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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)
 
 
Genome Sequence(s)
GenBank
EMBL
Organism Additional Information
Pedobacter heparinus is a Gram-negative, nonpathogenic soil organism.
 
 
Gene Information
Gene Name
hep B
NCBI Gene ID
GenBank Gene Sequence
 
 
Protein Information
Protein Name
Heparinase II
UniProtKB/SwissProt ID
NCBI RefSeq
EMBL-CDS
UniProtKB Sequence
>tr|Q46080|Q46080_PEDHE Heparinase II protein OS=Pedobacter heparinus GN=HepB PE
=1 SV=1 MKRQLYLYVIFVVVELMVFTTKGYSQTKADVVWKDVDGVSMPIPPKTHPRLYLREQQVPD LKNRMND
PKLKKVWADMIKMQEDWKPADIPEVKDFRFYFNQKGLTVRVELMALNYLMTKD PKVGREAITSIIDTLETATFKP
AGDISRGIGLFMVTGAIVYDWCYDQLKPEEKTRFVKAF VRLAKMLECGYPPVKDKSIVGHASEWMIMRDLLSVGI
AIYDEFPEMYNLAAGRFFKEHLV ARNWFYPSHNYHQGMSYLNVRFTNDLFALWILDRMGAGNVFNPGQQFILYDA
IYKRRPDG QILAGGDVDYSRKKPKYYTMPALLAGSYYKDEYLNYEFLKDPNVEPHCKLFEFLWRDTQL GSRKPD
DLPLSRYSGSPFGWMIARTGWGPESVIAEMKVNEYSFLNHQHQDAGAFQIYYKG PLAIDAGSYTGSSGGYNSPHN
KNFFKRTIAHNSLLIYDPKETFSSSGYGGSDHTDFAAND GGQRLPGKGWIAPRDLKEMLAGDFRTGKILAQGFGP
DNQTPDYTYLKGDITAAYSAKVKE VKRSFLFLNLKDAKVPAAMIVFDKVVASNPDFKKFWLLHSIEQPEIKGNQI
TIKRTKNGD SGMLVNTALLPDAANSNITSIGGKGKDFWVFGTNYTNDPKPGTDEALERGEWRVEITPKK AAAED
YYLNVIQIADNTQQKLHEVKRIDGDKVVGVQLADRIVTFSKTSETVDRPFGFSVV GKGTFKFVMTDLLPGTWQVL
KDGKILYPALSAKGDDGPLYFEGTEGTYRFLR
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
 
 
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 LKNRMND
PKLKKVWADMIKMQEDWKPADIPEVKDFRFYFNQKGLTVRVELMALNYLMTKD PKVGREAITSIIDT*(134)
LETATFKPAGDISRGIGLFMVTGAIVYDWCYDQLKPEEKTRFVKAF VRLAKMLECGYPPVKDKSIVGHASEWMIM
RDLLSVGIAIYDEFPEMYNLAAGRFFKEHLV ARNWFYPSHNYHQGMSYLNVRFTNDLFALWILDRMGAGNVFNPG
QQFILYDAIYKRRPDG QILAGGDVDYSRKKPKYYTMPALLAGSYYKDEYLNYEFLKDPNVEPHCKLFEFLWRDTQ
L GSRKPDDLPLSRYSGSPFGWMIARTGWGPESVIAEMKVNEYSFLNHQHQDAGAFQIYYKG PLAIDAGSYTGSS
GGYNSPHNKNFFKRTIAHNSLLIYDPKETFSSSGYGGSDHTDFAAND GGQRLPGKGWIAPRDLKEMLAGDFRTGK
ILAQGFGPDNQTPDYTYLKGDITAAYSAKVKE VKRSFLFLNLKDAKVPAAMIVFDKVVASNPDFKKFWLLHSIEQ
PEIKGNQITIKRTKNGD SGMLVNTALLPDAANSNITSIGGKGKDFWVFGTNYTNDPKPGTDEALERGEWRVEITP
KK AAAEDYYLNVIQIADNTQQKLHEVKRIDGDKVVGVQLADRIVTFSKTSETVDRPFGFSVV GKGTFKFVMTDL
LPGTWQVLKDGKILYPALSAKGDDGPLYFEGTEGTYRFLR
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.
Technique(s) used for Glycan Identification
Crystallographic analysis (electron density maps)
 
 
Protein Glycosylation linked (PGL) gene(s)
Characterized Accessory Gene(s)
Information currently not available with us.
PGL Additional Links
 
 
Literature
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
 
 
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