3V0M - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF THE FUCOSYLGALACTOSIDE ALPHA N-ACETYLGALACTOSAMINYLTRANSFERASE (GTA, CISAB MUTANT L266G, G268A) IN COMPLEX WITH A NOVEL UDP-GAL DERIVED INHIBITOR (5GW) AND H-ANTIGEN ACCEPTOR

Authors :   M. M. Palcic, R. Jorgensen

Date :   08 Dec 11 (Deposition) - 23 Jan 13 (Release) - 12 Nov 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.68

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

Keywords :   Gta, Abo, Cisab Mutant, Aa(Gly)B, Rossmann Fold, "Closed" Conformation, Glycosyltransferase, Glycoprotein, Blood Group Antigen, Udp-Galnac, Metal-Binding, Manganese, Glycosylation, Transmembrane, Golgi Apparatus, Secreted, Signal-Anchor, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Jrgensen, T. Pesnot, H. J. Lee, M. M. Palcic, G. K. Wagner
Base-Modified Donor Analogues Reveal Novel Dynamic Features Of A Glycosyltransferase.
J. Biol. Chem. V. 288 26201 2013
PubMed-ID: 23836908 | Reference-DOI: 10.1074/JBC.M113.465963

Molecule 1 - HISTO-BLOOD GROUP ABO SYSTEM TRANSFERASE
	Chains	:	A, B
	EC Number	:	2.4.1.40, 2.4.1.37
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PCW DELTA 1AC
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	EXTRACELLULAR CATALYTIC DOMAIN
	Gene	:	AB0, ABO
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	FUCOSYLGLYCOPROTEIN 3-ALPHA-GALACTOSYLTRANSFERASE, FUCOSYLGLYCOPROTEIN ALPHA-N-ACETYLGALACTOSAMINYLTRANSFERASE, GLYCOPROTEIN-FUCOSYLGALACTOSIDE ALPHA-N- ACETYLGALACTOSAMINYLTRANSFERASE, GLYCOPROTEIN-FUCOSYLGALACTOSIDE ALPHA-GALACTOSYLTRANSFERASE, HISTO-BLOOD GROUP A TRANSFERASE, A TRANSFERASE, HISTO-BLOOD GROUP B TRANSFERASE, B TRANSFERASE, NAGAT, FUCOSYLGLYCOPROTEIN ALPHA-N-ACETYLGALACTOSAMINYLTRANSFERASE SOLUBLE FORM

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 7)

No.	Name	Count	Type	Full Name
1	5GW	2	Ligand/Ion	5-PHENYLURIDINE 5'-(TRIHYDROGEN DIPHOSPHATE)
2	BHE	2	Ligand/Ion	OCTYL 2-O-(6-DEOXY-ALPHA-L-GALACTOPYRANOSYL)-BETA-D-GALACTOPYRANOSIDE
3	MN	2	Ligand/Ion	MANGANESE (II) ION
4	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:211 , ASP A:213 , HOH A:379 , 5GW A:450	BINDING SITE FOR RESIDUE MN A 1
2	AC2	SOFTWARE	MN A:1 , HOH A:42 , PHE A:121 , ILE A:123 , TYR A:126 , TRP A:181 , VAL A:184 , ASP A:211 , VAL A:212 , ASP A:213 , LYS A:346 , HOH A:379 , HOH A:408 , HOH A:457 , BHE A:475 , HOH A:481 , HOH A:489	BINDING SITE FOR RESIDUE 5GW A 450
3	AC3	SOFTWARE	HIS A:233 , GLY A:235 , PHE A:236 , THR A:245 , TRP A:300 , GLU A:303 , ASP A:326 , HOH A:419 , 5GW A:450 , HOH A:462 , HOH A:480 , HOH A:506 , HOH A:571 , HOH A:592 , ASN B:113	BINDING SITE FOR RESIDUE BHE A 475
4	AC4	SOFTWARE	ASP B:211 , ASP B:213 , 5GW B:450 , HOH B:462	BINDING SITE FOR RESIDUE MN B 1
5	AC5	SOFTWARE	MN B:1 , PHE B:121 , ILE B:123 , TYR B:126 , TRP B:181 , VAL B:184 , ARG B:188 , ASP B:211 , VAL B:212 , ASP B:213 , LYS B:346 , HOH B:367 , HOH B:409 , HOH B:462 , BHE B:475 , HOH B:490 , HOH B:540 , HOH B:585	BINDING SITE FOR RESIDUE 5GW B 450
6	AC6	SOFTWARE	HIS B:233 , GLY B:235 , PHE B:236 , THR B:245 , TRP B:300 , GLU B:303 , ASP B:326 , HOH B:386 , HOH B:437 , HOH B:438 , 5GW B:450 , HOH B:461 , HOH B:477 , HOH B:486 , HOH B:507 , HOH B:585	BINDING SITE FOR RESIDUE BHE B 475
7	AC7	SOFTWARE	SER B:171 , ARG B:199 , HOH B:470	BINDING SITE FOR RESIDUE SO4 B 355

(no "SS Bond" information available for 3V0M)

(no "Cis Peptide Bond" information available for 3V0M)

Asymmetric/Biological Unit (22, 43)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_019149	R	63	H	BGAT_HUMAN	Polymorphism	549446	A/B	M	63	H
02	UniProt	VAR_019150	P	74	S	BGAT_HUMAN	Polymorphism	512770	A/B	P	74	S
03	UniProt	VAR_003409	P	156	L	BGAT_HUMAN	Polymorphism	1053878	A/B	P	156	L
04	UniProt	VAR_019151	R	161	H	BGAT_HUMAN	Polymorphism	8176738	A/B	R	161	H
05	UniProt	VAR_036738	T	163	M	BGAT_HUMAN	Polymorphism	55756402	A/B	T	163	M
06	UniProt	VAR_003410	R	176	G	BGAT_HUMAN	Polymorphism	7853989	A/B	R	176	G
07	UniProt	VAR_036739	R	198	W	BGAT_HUMAN	Polymorphism	56223957	A	R	198	W
08	UniProt	VAR_019152	R	199	C	BGAT_HUMAN	Polymorphism	8176739	A/B	R	199	C
09	UniProt	VAR_036740	M	214	R	BGAT_HUMAN	Polymorphism	55827808	A/B	M	214	R
10	UniProt	VAR_019153	F	216	I	BGAT_HUMAN	Polymorphism	8176740	A/B	F	216	I
11	UniProt	VAR_036741	E	223	D	BGAT_HUMAN	Polymorphism	---	A/B	E	223	D
12	UniProt	VAR_055227	G	230	R	BGAT_HUMAN	Unclassified	---	A/B	G	230	R
13	UniProt	VAR_072628	P	234	A	BGAT_HUMAN	Polymorphism	---	A/B	P	234	A
14	UniProt	VAR_003411	G	235	S	BGAT_HUMAN	Polymorphism	8176743	A/B	G	235	S
15	UniProt	VAR_033540	P	257	L	BGAT_HUMAN	Polymorphism	8176745	A/B	P	257	L
16	UniProt	VAR_003412	L	266	M	BGAT_HUMAN	Polymorphism	8176746	A/B	G	266	M
17	UniProt	VAR_003413	G	268	A	BGAT_HUMAN	Polymorphism	8176747	A/B	A	268	A
18	UniProt	VAR_033541	G	268	R	BGAT_HUMAN	Polymorphism	8176747	A/B	A	268	R
19	UniProt	VAR_019154	V	277	M	BGAT_HUMAN	Polymorphism	8176748	A/B	V	277	M
20	UniProt	VAR_036742	M	288	R	BGAT_HUMAN	Polymorphism	---	A/B	M	288	R
21	UniProt	VAR_036743	D	291	N	BGAT_HUMAN	Polymorphism	---	A/B	D	291	N
22	UniProt	VAR_036744	K	346	M	BGAT_HUMAN	Polymorphism	---	A/B	K	346	M

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 3V0M)

(no "Exon" information available for 3V0M)

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:289
 aligned with BGAT_HUMAN | P16442 from UniProtKB/Swiss-Prot  Length:354

    Alignment length:293
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343   
           BGAT_HUMAN    54 AVREPDHLQRVSLPRMVYPQPKVLTPCRKDVLVVTPWLAPIVWEGTFNIDILNEQFRLQNTTIGLTVFAIKKYVAFLKLFLETAEKHFMVGHRVHYYVFTDQPAAVPRVTLGTGRQLSVLEVRAYKRWQDVSMRRMEMISDFCERRFLSEVDYLVCVDVDMEFRDHVGVEILTPLFGTLHPGFYGSSREAFTYERRPQSQAYIPKDEGDFYYLGGFFGGSVQEVQRLTRACHQAMMVDQANGIEAVWHDESHLNKYLLRHKPTKVLSPEYLWDQQLLGWPAVLRKLRFTAVPK 346
               SCOP domains d3v0    ma_ A: automated matches                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....----................................ee.....hhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhhhhhhh....eeeeeeee.hhhhh........eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhh.eeeee...eee....hhhhh..eeee.....................................eeeeehhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh...eee.hhhh.hhhhhh.........eee... Sec.struct. author
             SAPs(SNPs) (1) ---------H----------S---------------------------------------------------------------------------------L----H-M------------G---------------------WC--------------R-I------D------R---AS---------------------L--------M-A--------M----------R--N------------------------------------------------------M SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------R------------------------------------------------------------------------------ SAPs(SNPs) (2)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v0m A  58 AIGE----FMVSLPRMVYPQPKVLTPCRKDVLVVTPWLAPIVWEGTFNIDILNEQFRLQNTTIGLTVFAIKKYVAFLKLFLETAEKHFMVGHRVHYYVFTDQPAAVPRVTLGTGRQLSVLEVRAYKRWQDVSMRRMEMISDFCERRFLSEVDYLVCVDVDMEFRDHVGVEILTPLFGTLHPGFYGSSREAFTYERRPQSQAYIPKDEGDFYYGGAFFGGSVQEVQRLTRACHQAMMVDQANGIEAVWHDESHLNKYLLRHKPTKVLSPEYLWDQQLLGWPAVLRKLRFTAVPK 346
                               |    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343   
                              61   62

Chain B from PDB  Type:PROTEIN  Length:286
 aligned with BGAT_HUMAN | P16442 from UniProtKB/Swiss-Prot  Length:354

    Alignment length:293
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343   
           BGAT_HUMAN    54 AVREPDHLQRVSLPRMVYPQPKVLTPCRKDVLVVTPWLAPIVWEGTFNIDILNEQFRLQNTTIGLTVFAIKKYVAFLKLFLETAEKHFMVGHRVHYYVFTDQPAAVPRVTLGTGRQLSVLEVRAYKRWQDVSMRRMEMISDFCERRFLSEVDYLVCVDVDMEFRDHVGVEILTPLFGTLHPGFYGSSREAFTYERRPQSQAYIPKDEGDFYYLGGFFGGSVQEVQRLTRACHQAMMVDQANGIEAVWHDESHLNKYLLRHKPTKVLSPEYLWDQQLLGWPAVLRKLRFTAVPK 346
               SCOP domains d3v0    mb_ B: automated matches                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....----................................ee.....hhhhhhhhhhh...eeeeeeeehhhhhhhhhhhhhhhhhhh....eeeeeeee.hhhhh........eeeeeee.....hhhhhhhhhhhhhhhh---hhhhh..eeeee...eee....hhhhh..eeee........hhhhh........................eeeeehhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh...eee.hhhh.hhhhhh.........eee... Sec.struct. author
             SAPs(SNPs) (1) ---------H----------S---------------------------------------------------------------------------------L----H-M------------G----------------------C--------------R-I------D------R---AS---------------------L--------M-A--------M----------R--N------------------------------------------------------M SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------R------------------------------------------------------------------------------ SAPs(SNPs) (2)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v0m B  58 AIGE----FMVSLPRMVYPQPKVLTPCRKDVLVVTPWLAPIVWEGTFNIDILNEQFRLQNTTIGLTVFAIKKYVAFLKLFLETAEKHFMVGHRVHYYVFTDQPAAVPRVTLGTGRQLSVLEVRAYKRWQDVSMRRMEMISDF---RFLSEVDYLVCVDVDMEFRDHVGVEILTPLFGTLHPGFYGSSREAFTYERRPQSQAYIPKDEGDFYYGGAFFGGSVQEVQRLTRACHQAMMVDQANGIEAVWHDESHLNKYLLRHKPTKVLSPEYLWDQQLLGWPAVLRKLRFTAVPK 346
                               |    63        73        83        93       103       113       123       133       143       153       163       173       183       193 |   | 203       213       223       233       243       253       263       273       283       293       303       313       323       333       343   
                              61   62                                                                                                                                  195 199

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(

)

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: automated matches (38)

Human (Homo sapiens) [TaxId: 9606] (36)

1a	d3v0ma_	A:
1b	d3v0mb_	B:

(no "CATH Domain" information available for 3V0M)

(no "Pfam Domain" information available for 3V0M)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (BGAT_HUMAN | P16442)

molecular function
	GO:0004381	fucosylgalactoside 3-alpha-galactosyltransferase activity	Catalysis of the reaction: UDP-galactose + glycoprotein-alpha-L-fucosyl-(1,2)-D-galactose = UDP + glycoprotein-alpha-D-galactosyl-(1,3)-(alpha-L-fucosyl-(1,2))-D-galactose.
	GO:0004380	glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase activity	Catalysis of the reaction: UDP-N-acetyl-D-galactosamine + glycoprotein-alpha-L-fucosyl-(1,2)-D-galactose = UDP + glycoprotein-N-acetyl-alpha-D-galactosaminyl-(1,3)-(alpha-L-fucosyl-(1,2))-D-galactose.
	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: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:0032580	Golgi cisterna membrane	The lipid bilayer surrounding any of the thin, flattened compartments that form the central portion of the Golgi complex.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	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 3v0m)

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	3v0m
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3ioh	CRYSTAL STRUCTURE OF THE FUCOSYLGALACTOSIDE ALPHA N- ACETYLGALACTOSAMINYLTRANSFERASE (GTA, CISAB MUTANT L266G, G268A)
3ioi	CRYSTAL STRUCTURE OF THE FUCOSYLGALACTOSIDE ALPHA N- ACETYLGALACTOSAMINYLTRANSFERASE (GTA, CISAB MUTANT L266G, G268A) IN COMPLEX WITH A NOVEL UDP-GAL DERIVED INHIBITOR (1GW)
3ioj	CRYSTAL STRUCTURE OF THE FUCOSYLGALACTOSIDE ALPHA N- ACETYLGALACTOSAMINYLTRANSFERASE (GTA, CISAB MUTANT L266G, G268A) IN COMPLEX WITH UDP
3v0l
3v0n
3v0o
3v0p
3v0q

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (22, 43)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (13, 13)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File