ProGP133

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ProGP ID ProGP133
Validation Status Characterized
Organism Information
Organism NamePedobacter heparinus (Flavobacterium heparinum)
Domain Bacteria
Classification Family: Sphingobacteriaceae
Order: "Sphingobacteriales"
Class: "Sphingobacteria"
Division or phylum: "Bacteroidetes"
Taxonomic ID (NCBI) 984
Genome Sequence(s)
GenBank CP001681.1
EMBL U27585
Organism Additional Information Pedobacter heparinus is a Gram-negative, nonpathogenic soil organism.
Gene Information
Gene Namehep B
NCBI Gene ID 8253515
GenBank Gene Sequence 8253515
Protein Information
Protein NameHeparinase II
UniProtKB/SwissProt ID Q46080
NCBI RefSeq YP_003092674.1
EMBL-CDSAAB18277.1
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 LocationPeriplasm
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 ProteinT134
Experimentally Validated Glycosite(s ) in Mature ProteinT134
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
Technique(s) used for Glycosylation DetectionPresence 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.
Technique(s) used for Glycan Identification Crystallographic analysis (electron density maps)
Literature
Additional CommentSequon features: Asp-Thr consensus sequon is found in this protein.
Year of Identification1996
Year of Identification Month Wise1996.12.1
Year of Validation 2006
Reference1) 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]
AuthorShaya, D., Tocilj, A., Li, Y., Myette, J., Venkataraman, G., Sasisekharan, R. and Cygler, M.
Research GroupDepartment of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada.
Corresponding Author Cygler, M.
ContactDepartment of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada.
Reference 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]
Author Godavarti, R. Sasisekharan, R.
Research GroupDepartment of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA.
Corresponding Author Sasisekharan, R.
ContactDepartment of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA.
Reference 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]
Author Godavarti, R. Sasisekharan, R.
Research GroupDepartment of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA.
Corresponding Author Sasisekharan, R.
ContactDepartment of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA.