4mmh
From Proteopedia
(Difference between revisions)
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4mmh]] 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=4MMH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MMH FirstGlance]. <br> | <table><tr><td colspan='2'>[[4mmh]] 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=4MMH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4MMH FirstGlance]. <br> | ||
| - | </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> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2Å</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4mmh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mmh OCA], [https://pdbe.org/4mmh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mmh RCSB], [https://www.ebi.ac.uk/pdbsum/4mmh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mmh ProSAT]</span></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=4mmh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4mmh OCA], [https://pdbe.org/4mmh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4mmh RCSB], [https://www.ebi.ac.uk/pdbsum/4mmh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4mmh ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[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> | [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;"> | ||
| - | == 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. | ||
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| - | 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<ref>PMID:24437462</ref> | ||
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| - | </div> | ||
| - | <div class="pdbe-citations 4mmh" style="background-color:#fffaf0;"></div> | ||
== References == | == References == | ||
<references/> | <references/> | ||
Current revision
Crystal structure of heparan sulfate lyase HepC from Pedobacter heparinus
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