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Title :   CRYSTAL STRUCTURE OF MOUSE ALPHA-1,4-N-ACETYLHEXOSAMINOTRANSFERASE (EXTL2) IN COMPLEX WITH UDPGLCNAC

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

Date :   27 Feb 03 (Deposition) - 22 Apr 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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
(for further references see the PDB file header)

Compounds

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

Structural Features

Chains, Units

		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)

Ligands, Modified Residues, Ions (3, 6)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	MN	2	Ligand/Ion	MANGANESE (II) ION
3	UD1	2	Ligand/Ion	URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	MN	-1	Ligand/Ion	MANGANESE (II) ION
3	UD1	2	Ligand/Ion	URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE

Biological Unit 2 (2, 16)

No.	Name	Count	Type	Full Name
1	EDO	8	Ligand/Ion	1,2-ETHANEDIOL
2	MN	-1	Ligand/Ion	MANGANESE (II) ION
3	UD1	8	Ligand/Ion	URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE

Sites (6, 6)

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:153 , UD1 A:401 , HOH A:656 , HOH A:690 , HOH A:691	BINDING SITE FOR RESIDUE MN A 600
2	AC2	SOFTWARE	ASP B:153 , UD1 B:400 , HOH B:654 , HOH B:683 , HOH B:684	BINDING SITE FOR RESIDUE MN B 601
3	AC3	SOFTWARE	GLN B:72 , THR B:73 , TYR B:74 , ARG B:76 , ASN B:101 , ASN B:130 , MET B:132 , ARG B:135 , ASP B:151 , ASP B:152 , ASP B:153 , LEU B:213 , ASN B:243 , ASP B:245 , ASP B:246 , HIS B:289 , ARG B:293 , MN B:601 , HOH B:602 , HOH B:642 , HOH B:654 , HOH B:673	BINDING SITE FOR RESIDUE UD1 B 400
4	AC4	SOFTWARE	GLN A:72 , THR A:73 , TYR A:74 , ARG A:76 , ASN A:101 , ASN A:130 , MET A:132 , ARG A:135 , ASP A:151 , ASP A:152 , ASP A:153 , LEU A:213 , GLY A:215 , ASP A:245 , ASP A:246 , HIS A:289 , ARG A:293 , MN A:600 , HOH A:617 , HOH A:630 , HOH A:690 , HOH A:691	BINDING SITE FOR RESIDUE UD1 A 401
5	AC5	SOFTWARE	PHE A:171 , GLN A:174 , PRO A:260 , ILE A:263 , HOH A:631 , GLN B:170	BINDING SITE FOR RESIDUE EDO A 501
6	AC6	SOFTWARE	GLN A:170 , PHE A:171 , PHE B:171 , GLN B:174 , PRO B:260 , ILE B:314 , HOH B:633	BINDING SITE FOR RESIDUE EDO B 502

SS Bonds (2, 2)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (3, 6)

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:62-146	84 85
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 (gaps) B:170-327 (gaps)	158 158

Sequences/Alignments

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
	(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:254
 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 d1on6a_ A: Alpha-1,4-N-acetylhexosaminyltransferase (Alpha-GalNAcT EXTL2)                                                                                                                                                                                                 SCOP domains
               CATH domains 1on6A00 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..-----------..hhhhhhhhhhhhhhhhhh........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 (gaps) UniProt: 170-330 [INCOMPLETE]                                                                                                 Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------Exon 1.7  PDB: A:146-169-------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1on6 A  63 ALDSFTLIMQTYNRTDLLLRLLNHYQAVPSLHKVIVVWNNVGEKGPEELWNSLGPHPIPVIFKPQTANKMRNRLQVFPEVETNAVLMVDDDTLISAQDLVFAFSIWQQFPDQIIGFVPRKHVSTSSGIYSYGGFELQTPGPGNGDQYSMVLIGASFFNSKYLELFQKQPAAVHALIDETQNCDDIAMNFLVTRHTGKPSGIFVKPINMVNLE-----------RAEHFLQRSYCINKLVNIYDGMPLKYSNIMISQFGFPYANHK 327
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272 |       -   |   292       302       312       322     
                                                                                                                                                                                                                                             274         286

Chain B from PDB  Type:PROTEIN  Length:257
 aligned with EXTL2_MOUSE | Q9ES89 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:266
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321      
          EXTL2_MOUSE    62 SALDSFTLIMQTYNRTDLLLRLLNHYQAVPSLHKVIVVWNNVGEKGPEELWNSLGPHPIPVIFKPQTANKMRNRLQVFPEVETNAVLMVDDDTLISAQDLVFAFSIWQQFPDQIIGFVPRKHVSTSSGIYSYGGFELQTPGPGNGDQYSMVLIGASFFNSKYLELFQKQPAAVHALIDETQNCDDIAMNFLVTRHTGKPSGIFVKPINMVNLEKETNGYSGMWHRAEHFLQRSYCINKLVNIYDGMPLKYSNIMISQFGFPYANHK 327
               SCOP domains d1on6b_ B: Alpha-1,4-N-acetylhexosaminyltransferase (Alpha-GalNAcT EXTL2)                                                                                                                                                                                                  SCOP domains
               CATH domains 1on6B00 B:62-327 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                                              CATH domains
           Pfam domains (1) -----Glyco_transf_64-1on6B01 B:67-321                                                                                                                                                                                                                               ------ Pfam domains (1)
           Pfam domains (2) -----Glyco_transf_64-1on6B02 B:67-321                                                                                                                                                                                                                               ------ Pfam domains (2)
         Sec.struct. author hhhh.eeeeeee..hhhhhhhhhhhhh....eeeeeeee.......hhhhhhhh......eeeee....hhhhhhh........eeeee...eeehhhhhhhhhhhhhhh...eee..eeeeeeee..eeeee................ee...eeeeehhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhhhh...eeee....eee....---------.hhhhhhhhhhhhhhhhhh.........eeeee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6b  PDB: B:62-146 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)
                 1on6 B  62 SALDSFTLIMQTYNRTDLLLRLLNHYQAVPSLHKVIVVWNNVGEKGPEELWNSLGPHPIPVIFKPQTANKMRNRLQVFPEVETNAVLMVDDDTLISAQDLVFAFSIWQQFPDQIIGFVPRKHVSTSSGIYSYGGFELQTPGPGNGDQYSMVLIGASFFNSKYLELFQKQPAAVHALIDETQNCDDIAMNFLVTRHTGKPSGIFVKPINMVNLEKE---------RAEHFLQRSYCINKLVNIYDGMPLKYSNIMISQFGFPYANHK 327
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271    |    -    |  291       301       311       321      
                                                                                                                                                                                                                                                276       286

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	-	→ 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 '\|'

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GT-A (172)

Family: Glyco_transf_64 (4)

Mus musculus (Mouse) (4)

1a	Glyco_transf_64-1on6B01	B:67-321
1b	Glyco_transf_64-1on6B02	B:67-321

Gene Ontology (14, 14)

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