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Asym./Biol. Unit (Jmol Viewer)

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Title :   HUMAN BETA 1,3-GLUCURONYLTRANSFERASE I (GLCAT-I) IN COMPLEX WITH UDP AND GAL-GAL(6-SO4)-XYL(2-PO4)-O-SER

Authors :   Y. Tone, L. C. Pedersen, T. Yamamoto, H. Kitagawa, J. Nishihara- Shimizu, J. Tamura, M. Negishi, K. Sugahara

Date :   15 Apr 08 (Deposition) - 06 May 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Glcat-I, Glycosyltransferase, Heparan Sulfate Biosynthesis, Glycoprotein, Golgi Apparatus, Manganese, Membrane, Metal- Binding, Signal-Anchor, Transmembrane (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Tone, L. C. Pedersen, T. Yamamoto, T. Izumikawa, H. Kitagawa, J. Nishihara, J. Tamura, M. Negishi, K. Sugahara
2-O-Phosphorylation Of Xylose And 6-O-Sulfation Of Galactose In The Protein Linkage Region Of Glycosaminoglycans Influence The Glucuronyltransferase-I Activity Involved In The Linkage Region Synthesis.
J. Biol. Chem. V. 283 16801 2008
PubMed-ID: 18400750 | Reference-DOI: 10.1074/JBC.M709556200
(for further references see the PDB file header)

Molecule 1 - GALACTOSYLGALACTOSYLXYLOSYLPROTEIN 3-BETA- GLUCURONOSYLTRANSFERASE 3
	Chains	:	A, B
	EC Number	:	2.4.1.135
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET28A
	Expression System Vector Type	:	PLASMID
	Fragment	:	CATALYTIC DOMAIN, UNP RESIDUES 76-335
	Gene	:	B3GAT3
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 10)

No.	Name	Count	Type	Full Name
1	GAL	4	Ligand/Ion	BETA-D-GALACTOSE
2	MN	2	Ligand/Ion	MANGANESE (II) ION
3	SO4	2	Ligand/Ion	SULFATE ION
4	UDP	2	Ligand/Ion	URIDINE-5'-DIPHOSPHATE

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY B:222 , GLU B:227 , TRP B:243 , ARG B:247 , ASP B:252 , GLU B:281 , HOH B:552 , HOH B:586	BINDING SITE FOR RESIDUE GAL B 1
02	AC2	SOFTWARE	TRP B:243 , ARG B:277 , HOH B:507 , HOH B:586	BINDING SITE FOR RESIDUE GAL B 2
03	AC3	SOFTWARE	GLU A:227 , ARG A:247 , ASP A:252 , GLU A:281 , HOH A:508 , HOH A:532 , HOH A:558 , HOH A:569 , HOH A:581	BINDING SITE FOR RESIDUE GAL A 1
04	AC4	SOFTWARE	GLY A:222 , TRP A:243 , ARG A:277 , HOH A:532 , HOH A:569	BINDING SITE FOR RESIDUE GAL A 2
05	AC5	SOFTWARE	LYS A:317 , GLN A:318 , GLY B:223 , TRP B:243	BINDING SITE FOR RESIDUE SO4 B 3
06	AC6	SOFTWARE	GLY A:223 , TRP A:243 , LYS B:317 , GLN B:318	BINDING SITE FOR RESIDUE SO4 A 3
07	AC7	SOFTWARE	ASP A:196 , HOH A:504 , HOH A:505	BINDING SITE FOR RESIDUE MN A 502
08	AC8	SOFTWARE	ASP B:196 , HOH B:505 , HOH B:506	BINDING SITE FOR RESIDUE MN B 504
09	AC9	SOFTWARE	PRO A:82 , THR A:83 , TYR A:84 , ARG A:86 , ASP A:113 , ARG A:156 , GLY A:157 , ASP A:194 , ASP A:195 , ASP A:196 , HIS A:308 , ARG A:310 , HOH A:505 , HOH A:508 , HOH A:540 , HOH A:547 , HOH A:588 , HOH A:600 , HOH A:615 , HOH A:631	BINDING SITE FOR RESIDUE UDP A 501
10	BC1	SOFTWARE	HOH A:514 , HOH A:571 , HOH A:597 , HOH A:623 , PRO B:82 , THR B:83 , TYR B:84 , ASP B:113 , PRO B:155 , ARG B:156 , GLY B:157 , ASP B:194 , ASP B:195 , ASP B:196 , HIS B:308 , ARG B:310 , HOH B:529	BINDING SITE FOR RESIDUE UDP A 503

(no "SS Bond" information available for 3CU0)

(no "Cis Peptide Bond" information available for 3CU0)

Asymmetric/Biological Unit (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_075370	P	140	L	B3GA3_HUMAN	Disease (JDSCD)	879255269	A/B	P	140	L
2	UniProt	VAR_075371	G	223	S	B3GA3_HUMAN	Unclassified (JDSCD)	372487178	A/B	G	223	S
3	UniProt	VAR_066624	R	277	Q	B3GA3_HUMAN	Disease (JDSCD)	387906937	A/B	R	277	Q

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

(no "PROSITE Motif" information available for 3CU0)

Asymmetric/Biological Unit (4, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000265471	1a	ENSE00002142592	chr11:62389647-62389338	310	B3GA3_HUMAN	1-28	28	0	-	-
1.3	ENST00000265471	3	ENSE00001118980	chr11:62388143-62387969	175	B3GA3_HUMAN	28-86	59	2	A:75-86 B:75-86	12 12
1.4c	ENST00000265471	4c	ENSE00000991160	chr11:62384819-62384459	361	B3GA3_HUMAN	86-206	121	2	A:86-206 (gaps) B:86-206 (gaps)	121 121
1.5b	ENST00000265471	5b	ENSE00000991161	chr11:62384268-62383978	291	B3GA3_HUMAN	207-303	97	2	A:207-303 B:207-303	97 97
1.6d	ENST00000265471	6d	ENSE00001293049	chr11:62383271-62382768	504	B3GA3_HUMAN	304-335	32	2	A:304-335 B:304-335	32 32

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:250
 aligned with B3GA3_HUMAN | O94766 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:261
                                    84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334 
          B3GA3_HUMAN    75 PTIYVVTPTYARLVQKAELVRLSQTLSLVPRLHWLLVEDAEGPTPLVSGLLAASGLLFTHLVVLTPKAQRLREGEPGWVHPRGVEQRNKALDWLRGRGGAVGGEKDPPPPGTQGVVYFADDDNTYSRELFEEMRWTRGVSVWPVGLVGGLRFEGPQVQDGRVVGFHTAWEPSRPFPVDMAGFAVALPLLLDKPNAQFDSTAPRGHLESSLLSHLVDPKDLEPRAANCTRVLVWHTRTEKPKMKQEEQLQRQGRGSDPAIEV 335
               SCOP domains d3cu0a_ A: 1,3-Glucuronyltransferase I (glcAT-I)                                                                                                                                                                                                                      SCOP domains
               CATH domains 3cu0A00 A:75-335 Spore Coat Polysaccharide Biosynthesis Protein Sp           sA; Chain A                                                                                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....hhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhhhh.eeeeee....-----------.....hhhhhhhhhhhhh....eeee..........eeeee.....eehhhhhhhhh....eee..eeee..eeeeeeeee..eeeeee...........hhh.eeeehhhhhhh............hhhhhhhh...hhhhheehhhhhh...ee........hhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------L----------------------------------------------------------------------------------S-----------------------------------------------------Q---------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3    ------------------------------------------------------------------------------------------------------------------------Exon 1.5b  PDB: A:207-303 UniProt: 207-303                                                       Exon 1.6d  PDB: A:304-335        Transcript 1 (1)
           Transcript 1 (2) -----------Exon 1.4c  PDB: A:86-206 (gaps) UniProt: 86-206                                                                          --------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3cu0 A  75 MTIYVVTPTYARLVQKAELVRLSQTLSLVPRLHWLLVEDAEGPTPLVSGLLAASGLLFTHLVVLTP-----------WVHPRGVEQRNKALDWLRGRGGAVGGEKDPPPPGTQGVVYFADDDNTYSRELFEEMRWTRGVSVWPVGLVGGLRFEGPQVQDGRVVGFHTAWEPSRPFPVDMAGFAVALPLLLDKPNAQFDSTAPRGHLESSLLSHLVDPKDLEPRAANCTRVLVWHTRTEKPKMKQEEQLQRQGRGSDPAIEV 335
                                    84        94       104       114       124       134     |   -       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334 
                                                                                           140         152

Chain B from PDB  Type:PROTEIN  Length:247
 aligned with B3GA3_HUMAN | O94766 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:261
                                    84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334 
          B3GA3_HUMAN    75 PTIYVVTPTYARLVQKAELVRLSQTLSLVPRLHWLLVEDAEGPTPLVSGLLAASGLLFTHLVVLTPKAQRLREGEPGWVHPRGVEQRNKALDWLRGRGGAVGGEKDPPPPGTQGVVYFADDDNTYSRELFEEMRWTRGVSVWPVGLVGGLRFEGPQVQDGRVVGFHTAWEPSRPFPVDMAGFAVALPLLLDKPNAQFDSTAPRGHLESSLLSHLVDPKDLEPRAANCTRVLVWHTRTEKPKMKQEEQLQRQGRGSDPAIEV 335
               SCOP domains d3cu0b_ B: 1,3-Glucuronyltransferase I (glcAT-I)                                                                                                                                                                                                                      SCOP domains
               CATH domains 3cu0B00 B:75-335 Spore Coat Polysaccharide Biosynthesis Protein Sp              sA; Chain A                                                                                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....hhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhhhh.eeeeee....--------------..hhhhhhhhhhhhh......ee...........eeee.....eehhhhhhhhh....eee..eeee..eeeeeeeee..eeeeee...........hhh.eeeehhhhhhh............hhhhhhhhhhhhhhhheehhhhhh...ee........hhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------L----------------------------------------------------------------------------------S-----------------------------------------------------Q---------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3    ------------------------------------------------------------------------------------------------------------------------Exon 1.5b  PDB: B:207-303 UniProt: 207-303                                                       Exon 1.6d  PDB: B:304-335        Transcript 1 (1)
           Transcript 1 (2) -----------Exon 1.4c  PDB: B:86-206 (gaps) UniProt: 86-206                                                                          --------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3cu0 B  75 MTIYVVTPTYARLVQKAELVRLSQTLSLVPRLHWLLVEDAEGPTPLVSGLLAASGLLFTHLVVLTP--------------PRGVEQRNKALDWLRGRGGAVGGEKDPPPPGTQGVVYFADDDNTYSRELFEEMRWTRGVSVWPVGLVGGLRFEGPQVQDGRVVGFHTAWEPSRPFPVDMAGFAVALPLLLDKPNAQFDSTAPRGHLESSLLSHLVDPKDLEPRAANCTRVLVWHTRTEKPKMKQEEQLQRQGRGSDPAIEV 335
                                    84        94       104       114       124       134     |   -         -|      164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334 
                                                                                           140            155

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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( (-)

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Families(

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Protein Domains( (-)

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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: 1,3-glucuronyltransferase (7)

Protein domain: 1,3-Glucuronyltransferase I (glcAT-I) (3)

Human (Homo sapiens) [TaxId: 9606] (3)

1a	d3cu0a_	A:
1b	d3cu0b_	B:

Asymmetric/Biological Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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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)

Human (Homo sapiens) (73)

1a	3cu0A00	A:75-335
1b	3cu0B00	B:75-335

(no "Pfam Domain" information available for 3CU0)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (B3GA3_HUMAN | O94766)

molecular function
	GO:0015018	galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity	Catalysis of the reaction: UDP-glucuronate + 3-beta-D-galactosyl-4-beta-D-galactosyl-O-beta-D-xylosylprotein = UDP + 3-beta-D-glucuronosyl-3-beta-D-galactosyl-4-beta-D-galactosyl-O-beta-D-xylosylprotein.
	GO:0015020	glucuronosyltransferase activity	Catalysis of the reaction: UDP-glucuronate + acceptor = UDP + acceptor beta-D-glucuronoside.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0072542	protein phosphatase activator activity	Increases the activity of a protein phosphatase, an enzyme which catalyzes of the removal of a phosphate group from a protein substrate molecule.
	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.
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:0030204	chondroitin sulfate metabolic process	The chemical reactions and pathways involving chondroitin sulfate, any member of a group of 10-60 kDa glycosaminoglycans, widely distributed in cartilage and other mammalian connective tissues, the repeat units of which consist of beta-(1,4)-linked D-glucuronyl beta-(1,3)-N-acetyl-D-galactosamine sulfate. They usually occur linked to a protein to form proteoglycans. Two subgroups exist, one in which the sulfate is on the 4-position (chondroitin sulfate A) and the second in which it is in the 6-position (chondroitin sulfate C). They often are polydisperse and often differ in the degree of sulfation from tissue to tissue. The chains of repeating disaccharide are covalently linked to the side chains of serine residues in the polypeptide backbone of a protein by a glycosidic attachment through the trisaccharide unit galactosyl-galactosyl-xylosyl. Chondroitin sulfate B is more usually known as dermatan sulfate.
	GO:0050650	chondroitin sulfate proteoglycan biosynthetic process	The chemical reactions and pathways resulting in the formation of chondroitin sulfate proteoglycan, any glycoprotein whose glycosaminoglycan units are chondroitin sulfate. Chondroitin sulfates are a group of 10-60 kDa glycosaminoglycans, widely distributed in cartilage and other mammalian connective tissues; the repeat units consist of beta-(1,4)-linked D-glucuronyl beta-(1,3)-N-acetyl-D-galactosamine sulfate.
	GO:0050651	dermatan sulfate proteoglycan biosynthetic process	The chemical reactions and pathways resulting in the formation of dermatan sulfate proteoglycan, any glycoprotein whose glycosaminoglycan units are dermatan sulfate (chondroitin sulfate B). Dermatan sulfate is a glycosaminoglycan with repeats consisting of beta-(1,4)-linked L-iduronyl-beta-(1,3)-N-acetyl-D-galactosamine 4-sulfate units.
	GO:0006024	glycosaminoglycan biosynthetic process	The chemical reactions and pathways resulting in the formation of glycosaminoglycans, any of a group of polysaccharides that contain amino sugars.
	GO:0030203	glycosaminoglycan metabolic process	The chemical reactions and pathways involving glycosaminoglycans, any one of a group of polysaccharides that contain amino sugars. Formerly known as mucopolysaccharides, they include hyaluronic acid and chondroitin, which provide lubrication in joints and form part of the matrix of cartilage. The three-dimensional structure of these molecules enables them to trap water, which forms a gel and gives glycosaminoglycans their elastic properties.
	GO:0015012	heparan sulfate proteoglycan biosynthetic process	The chemical reactions and pathways resulting in the formation of the heparan sulfate proteoglycan, a glycosaminoglycan with repeat unit consisting of alternating alpha-(1->4)-linked hexuronic acid and glucosamine residues; the former are a mixture of sulfated and nonsulfated D-glucuronic acid and L-iduronic acid; the L-iduronic acid is either sulfated or acetylated on its amino group as well as being sulfated on one of its hydroxyl groups; heparan sulfate chains are covalently linked to peptidyl-serine by a glycosidic attachment through the trisaccharide galactosyl-galactosyl-xylosyl to serine residues.
	GO:0043085	positive regulation of catalytic activity	Any process that activates or increases the activity of an enzyme.
	GO:0090316	positive regulation of intracellular protein transport	Any process that activates or increases the frequency, rate or extent of the directed movement of proteins within cells.
	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:0000139	Golgi membrane	The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
	GO:0005801	cis-Golgi network	The network of interconnected tubular and cisternal structures located at the convex side of the Golgi apparatus, which abuts the endoplasmic reticulum.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	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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	3cu0
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	B3GA3_HUMAN \| O94766	:	1fgg 1kws

Description

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Ligands, Modified Residues, Ions (4, 10)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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