ProGP133 (Heparinase II)
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| ProGP ID | ProGP133 (Heparinase II) |
| Validation Status | Characterized |
| Organism Information | |
| Organism Name | Pedobacter heparinus (Flavobacterium heparinum) |
| Domain | Bacteria |
| Classification | Phylum : Bacteroidetes Class : Sphingobacteriia Orders : Sphingobaccteriales Family : Sphingobacteriaceae Genus : Pedobacter Species : heparinus |
| Taxonomic ID (NCBI) | 984 |
| Genome Information | |
| GenBank | CP001681.1 |
| EMBL | U27585 |
| Organism Additional Information | Pedobacter heparinus is a Gram-negative, non-pathogenic soil organism. |
| Gene Information | |
| Gene Name | hep B |
| NCBI Gene ID | 8253515 |
| GenBank Gene Sequence | NC_013061 |
| Protein Information | |
| Protein Name | Heparinase II |
| UniProtKB/SwissProt ID | C6XZB6 |
| NCBI RefSeq | WP_015808224.1 |
| 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 |
| 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) |
| 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. |
| GlyTouCan | G07644FE |
| Technique(s) used for Glycan Identification | Crystallographic analysis (electron density maps) |
| Protein Glycosylation linked (PGL) gene(s) | |
| Additional Comment | Sequon features: Asp-Thr consensus sequon is found in this protein. |
| Literature | |
| Year of Identification | 1996 |
| Year of Identification Month Wise | 1996.12.1 |
| Year of Validation | 2006 |
| Reference | 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. Journal of Biological Chemistry, 281(22), pp.15525-15535. |
| Corresponding Author | Miroslaw Cygler |
| Contact | Biotechnology Research Institute, 6100 Royalmount Avenue, Montréal, Québec H4P 2R2 Canada. |
| Reference | Godavarti, R. and Sasisekharan, R., 1996. A Comparative Analysis of the Primary Sequences and Characteristics of Heparinases I, II, and III fromFlavobacterium heparinum. Biochemical and biophysical research communications, 229(3), pp.770-777. |
| Reference | Zilliges Y, Kehr JC, Mikkat S, Bouchier C, de Marsac NT, Börner T, Dittmann E. (2008) An extracellular glycoprotein is implicated in cell-cell contacts in the toxic cyanobacterium Microcystis aeruginosa PCC 7806. J Bacteriol., 190(8), 2871-9. [PubMed: 182 |
| Corresponding Author | Elke Dittmann |
| Contact | Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA. |