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1ym0

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(New page: 200px<br /><applet load="1ym0" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ym0, resolution 2.06&Aring;" /> '''Crystal Structure of...)
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[[Image:1ym0.gif|left|200px]]<br /><applet load="1ym0" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1ym0, resolution 2.06&Aring;" />
 
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'''Crystal Structure of Earthworm Fibrinolytic Enzyme Component B: a Novel, Glycosylated Two-chained Trypsin'''<br />
 
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==Overview==
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==Crystal Structure of Earthworm Fibrinolytic Enzyme Component B: a Novel, Glycosylated Two-chained Trypsin==
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The earthworm fibrinolytic enzyme (EFE), belonging to a group of serine, proteases with strong fibrinolytic activity, has been used in a mixture as, an oral drug for prevention and treatment of thrombosis in East Asia. The, EFE component b (EFE-b) is one of seven EFE components from Eisenia, fetida, and among them it has nearly the highest fibrinolytic activity., Here, we report its crystal structure at a resolution of 2.06A. The, structural analysis shows that EFE-b should be classified as a trypsin, from earthworm. However, it is distinct from other trypsins. It is a, two-chained protease with an N-terminal, pyroglutamated light chain and an, N-glycosylated heavy chain. Furthermore, the heavy chain contains a novel, structural motif, an eight-membered ring resulting from a disulfide bridge, between two neighboring cysteine residues, and a cis peptide bond exists, between these two cysteine residues. The crystal structure of EFE-b, provides the structural basis for its high level of stability and reveals, its complicated post-translational modifications in earthworm. This, structure is the first reported for a glycosylated two-chained trypsin, which may provide useful clues to explain the origin and evolution of the, chymotrypsin family.
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<StructureSection load='1ym0' size='340' side='right'caption='[[1ym0]], [[Resolution|resolution]] 2.06&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1ym0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Eisenia_fetida Eisenia fetida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YM0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YM0 FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.06&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ym0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ym0 OCA], [https://pdbe.org/1ym0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ym0 RCSB], [https://www.ebi.ac.uk/pdbsum/1ym0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ym0 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q3HR18_EISFE Q3HR18_EISFE]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ym/1ym0_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1ym0 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The earthworm fibrinolytic enzyme (EFE), belonging to a group of serine proteases with strong fibrinolytic activity, has been used in a mixture as an oral drug for prevention and treatment of thrombosis in East Asia. The EFE component b (EFE-b) is one of seven EFE components from Eisenia fetida, and among them it has nearly the highest fibrinolytic activity. Here, we report its crystal structure at a resolution of 2.06A. The structural analysis shows that EFE-b should be classified as a trypsin from earthworm. However, it is distinct from other trypsins. It is a two-chained protease with an N-terminal, pyroglutamated light chain and an N-glycosylated heavy chain. Furthermore, the heavy chain contains a novel structural motif, an eight-membered ring resulting from a disulfide bridge between two neighboring cysteine residues, and a cis peptide bond exists between these two cysteine residues. The crystal structure of EFE-b provides the structural basis for its high level of stability and reveals its complicated post-translational modifications in earthworm. This structure is the first reported for a glycosylated two-chained trypsin, which may provide useful clues to explain the origin and evolution of the chymotrypsin family.
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==About this Structure==
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Crystal structure of earthworm fibrinolytic enzyme component B: a novel, glycosylated two-chained trypsin.,Wang F, Wang C, Li M, Zhang JP, Gui LL, An XM, Chang WR J Mol Biol. 2005 May 6;348(3):671-85. PMID:15826663<ref>PMID:15826663</ref>
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1YM0 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Eisenia_fetida Eisenia fetida] with MG and SO4 as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1YM0 OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Crystal structure of earthworm fibrinolytic enzyme component B: a novel, glycosylated two-chained trypsin., Wang F, Wang C, Li M, Zhang JP, Gui LL, An XM, Chang WR, J Mol Biol. 2005 May 6;348(3):671-85. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15826663 15826663]
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</div>
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<div class="pdbe-citations 1ym0" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Eisenia fetida]]
[[Category: Eisenia fetida]]
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[[Category: Protein complex]]
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[[Category: Large Structures]]
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[[Category: An, X.M.]]
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[[Category: An XM]]
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[[Category: Chang, W.R.]]
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[[Category: Chang WR]]
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[[Category: Gui, L.L.]]
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[[Category: Gui LL]]
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[[Category: Li, M.]]
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[[Category: Li M]]
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[[Category: Wang, C.]]
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[[Category: Wang C]]
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[[Category: Wang, F.]]
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[[Category: Wang F]]
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[[Category: Zhang, J.P.]]
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[[Category: Zhang JP]]
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[[Category: MG]]
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[[Category: SO4]]
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[[Category: cis peptide bond]]
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[[Category: eight-membered ring]]
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[[Category: glycosylation]]
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[[Category: pyroglutamation]]
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[[Category: two chains]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 04:19:53 2007''
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Current revision

Crystal Structure of Earthworm Fibrinolytic Enzyme Component B: a Novel, Glycosylated Two-chained Trypsin

PDB ID 1ym0

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