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GlyCosmos6-Glycan-Motif-Image

Id Subject Object Predicate Lexical cue image
T1 134-141 Glycan_Motif denotes heparin https://api.glycosmos.org/wurcs2image/0.10.0/png/binary/G54161DR|https://api.glycosmos.org/wurcs2image/0.10.0/png/binary/G00021MO
T3 417-428 Glycan_Motif denotes chondroitin https://api.glycosmos.org/wurcs2image/0.10.0/png/binary/G43702JT
T4 484-491 Glycan_Motif denotes heparin https://api.glycosmos.org/wurcs2image/0.10.0/png/binary/G54161DR|https://api.glycosmos.org/wurcs2image/0.10.0/png/binary/G00021MO
T6 684-691 Glycan_Motif denotes heparin https://api.glycosmos.org/wurcs2image/0.10.0/png/binary/G54161DR|https://api.glycosmos.org/wurcs2image/0.10.0/png/binary/G00021MO
T8 1006-1017 Glycan_Motif denotes chondroitin https://api.glycosmos.org/wurcs2image/0.10.0/png/binary/G43702JT
T9 1961-1968 Glycan_Motif denotes heparin https://api.glycosmos.org/wurcs2image/0.10.0/png/binary/G54161DR|https://api.glycosmos.org/wurcs2image/0.10.0/png/binary/G00021MO

Glycosmos6-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T1 146-161 GlycoEpitope denotes heparan sulfate http://www.glycoepitope.jp/epitopes/EP0086
T2 417-428 GlycoEpitope denotes chondroitin http://www.glycoepitope.jp/epitopes/EP0081
T3 1006-1017 GlycoEpitope denotes chondroitin http://www.glycoepitope.jp/epitopes/EP0081
T4 1973-1988 GlycoEpitope denotes heparan-sulfate http://www.glycoepitope.jp/epitopes/EP0086

sentences

Id Subject Object Predicate Lexical cue
T1 0-105 Sentence denotes Crystal structure of heparinase II from Pedobacter heparinus and its complex with a disaccharide product.
T2 106-273 Sentence denotes Heparinase II depolymerizes heparin and heparan sulfate glycosaminoglycans, yielding unsaturated oligosaccharide products through an elimination degradation mechanism.
T3 274-439 Sentence denotes This enzyme cleaves the oligosaccharide chain on the nonreducing end of either glucuronic or iduronic acid, sharing this characteristic with a chondroitin ABC lyase.
T4 440-725 Sentence denotes We have determined the first structure of a heparin-degrading lyase, that of heparinase II from Pedobacter heparinus (formerly Flavobacterium heparinum), in a ligand-free state at 2.15 A resolution and in complex with a disaccharide product of heparin degradation at 2.30 A resolution.
T5 726-902 Sentence denotes The protein is composed of three domains: an N-terminal alpha-helical domain, a central two-layered beta-sheet domain, and a C-terminal domain forming a two-layered beta-sheet.
T6 903-1049 Sentence denotes Heparinase II shows overall structural similarities to the polysaccharide lyase family 8 (PL8) enzymes chondroitin AC lyase and hyaluronate lyase.
T7 1050-1189 Sentence denotes In contrast to PL8 enzymes, however, heparinase II forms stable dimers, with the two active sites formed independently within each monomer.
T8 1190-1309 Sentence denotes The structure of the N-terminal domain of heparinase II is also similar to that of alginate lyases from the PL5 family.
T9 1310-1473 Sentence denotes A Zn2+ ion is bound within the central domain and plays an essential structural role in the stabilization of a loop forming one wall of the substrate-binding site.
T10 1474-1610 Sentence denotes The disaccharide binds in a long, deep canyon formed at the top of the N-terminal domain and by loops extending from the central domain.
T11 1611-1801 Sentence denotes Based on structural comparison with the lyases from the PL5 and PL8 families having bound substrates or products, the disaccharide found in heparinase II occupies the "+1" and "+2" subsites.
T12 1802-2001 Sentence denotes The structure of the enzyme-product complex, combined with data from previously characterized mutations, allows us to propose a putative chemical mechanism of heparin and heparan-sulfate degradation.

GlyCosmos6-Glycan-Motif-Structure

Id Subject Object Predicate Lexical cue
T1 134-141 https://glytoucan.org/Structures/Glycans/G00021MO denotes heparin
T2 134-141 https://glytoucan.org/Structures/Glycans/G54161DR denotes heparin
T3 417-428 https://glytoucan.org/Structures/Glycans/G43702JT denotes chondroitin
T4 484-491 https://glytoucan.org/Structures/Glycans/G00021MO denotes heparin
T5 484-491 https://glytoucan.org/Structures/Glycans/G54161DR denotes heparin
T6 684-691 https://glytoucan.org/Structures/Glycans/G00021MO denotes heparin
T7 684-691 https://glytoucan.org/Structures/Glycans/G54161DR denotes heparin
T8 1006-1017 https://glytoucan.org/Structures/Glycans/G43702JT denotes chondroitin
T9 1961-1968 https://glytoucan.org/Structures/Glycans/G00021MO denotes heparin
T10 1961-1968 https://glytoucan.org/Structures/Glycans/G54161DR denotes heparin

GlyCosmos15-Glycan

Id Subject Object Predicate Lexical cue image
T1 417-428 Glycan denotes chondroitin https://api.glycosmos.org/wurcs2image/latest/png/binary/G43702JT
T2 1006-1017 Glycan denotes chondroitin https://api.glycosmos.org/wurcs2image/latest/png/binary/G43702JT
T3 146-161 Glycan denotes heparan sulfate https://api.glycosmos.org/wurcs2image/latest/png/binary/G17927IW
T6 1973-1988 Glycan denotes heparan-sulfate https://api.glycosmos.org/wurcs2image/latest/png/binary/G17927IW

Glycan-GlyCosmos

Id Subject Object Predicate Lexical cue image
T1 417-428 Glycan denotes chondroitin https://api.glycosmos.org/wurcs2image/latest/png/binary/G43702JT
T2 1006-1017 Glycan denotes chondroitin https://api.glycosmos.org/wurcs2image/latest/png/binary/G43702JT
T4 146-161 Glycan denotes heparan sulfate https://api.glycosmos.org/wurcs2image/latest/png/binary/G17927IW

GlyCosmos-GlycoEpitope

Id Subject Object Predicate Lexical cue glycoepitope_id
T1 146-161 http://purl.jp/bio/12/glyco/glycan#Glycan_epitope denotes heparan sulfate http://www.glycoepitope.jp/epitopes/EP0086
T2 417-428 http://purl.jp/bio/12/glyco/glycan#Glycan_epitope denotes chondroitin http://www.glycoepitope.jp/epitopes/EP0081
T3 1006-1017 http://purl.jp/bio/12/glyco/glycan#Glycan_epitope denotes chondroitin http://www.glycoepitope.jp/epitopes/EP0081
T4 1973-1988 http://purl.jp/bio/12/glyco/glycan#Glycan_epitope denotes heparan-sulfate http://www.glycoepitope.jp/epitopes/EP0086

GlyCosmos15-Taxon

Id Subject Object Predicate Lexical cue db_id
T1 40-60 Organism denotes Pedobacter heparinus 984
T2 536-556 Organism denotes Pedobacter heparinus 984
T3 567-591 Organism denotes Flavobacterium heparinum 984

GlyCosmos15-GlycoEpitope

Id Subject Object Predicate Lexical cue glycoepitope_id
T1 146-161 http://purl.jp/bio/12/glyco/glycan#Glycan_epitope denotes heparan sulfate http://www.glycoepitope.jp/epitopes/EP0086
T2 417-428 http://purl.jp/bio/12/glyco/glycan#Glycan_epitope denotes chondroitin http://www.glycoepitope.jp/epitopes/EP0081
T3 1006-1017 http://purl.jp/bio/12/glyco/glycan#Glycan_epitope denotes chondroitin http://www.glycoepitope.jp/epitopes/EP0081
T4 1973-1988 http://purl.jp/bio/12/glyco/glycan#Glycan_epitope denotes heparan-sulfate http://www.glycoepitope.jp/epitopes/EP0086

GlyCosmos15-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 1438-1442 Body_part denotes wall http://purl.obolibrary.org/obo/UBERON_0000060

GlyCosmos15-Sentences

Id Subject Object Predicate Lexical cue
T1 0-105 Sentence denotes Crystal structure of heparinase II from Pedobacter heparinus and its complex with a disaccharide product.
T2 106-273 Sentence denotes Heparinase II depolymerizes heparin and heparan sulfate glycosaminoglycans, yielding unsaturated oligosaccharide products through an elimination degradation mechanism.
T3 274-439 Sentence denotes This enzyme cleaves the oligosaccharide chain on the nonreducing end of either glucuronic or iduronic acid, sharing this characteristic with a chondroitin ABC lyase.
T4 440-725 Sentence denotes We have determined the first structure of a heparin-degrading lyase, that of heparinase II from Pedobacter heparinus (formerly Flavobacterium heparinum), in a ligand-free state at 2.15 A resolution and in complex with a disaccharide product of heparin degradation at 2.30 A resolution.
T5 726-902 Sentence denotes The protein is composed of three domains: an N-terminal alpha-helical domain, a central two-layered beta-sheet domain, and a C-terminal domain forming a two-layered beta-sheet.
T6 903-1049 Sentence denotes Heparinase II shows overall structural similarities to the polysaccharide lyase family 8 (PL8) enzymes chondroitin AC lyase and hyaluronate lyase.
T7 1050-1189 Sentence denotes In contrast to PL8 enzymes, however, heparinase II forms stable dimers, with the two active sites formed independently within each monomer.
T8 1190-1309 Sentence denotes The structure of the N-terminal domain of heparinase II is also similar to that of alginate lyases from the PL5 family.
T9 1310-1473 Sentence denotes A Zn2+ ion is bound within the central domain and plays an essential structural role in the stabilization of a loop forming one wall of the substrate-binding site.
T10 1474-1610 Sentence denotes The disaccharide binds in a long, deep canyon formed at the top of the N-terminal domain and by loops extending from the central domain.
T11 1611-1801 Sentence denotes Based on structural comparison with the lyases from the PL5 and PL8 families having bound substrates or products, the disaccharide found in heparinase II occupies the "+1" and "+2" subsites.
T12 1802-2001 Sentence denotes The structure of the enzyme-product complex, combined with data from previously characterized mutations, allows us to propose a putative chemical mechanism of heparin and heparan-sulfate degradation.

NCBITAXON

Id Subject Object Predicate Lexical cue db_id
T1 40-60 OrganismTaxon denotes Pedobacter heparinus 984
T2 536-556 OrganismTaxon denotes Pedobacter heparinus 984
T3 567-591 OrganismTaxon denotes Flavobacterium heparinum 984

Anatomy-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 1438-1442 Body_part denotes wall http://purl.obolibrary.org/obo/UBERON_0000060