ProGlyProt ID BC162 Organism Information Organism Name Pedobacter heparinus (Flavobacterium heparinum) Domain Bacteria Classification Family: Sphingobacteriaceae Order: "Sphingobacteriales" Class: "Sphingobacteria" Division or phylum: "Bacteroidetes" Taxonomic ID (NCBI) 984 Genome Sequence (s) GeneBank CP001681.1 EMBL U27585 Gene Information Gene Name hep B NCBI Gene ID 8253515 GenBank Gene Sequence 8253515 Protein Information Protein Name Heparinase II UniProtKB/SwissProt ID Q46080 NCBI RefSeq YP_003092674.1 EMBL-CDS AAB18277.1 UniProtKB Sequence >tr|Q46080|Q46080_PEDHE Heparinase II protein OS=Pedobacter heparinus GN=HepB PE=1 SV=1 MKRQLYLYVIFVVVELMVFTTKGYSQTKADVVWKDVDGVSMPIPPKTHPRLYLREQQVPD LKNRMNDPKLKKVWADMIKMQEDWKPADIPEVKDFRFYFNQKGLTVRVELMALNYLMTKD PKVGREAITSIIDTLETATFKPAGDISRGIGLFMVTGAIVYDWCYDQLKPEEKTRFVKAF VRLAKMLECGYPPVKDKSIVGHASEWMIMRDLLSVGIAIYDEFPEMYNLAAGRFFKEHLV ARNWFYPSHNYHQGMSYLNVRFTNDLFALWILDRMGAGNVFNPGQQFILYDAIYKRRPDG QILAGGDVDYSRKKPKYYTMPALLAGSYYKDEYLNYEFLKDPNVEPHCKLFEFLWRDTQL GSRKPDDLPLSRYSGSPFGWMIARTGWGPESVIAEMKVNEYSFLNHQHQDAGAFQIYYKG PLAIDAGSYTGSSGGYNSPHNKNFFKRTIAHNSLLIYDPKETFSSSGYGGSDHTDFAAND GGQRLPGKGWIAPRDLKEMLAGDFRTGKILAQGFGPDNQTPDYTYLKGDITAAYSAKVKE VKRSFLFLNLKDAKVPAAMIVFDKVVASNPDFKKFWLLHSIEQPEIKGNQITIKRTKNGD SGMLVNTALLPDAANSNITSIGGKGKDFWVFGTNYTNDPKPGTDEALERGEWRVEITPKK AAAEDYYLNVIQIADNTQQKLHEVKRIDGDKVVGVQLADRIVTFSKTSETVDRPFGFSVV GKGTFKFVMTDLLPGTWQVLKDGKILYPALSAKGDDGPLYFEGTEGTYRFLR Sequence length 772 AA Subcellular Location Periplasm Function GAG lyase. It acts in an endolytic manner and displays broad selectivity, catalyzing the cleavage of linkages adjacent not only to IdoA and GlcA but also to the rare -L-galacturonic acid residues present in the polymer. Although HepII has greater affinity for heparin, its turnover rate for heparan sulfate is higher. Protein Structure PDB ID 2FUQ, 2FUT Glycosylation Status Glycosylation Type O (Thr) linked Experimentally Validated Glycosite(s) in Full Length Protein T134 Experimentally Validated Glycosite(s ) in Mature Protein T134 Glycosite(s) Annotated Protein Sequence >tr|Q46080|Q46080_PEDHE Heparinase II protein OS=Pedobacter heparinus GN=HepB PE=1 SV=1 MKRQLYLYVIFVVVELMVFTTKGYSQTKADVVWKDVDGVSMPIPPKTHPRLYLREQQVPD LKNRMNDPKLKKVWADMIKMQEDWKPADIPEVKDFRFYFNQKGLTVRVELMALNYLMTKD PKVGREAITSIIDT*(134)LETATFKPAGDISRGIGLFMVTGAIVYDWCYDQLKPEEKTRFVKAF VRLAKMLECGYPPVKDKSIVGHASEWMIMRDLLSVGIAIYDEFPEMYNLAAGRFFKEHLV ARNWFYPSHNYHQGMSYLNVRFTNDLFALWILDRMGAGNVFNPGQQFILYDAIYKRRPDG QILAGGDVDYSRKKPKYYTMPALLAGSYYKDEYLNYEFLKDPNVEPHCKLFEFLWRDTQL GSRKPDDLPLSRYSGSPFGWMIARTGWGPESVIAEMKVNEYSFLNHQHQDAGAFQIYYKG PLAIDAGSYTGSSGGYNSPHNKNFFKRTIAHNSLLIYDPKETFSSSGYGGSDHTDFAAND GGQRLPGKGWIAPRDLKEMLAGDFRTGKILAQGFGPDNQTPDYTYLKGDITAAYSAKVKE VKRSFLFLNLKDAKVPAAMIVFDKVVASNPDFKKFWLLHSIEQPEIKGNQITIKRTKNGD SGMLVNTALLPDAANSNITSIGGKGKDFWVFGTNYTNDPKPGTDEALERGEWRVEITPKK AAAEDYYLNVIQIADNTQQKLHEVKRIDGDKVVGVQLADRIVTFSKTSETVDRPFGFSVV GKGTFKFVMTDLLPGTWQVLKDGKILYPALSAKGDDGPLYFEGTEGTYRFLR Sequence Around Glycosites (21 AA) GREAITSIIDTLETATFKPAG Glycosite Sequence Logo seqlogo Glycosite Sequence Logo Technique(s) used for Glycosylation Detection Presence of multiple isoforms in the RPHPLC (reverse-phase high pressure liquid chromatography) profile, and mass excess (approx. 1.3 kDa) detected using mass spectrometry. Technique(s) used for Glycosylated Residue(s) Detection Crystallographic analysis (electron density maps) Protein Glycosylation- Implication Glycan Information Glycan Annotation Linkage: Man-Thr. Tetrasaccharide glycan observed in crystal structure: Man-(Rha)-GlcUA-Xyl (xylose-β (1–4)glucuronic acid-α(1–2)[rhamnose-α(1–4)]mannose-α(1-O)Ser. Two more sugars were visible but their density was too weak to be reliably modeled. The branched Rha sugar fills a depression in the protein surface while the remaining sugars extend away from the surface of the protein. Technique(s) used for Glycan Identification Crystallographic analysis (electron density maps) Protein Glycosylation linked (PGL) gene(s) OST Gene Name OST NCBI Gene ID OST GenBank Gene Sequence OST Protein Name OST UniProtKB/ SwissProt ID OST NCBI RefSeq OST EMBL-CDS OST UniProtKB Sequence OST EC Number (BRENDA) OST Genome Context Characterized Accessory Gene(s) Information currently not available with us. PGL Additional Links CAZy Literatures Reference(s) 1) Shaya, D., Tocilj, A., Li, Y., Myette, J., Venkataraman, G., Sasisekharan, R. and Cygler, M. (2006) Crystal structure of heparinase II from Pedobacter heparinus and its complex with a disaccharide product. J Biol Chem, 281, 15525-15535. [PubMed: 16565082] 2) Godavarti, R. and Sasisekharan, R. (1996) A comparative analysis of the primary sequences and characteristics of heparinases I, II, and III from Flavobacterium heparinum. Biochem Biophys Res Commun, 229, 770-777. [PubMed: 8954971] Additional Comments Sequon features: Asp-Thr consensus sequon is found in this protein. Year of Identification 1996 Year of Validation 2006