TRUNCATED MUTANT-C3) IN COMPLEX WITH UDP AND TRIS

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

Date :   25 Dec 06 (Deposition) - 22 May 07 (Release) - 29 Mar 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.02

Chains :   Asym./Biol. Unit : A

Keywords :   Substrate Specificity, 3 Galactosyltransferase, Alpha-1, Enzyme Mechanism, Glycosyltransferase Galactosyltransferase, Transmembrane, Golgi Apparatus, Glycoprotein, Metal-Binding, Signal-Anchor, Membrane, Manganese, Transferase, Glycosyltransferase (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

Compounds

Molecule 1 - N-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYLTRANSFERASE
	Chains	:	A
	EC Number	:	2.4.1.151
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Fragment	:	CATALYTIC DOMAIN RESIDUES 80-365
	Organism Common	:	BOVINE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Other Details	:	URIDINE-5'-DIPHOSPHATE, 2-AMINO-2-HYDROXYMETHYL- PROPANE-1,3-DIOL (TRIS), 2-METHYL-2,4-PENTANEDIOL (MPD), GLYCEROL (GOL)
	Synonym	:	ALPHA-1,3 GALACTOSYLTRANSFERASE, GALACTOSYLTRANSFERASE, UDP- GALACTOSE: BETA-D-GALACTOSYL-1,4-N-ACETYL-D-GLUCOSAMINIDE ALPHA-1,3- GALACTOSYLTRANSFERASE

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 5)

Sites (5, 5)

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:225 , ASP A:227 , UDP A:1366 , HOH A:2200	BINDING SITE FOR RESIDUE MN A1367
2	AC2	SOFTWARE	LYS A:102 , LYS A:104 , 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 , GLU A:360 , MN A:1367 , TRS A:1369 , HOH A:2097 , HOH A:2199 , HOH A:2201	BINDING SITE FOR RESIDUE UDP A1366
3	AC3	SOFTWARE	LYS A:104 , GLN A:247 , TYR A:278 , HIS A:280 , GLU A:317 , TRP A:356 , GLU A:360 , UDP A:1366 , HOH A:2125 , HOH A:2201 , HOH A:2202	BINDING SITE FOR RESIDUE TRS A1369
4	AC4	SOFTWARE	TYR A:341 , ILE A:349 , LYS A:350 , LEU A:351 , VAL A:352 , HOH A:2189	BINDING SITE FOR RESIDUE MPD A1368
5	AC5	SOFTWARE	PRO A:174 , LEU A:175 , ILE A:176 , PHE A:184 , HOH A:2203	BINDING SITE FOR RESIDUE GOL A1370

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (3, 3)

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
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Chain A from PDB  Type:PROTEIN  Length:284
 aligned with GGTA1_BOVIN | P14769 from UniProtKB/Swiss-Prot  Length:368

    Alignment length:284
                                    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 KLKLSDWFNPFKRPEVVTMTKWKAPVVWEGTYNRAVLDNYYAKQKITVGLTVFAVGRYIEHYLEEFLTSANKHFMVGHPVIFYIMVDDVSRMPLIELGPLRSFKVFKIKPEKRWQDISMMRMKTIGEHIVAHIQHEVDFLFCMDVDQVFQDKFGVETLGESVAQLQAWWYKADPNDFTYERRKESAAYIPFGEGDFYYHAAIFGGTPTQVLNITQECFKGILKDKKNDIEAQWHDESHLNKYFLLNKPTKILSPEYCWDYHIGLPADIKLVKMSWQTKEYNVVR 365
               SCOP domains d2jcja_ A: alpha-1,3-galactosyltransferase catalytic domain                                                                                                                                                                                                                                  SCOP domains
               CATH domains 2jcjA00 A:82-365 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                                                                CATH domains
               Pfam domains Glyco_transf_6-2jcjA01 A:82-365                                                                                                                                                                                                                                                              Pfam domains
         Sec.struct. author ..hhhhh.hhhhh............ee.....hhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhhhhh.....eeeeeee..............eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhh.eeeee...eee....hhhhh..eeeee.......hhhhh....................eeeeeeeehhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh...eee.hhhh.hhhhh.........eee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.7   ---------------------------------------------Exon 1.9  PDB: A:138-365 UniProt: 138-368 [INCOMPLETE]                                                                                                                                                                               Transcript 1 (1)
           Transcript 1 (2) ----------Exon 1.8  PDB: A:92-138 UniProt: 92-138        ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2jcj A  82 KLKLSDWFNPFKRPEVVTMTKWKAPVVWEGTYNRAVLDNYYAKQKITVGLTVFAVGRYIEHYLEEFLTSANKHFMVGHPVIFYIMVDDVSRMPLIELGPLRSFKVFKIKPEKRWQDISMMRMKTIGEHIVAHIQHEVDFLFCMDVDQVFQDKFGVETLGESVAQLQAWWYKADPNDFTYERRKESAAYIPFGEGDFYYHAAIFGGTPTQVLNITQECFKGILKDKKNDIEAQWHDESHLNKYFLLNKPTKILSPEYCWDYHIGLPADIKLVKMSWQTKEYNVVR 365
                                    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, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (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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	2jcj
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	GGTA1_BOVIN \| P14769
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	2.4.1.151
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Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

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