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| | ==Crystal structure of heparan sulfate lyase HepC mutant from Pedobacter heparinus== | | ==Crystal structure of heparan sulfate lyase HepC mutant from Pedobacter heparinus== |
| - | <StructureSection load='4mmi' size='340' side='right' caption='[[4mmi]], [[Resolution|resolution]] 2.40Å' scene=''> | + | <StructureSection load='4mmi' size='340' side='right'caption='[[4mmi]], [[Resolution|resolution]] 2.40Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4mmi]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_13125 Atcc 13125]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MMI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4MMI FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4mmi]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pedobacter_heparinus Pedobacter heparinus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4MMI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MMI FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4mmh|4mmh]]</td></tr>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4mmi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mmi OCA], [https://pdbe.org/4mmi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mmi RCSB], [https://www.ebi.ac.uk/pdbsum/4mmi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mmi ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">HepC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=984 ATCC 13125])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Heparin-sulfate_lyase Heparin-sulfate lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.8 4.2.2.8] </span></td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4mmi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mmi OCA], [http://pdbe.org/4mmi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4mmi RCSB], [http://www.ebi.ac.uk/pdbsum/4mmi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4mmi ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/HEPC_PEDHD HEPC_PEDHD]] Specifically cleaves heparan sulfate-rich regions of acidic polysaccharides. Does not act on N,O-desulfated glucosamine or N-acetyl-O-sulfated glucosamine linkages. Functions in cleaving metazoan heparan sulfate and providing carbon, nitrogen and sulfate sources for microorganisms.<ref>PMID:8702264</ref> <ref>PMID:10747789</ref> | + | [https://www.uniprot.org/uniprot/HEPC_PEDHD HEPC_PEDHD] Specifically cleaves heparan sulfate-rich regions of acidic polysaccharides. Does not act on N,O-desulfated glucosamine or N-acetyl-O-sulfated glucosamine linkages. Functions in cleaving metazoan heparan sulfate and providing carbon, nitrogen and sulfate sources for microorganisms.<ref>PMID:8702264</ref> <ref>PMID:10747789</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 13125]] | + | [[Category: Large Structures]] |
| - | [[Category: Heparin-sulfate lyase]] | + | [[Category: Pedobacter heparinus]] |
| - | [[Category: Hashimoto, W]] | + | [[Category: Hashimoto W]] |
| - | [[Category: Maruyama, Y]] | + | [[Category: Maruyama Y]] |
| - | [[Category: Mikami, B]] | + | [[Category: Mikami B]] |
| - | [[Category: Murata, K]] | + | [[Category: Murata K]] |
| - | [[Category: Nakamichi, Y]] | + | [[Category: Nakamichi Y]] |
| - | [[Category: Alpha/alpha barrel anti-parallel beta-sheet]]
| + | |
| - | [[Category: Heparinase]]
| + | |
| - | [[Category: Lyase]]
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| Structural highlights
Function
HEPC_PEDHD Specifically cleaves heparan sulfate-rich regions of acidic polysaccharides. Does not act on N,O-desulfated glucosamine or N-acetyl-O-sulfated glucosamine linkages. Functions in cleaving metazoan heparan sulfate and providing carbon, nitrogen and sulfate sources for microorganisms.[1] [2]
Publication Abstract from PubMed
Pedobacter heparinus (formerly known as Flavobacterium heparinum) is a typical glycosaminoglycan-degrading bacterium that produces three heparin lyases, Hep I, Hep II, and Hep III, which act on heparins with 1,4-glycoside bonds between uronate and amino sugar residues. Being different from Hep I and Hep II, Hep III is specific for heparan sulfate. Here we describe the crystal structure of Hep III with the active site located in a deep cleft. The X-ray crystallographic structure of Hep III was determined at 2.20 A resolution using single-wavelength anomalous diffraction. This enzyme comprised an N-terminal alpha/alpha-barrel domain and a C-terminal antiparallel beta-sheet domain as its basic scaffold. Overall structures of Hep II and Hep III were similar, although Hep III exhibited an open form compared with the closed form of Hep II. Superimposition of Hep III and heparin tetrasaccharide-bound Hep II suggested that an active site of Hep III was located in the deep cleft at the interface between its two domains. Three mutants (N240A, Y294F, and H424A) with mutations at the active site had significantly reduced enzyme activity. This is the first report of the structure-function relationship of P. heparinus Hep III.
Crystal Structure of Pedobacter heparinus Heparin Lyase Hep III with the Active Site in a Deep Cleft.,Hashimoto W, Maruyama Y, Nakamichi Y, Mikami B, Murata K Biochemistry. 2014 Feb 4;53(4):777-86. doi: 10.1021/bi4012463. Epub 2014 Jan 27. PMID:24437462[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Su H, Blain F, Musil RA, Zimmermann JJ, Gu K, Bennett DC. Isolation and expression in Escherichia coli of hepB and hepC, genes coding for the glycosaminoglycan-degrading enzymes heparinase II and heparinase III, respectively, from Flavobacterium heparinum. Appl Environ Microbiol. 1996 Aug;62(8):2723-34. PMID:8702264
- ↑ Pojasek K, Shriver Z, Hu Y, Sasisekharan R. Histidine 295 and histidine 510 are crucial for the enzymatic degradation of heparan sulfate by heparinase III. Biochemistry. 2000 Apr 11;39(14):4012-9. PMID:10747789
- ↑ Hashimoto W, Maruyama Y, Nakamichi Y, Mikami B, Murata K. Crystal Structure of Pedobacter heparinus Heparin Lyase Hep III with the Active Site in a Deep Cleft. Biochemistry. 2014 Feb 4;53(4):777-86. doi: 10.1021/bi4012463. Epub 2014 Jan 27. PMID:24437462 doi:http://dx.doi.org/10.1021/bi4012463
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