1ym0: Difference between revisions

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-[[Image:1ym0.png|left|200px]]
-<!--
+==Crystal Structure of Earthworm Fibrinolytic Enzyme Component B: a Novel, Glycosylated Two-chained Trypsin==
-The line below this paragraph, containing "STRUCTURE_1ym0", creates the "Structure Box" on the page.
+<StructureSection load='1ym0' size='340' side='right'caption='[[1ym0]], [[Resolution|resolution]] 2.06&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<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>
-or leave the SCENE parameter empty for the default display.
+</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>
--->
+<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>
-{{STRUCTURE_1ym0|  PDB=1ym0  |  SCENE=  }}
+<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>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q3HR18_EISFE Q3HR18_EISFE]
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ym/1ym0_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+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.
-===Crystal Structure of Earthworm Fibrinolytic Enzyme Component B: a Novel, Glycosylated Two-chained Trypsin===
+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>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_15826663}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1ym0" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 15826663 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_15826663}}
+__TOC__
+</StructureSection>
-==About this Structure==
-[[1ym0]] is a 2 chain structure with sequence from [http://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].
-==Reference==
-<ref group="xtra">PMID:15826663</ref><ref group="xtra">PMID:15103143</ref><references group="xtra"/>
 [[Category: Eisenia fetida]]
-[[Category: An, X M.]]
+[[Category: Large Structures]]
-[[Category: Chang, W R.]]
+[[Category: An XM]]
-[[Category: Gui, L L.]]
+[[Category: Chang WR]]
-[[Category: Li, M.]]
+[[Category: Gui LL]]
-[[Category: Wang, C.]]
+[[Category: Li M]]
-[[Category: Wang, F.]]
+[[Category: Wang C]]
-[[Category: Zhang, J P.]]
+[[Category: Wang F]]
-[[Category: Cis peptide bond]]
+[[Category: Zhang JP]]
-[[Category: Eight-membered ring]]
-[[Category: Glycosylation]]
-[[Category: Hydrolase]]
-[[Category: Pyroglutamation]]
-[[Category: Two chain]]