1ON8 - JenaLib

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Title :   CRYSTAL STRUCTURE OF MOUSE ALPHA-1,4-N-ACETYLHEXOSAMINYLTRANSFERASE (EXTL2) WITH UDP AND GLCUAB(1-3)GALB(1-O)-NAPHTHALENELMETHANOL AN ACCEPTOR SUBSTRATE ANALOG

Authors :   L. C. Pedersen, J. Dong, F. Taniguchi, H. Kitagawa, J. M. Krahn, L. G. Ped K. Sugahara, M. Negishi

Date :   27 Feb 03 (Deposition) - 22 Apr 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A,B  (4x)

Keywords :   Rossmann Fold, Dxd Motif, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. C. Pedersen, J. Dong, F. Taniguchi, H. Kitagawa, J. M. Krahn, L. G. Pedersen, K. Sugahara, M. Negishi
Crystal Structure Of An Alpha-1, 4-N-Acetylhexosaminyltransferase (Extl2), A Member Of The Exostosin Gene Family Involved In Heparan Sulfate Biosynthesis
J. Biol. Chem. V. 278 14420 2003
PubMed-ID: 12562774 | Reference-DOI: 10.1074/JBC.M210532200

Molecule 1 - ALPHA-1,4-N-ACETYLHEXOSAMINYLTRANSFERASE EXTL2
	Chains	:	A, B
	EC Number	:	2.4.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PMAL-2C
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	CATALYTIC DOMAIN
	Gene	:	EXTL2 OR EXTR2
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	ALPHA-GALNACT EXTL2, EXT-RELATED PROTEIN 2, EXOSTOSIN-LIKE 2

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (4x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 10)

No.	Name	Count	Type	Full Name
1	BDP	2	Ligand/Ion	BETA-D-GLUCOPYRANURONIC ACID
2	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
3	GAL	2	Ligand/Ion	BETA-D-GALACTOSE
4	MN	2	Ligand/Ion	MANGANESE (II) ION
5	UDP	2	Ligand/Ion	URIDINE-5'-DIPHOSPHATE

Biological Unit 1 (4, 8)

No.	Name	Count	Type	Full Name
1	BDP	2	Ligand/Ion	BETA-D-GLUCOPYRANURONIC ACID
2	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
3	GAL	2	Ligand/Ion	BETA-D-GALACTOSE
4	MN	-1	Ligand/Ion	MANGANESE (II) ION
5	UDP	2	Ligand/Ion	URIDINE-5'-DIPHOSPHATE

Biological Unit 2 (4, 32)

No.	Name	Count	Type	Full Name
1	BDP	8	Ligand/Ion	BETA-D-GLUCOPYRANURONIC ACID
2	EDO	8	Ligand/Ion	1,2-ETHANEDIOL
3	GAL	8	Ligand/Ion	BETA-D-GALACTOSE
4	MN	-1	Ligand/Ion	MANGANESE (II) ION
5	UDP	8	Ligand/Ion	URIDINE-5'-DIPHOSPHATE

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:181 , TYR A:193 , HIS A:289 , ARG A:293 , UDP A:351 , GAL A:510	BINDING SITE FOR RESIDUE BDP A 509
02	AC2	SOFTWARE	ARG A:82 , ARG A:181 , BDP A:509 , HOH A:626	BINDING SITE FOR RESIDUE GAL A 510
03	AC3	SOFTWARE	ARG B:181 , TYR B:193 , HIS B:289 , ARG B:293 , UDP B:352 , GAL B:520 , HOH B:615	BINDING SITE FOR RESIDUE BDP B 519
04	AC4	SOFTWARE	ARG B:82 , ARG B:181 , BDP B:519 , HOH B:642	BINDING SITE FOR RESIDUE GAL B 520
05	AC5	SOFTWARE	ASP A:153 , UDP A:351 , HOH A:604 , HOH A:605 , HOH A:606	BINDING SITE FOR RESIDUE MN A 600
06	AC6	SOFTWARE	ASP B:153 , UDP B:352 , HOH B:613 , HOH B:614 , HOH B:615	BINDING SITE FOR RESIDUE MN B 601
07	AC7	SOFTWARE	GLN A:72 , THR A:73 , TYR A:74 , ARG A:76 , ASN A:101 , ASN A:130 , MET A:132 , ASP A:151 , ASP A:152 , ASP A:153 , TYR A:280 , MET A:283 , TRP A:284 , BDP A:509 , MN A:600 , HOH A:604 , HOH A:605 , HOH A:606 , HOH A:639	BINDING SITE FOR RESIDUE UDP A 351
08	AC8	SOFTWARE	GLN B:72 , THR B:73 , TYR B:74 , ARG B:76 , ASN B:101 , ASN B:130 , MET B:132 , ASP B:151 , ASP B:152 , ASP B:153 , MET B:283 , TRP B:284 , HIS B:289 , BDP B:519 , MN B:601 , HOH B:613 , HOH B:615	BINDING SITE FOR RESIDUE UDP B 352
09	AC9	SOFTWARE	PHE A:171 , GLN A:174 , PRO A:260 , ILE A:314 , HOH A:622	BINDING SITE FOR RESIDUE EDO A 401
10	BC1	SOFTWARE	GLN A:170 , PHE B:171 , GLN B:174 , PRO B:260 , HOH B:604	BINDING SITE FOR RESIDUE EDO B 402

Asymmetric Unit

No.	Residues
1	A:244	-	A:296
2	B:244	-	B:296

Asymmetric Unit

No.	Residues
1	Gly A:116	-	Pro A:117
2	Phe A:321	-	Pro A:322
3	Gly B:116	-	Pro B:117
4	Phe B:321	-	Pro B:322

(no "SAP(SNP)/Variant" information available for 1ON8)

(no "PROSITE Motif" information available for 1ON8)

Asymmetric Unit (3, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENSMUST00000029575	1a	ENSMUSE00000501817	chr3:115710380-115710800	421	EXTL2_MOUSE	-	0	0	-	-
1.3	ENSMUST00000029575	3	ENSMUSE00000901963	chr3:115713540-115713614	75	EXTL2_MOUSE	1-3	3	0	-	-
1.6b	ENSMUST00000029575	6b	ENSMUSE00000587207	chr3:115726925-115727352	428	EXTL2_MOUSE	3-146	144	2	A:63-146 B:63-146	84 84
1.7	ENSMUST00000029575	7	ENSMUSE00000174716	chr3:115728243-115728313	71	EXTL2_MOUSE	146-169	24	2	A:146-169 B:146-169	24 24
1.8c	ENSMUST00000029575	8c	ENSMUSE00000325875	chr3:115729931-115731934	2004	EXTL2_MOUSE	170-330	161	2	A:170-327 B:170-327 (gaps)	158 158

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:265
 aligned with EXTL2_MOUSE | Q9ES89 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:265
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322     
          EXTL2_MOUSE    63 ALDSFTLIMQTYNRTDLLLRLLNHYQAVPSLHKVIVVWNNVGEKGPEELWNSLGPHPIPVIFKPQTANKMRNRLQVFPEVETNAVLMVDDDTLISAQDLVFAFSIWQQFPDQIIGFVPRKHVSTSSGIYSYGGFELQTPGPGNGDQYSMVLIGASFFNSKYLELFQKQPAAVHALIDETQNCDDIAMNFLVTRHTGKPSGIFVKPINMVNLEKETNGYSGMWHRAEHFLQRSYCINKLVNIYDGMPLKYSNIMISQFGFPYANHK 327
               SCOP domains d1on8a_ A: Alpha-1,4-N-acetylhexosaminyltransferase (Alpha-GalNAcT EXTL2)                                                                                                                                                                                                 SCOP domains
               CATH domains 1on8A00 A:63-327 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee..hhhhhhhhhhhhh....eeeeeeee.......hhhhhhhh......eeeee....hhhhhhh........eeeee...eeehhhhhhhhhhhhh.....eee..eeeeeeee..eeeee................ee...eeeeehhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhhhh...eeee....eee...............hhhhhhhhhhhhhhhhh.........eeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6b  PDB: A:63-146 UniProt: 3-146 [INCOMPLETE]                                -----------------------Exon 1.8c  PDB: A:170-327 UniProt: 170-330 [INCOMPLETE]                                                                                                        Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------Exon 1.7  PDB: A:146-169-------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1on8 A  63 ALDSFTLIMQTYNRTDLLLRLLNHYQAVPSLHKVIVVWNNVGEKGPEELWNSLGPHPIPVIFKPQTANKMRNRLQVFPEVETNAVLMVDDDTLISAQDLVFAFSIWQQFPDQIIGFVPRKHVSTSSGIYSYGGFELQTPGPGNGDQYSMVLIGASFFNSKYLELFQKQPAAVHALIDETQNCDDIAMNFLVTRHTGKPSGIFVKPINMVNLEKETNGYSGMWHRAEHFLQRSYCINKLVNIYDGMPLKYSNIMISQFGFPYANHK 327
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322

Chain B from PDB  Type:PROTEIN  Length:262
 aligned with EXTL2_MOUSE | Q9ES89 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:265
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322     
          EXTL2_MOUSE    63 ALDSFTLIMQTYNRTDLLLRLLNHYQAVPSLHKVIVVWNNVGEKGPEELWNSLGPHPIPVIFKPQTANKMRNRLQVFPEVETNAVLMVDDDTLISAQDLVFAFSIWQQFPDQIIGFVPRKHVSTSSGIYSYGGFELQTPGPGNGDQYSMVLIGASFFNSKYLELFQKQPAAVHALIDETQNCDDIAMNFLVTRHTGKPSGIFVKPINMVNLEKETNGYSGMWHRAEHFLQRSYCINKLVNIYDGMPLKYSNIMISQFGFPYANHK 327
               SCOP domains d1on8b_ B: Alpha-1,4-N-acetylhexosaminyltransferase (Alpha-GalNAcT EXTL2)                                                                                                                                                                                                 SCOP domains
               CATH domains 1on8B00 B:63-327 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                                             CATH domains
           Pfam domains (1) ----Glyco_transf_64-1on8B01 B:67-321                                                                                                                                                                                                                               ------ Pfam domains (1)
           Pfam domains (2) ----Glyco_transf_64-1on8B02 B:67-321                                                                                                                                                                                                                               ------ Pfam domains (2)
         Sec.struct. author ....eeeeeee..hhhhhhhhhhhhh....eeeeeeee.......hhhhhhhh......eeeee....hhhhhhh........eeeee...eeehhhhhhhhhhhhh.....eee..eeeeee.....eeee................ee...eeeeehhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhhhh...eeee....eee.....---.......hhhhhhhhhhhhhhhhh.........eeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6b  PDB: B:63-146 UniProt: 3-146 [INCOMPLETE]                                -----------------------Exon 1.8c  PDB: B:170-327 (gaps) UniProt: 170-330 [INCOMPLETE]                                                                                                 Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------Exon 1.7  PDB: B:146-169-------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1on8 B  63 ALDSFTLIMQTYNRTDLLLRLLNHYQAVPSLHKVIVVWNNVGEKGPEELWNSLGPHPIPVIFKPQTANKMRNRLQVFPEVETNAVLMVDDDTLISAQDLVFAFSIWQQFPDQIIGFVPRKHVSTSSGIYSYGGFELQTPGPGNGDQYSMVLIGASFFNSKYLELFQKQPAAVHALIDETQNCDDIAMNFLVTRHTGKPSGIFVKPINMVNLEKET---SGMWHRAEHFLQRSYCINKLVNIYDGMPLKYSNIMISQFGFPYANHK 327
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272    |  282       292       302       312       322     
                                                                                                                                                                                                                                                277 281

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(

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Folds(

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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: Exostosin (4)

Protein domain: Alpha-1,4-N-acetylhexosaminyltransferase (Alpha-GalNAcT EXTL2) (4)

Mouse (Mus musculus) [TaxId: 10090] (4)

1a	d1on8a_	A:
1b	d1on8b_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

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Topologies( (-)

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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)

House mouse (Mus musculus) (18)

1a	1on8A00	A:63-327
1b	1on8B00	B:63-327

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GT-A (172)

Family: Glyco_transf_64 (4)

Mus musculus (Mouse) (4)

1a	Glyco_transf_64-1on8B01	B:67-321
1b	Glyco_transf_64-1on8B02	B:67-321

Asymmetric Unit(hide GO term definitions)

Chain A,B (EXTL2_MOUSE | Q9ES89)

molecular function
	GO:0035248	alpha-1,4-N-acetylgalactosaminyltransferase activity	Catalysis of the transfer of an N-acetylgalactosaminyl residue from UDP-N-acetyl-galactosamine to an acceptor molecule, forming an alpha-1,4 linkage.
	GO:0001888	glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity	Catalysis of the reaction: UDP-N-acetyl-D-glucosamine + beta-D-glucuronosyl-(1->3)-beta-D-galactosyl-(1->3)-beta-D-galactosyl-(1->4)-beta-D-xylosyl-proteoglycan = UDP + alpha-N-acetyl-D-glucosaminyl-(1->4)-beta-D-glucuronosyl-(1->3)-beta-D-galactosyl-(1->3)-beta-D-galactosyl-(1->4)-beta-D-xylosyl-proteoglycan.
	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).
biological process
	GO:0006044	N-acetylglucosamine metabolic process	The chemical reactions and pathways involving N-acetylglucosamine. The D isomer is a common structural unit of glycoproteins in plants, bacteria and animals; it is often the terminal sugar of an oligosaccharide group of a glycoprotein.
	GO:0019276	UDP-N-acetylgalactosamine metabolic process	The chemical reactions and pathways involving UDP-N-acetylgalactosamine, a substance composed of N-acetylgalactosamine, a common structural unit of oligosaccharides, in glycosidic linkage with uridine diphosphate.
	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: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.
cellular component
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding 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.

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	Cis Peptide Bonds
		Gly A:116 - Pro A:117	[ RasMol ]
		Gly B:116 - Pro B:117	[ RasMol ]
		Phe A:321 - Pro A:322	[ RasMol ]
		Phe B:321 - Pro B:322	[ RasMol ]

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Access by PDB/NDB ID
	1on8
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	EXTL2_MOUSE \| Q9ES89
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	2.4.1.-
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UniProtKB/Swiss-Prot
	EXTL2_MOUSE \| Q9ES89	:	1omx 1omz 1on6

1omx	APO ENZYME
1omz	WITH DONOR SUBSTRATE UDPGALNAC
1on6	WITH DONOR SUBSTRATE UDPGLCNAC

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 10)

Sites (10, 10)

SS Bonds (2, 2)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (3, 6)

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