1bui: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:1bui.png|left|200px]]
-<!--
+==Structure of the ternary microplasmin-staphylokinase-microplasmin complex: a proteinase-cofactor-substrate complex in action==
-The line below this paragraph, containing "STRUCTURE_1bui", creates the "Structure Box" on the page.
+<StructureSection load='1bui' size='340' side='right'caption='[[1bui]], [[Resolution|resolution]] 2.65&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'>[[1bui]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Staphylococcus_phage_42D.m Staphylococcus phage 42D.m]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BUI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BUI 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]] 2.65&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0GJ:L-ALPHA-GLUTAMYL-N-{(1S)-4-{[AMINO(IMINIO)METHYL]AMINO}-1-[(1S)-2-CHLORO-1-HYDROXYETHYL]BUTYL}GLYCINAMIDE'>0GJ</scene></td></tr>
-{{STRUCTURE_1bui|  PDB=1bui  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1bui FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bui OCA], [https://pdbe.org/1bui PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bui RCSB], [https://www.ebi.ac.uk/pdbsum/1bui PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bui ProSAT]</span></td></tr>
+</table>
+== Disease ==
+[https://www.uniprot.org/uniprot/PLMN_HUMAN PLMN_HUMAN] Defects in PLG are the cause of plasminogen deficiency (PLGD) [MIM:[https://omim.org/entry/217090 217090]. PLGD is characterized by decreased serum plasminogen activity. Two forms of the disorder are distinguished: type 1 deficiency is additionally characterized by decreased plasminogen antigen levels and clinical symptoms, whereas type 2 deficiency, also known as dysplasminogenemia, is characterized by normal, or slightly reduced antigen levels, and absence of clinical manifestations. Plasminogen deficiency type 1 results in markedly impaired extracellular fibrinolysis and chronic mucosal pseudomembranous lesions due to subepithelial fibrin deposition and inflammation. The most common clinical manifestation of type 1 deficiency is ligneous conjunctivitis in which pseudomembranes formation on the palpebral surfaces of the eye progresses to white, yellow-white, or red thick masses with a wood-like consistency that replace the normal mucosa.<ref>PMID:1986355</ref> <ref>PMID:8392398</ref> <ref>PMID:6216475</ref> <ref>PMID:6238949</ref> <ref>PMID:1427790</ref> <ref>PMID:9242524</ref> <ref>PMID:9858247</ref> <ref>PMID:10233898</ref>
+== Function ==
+[https://www.uniprot.org/uniprot/PLMN_HUMAN PLMN_HUMAN] Plasmin dissolves the fibrin of blood clots and acts as a proteolytic factor in a variety of other processes including embryonic development, tissue remodeling, tumor invasion, and inflammation. In ovulation, weakens the walls of the Graafian follicle. It activates the urokinase-type plasminogen activator, collagenases and several complement zymogens, such as C1 and C5. Cleavage of fibronectin and laminin leads to cell detachment and apoptosis. Also cleaves fibrin, thrombospondin and von Willebrand factor. Its role in tissue remodeling and tumor invasion may be modulated by CSPG4. Binds to cells.<ref>PMID:14699093</ref>   Angiostatin is an angiogenesis inhibitor that blocks neovascularization and growth of experimental primary and metastatic tumors in vivo.<ref>PMID:14699093</ref>
+== 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/bu/1bui_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=1bui ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The serine proteinase plasmin is the key fibrinolytic enzyme that dissolves blood clots and also promotes cell migration and tissue remodeling. Here, we report the 2.65 A crystal structure of a ternary complex of microplasmin-staphylokinase bound to a second microplasmin. The staphylokinase 'cofactor' does not affect the active-site geometry of the plasmin 'enzyme', but instead modifies its subsite specificity by providing additional docking sites for enhanced presentation of the plasminogen 'substrate' to the 'enzymes's' active site. The activation loop of the plasmin 'substrate', cleaved in these crystals, can be reconstructed to show how it runs across the active site of the plasmin 'enzyme' prior to activation cleavage. This is the first experimental structure of a productive proteinase-cofactor-macromolecular substrate complex. Furthermore, it provides a template for the design of improved plasminogen activators and plasmin inhibitors with considerable therapeutical potential.
-===STRUCTURE OF THE TERNARY MICROPLASMIN-STAPHYLOKINASE-MICROPLASMIN COMPLEX: A PROTEINASE-COFACTOR-SUBSTRATE COMPLEX IN ACTION.===
+The ternary microplasmin-staphylokinase-microplasmin complex is a proteinase-cofactor-substrate complex in action.,Parry MA, Fernandez-Catalan C, Bergner A, Huber R, Hopfner KP, Schlott B, Guhrs KH, Bode W Nat Struct Biol. 1998 Oct;5(10):917-23. PMID:9783753<ref>PMID:9783753</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1bui" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_9783753}}, adds the Publication Abstract to the page
+*[[Plasminogen 3D structures|Plasminogen 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 9783753 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_9783753}}
+__TOC__
+</StructureSection>
-==About this Structure==
-BUI is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BUI OCA].
-==Reference==
-The ternary microplasmin-staphylokinase-microplasmin complex is a proteinase-cofactor-substrate complex in action., Parry MA, Fernandez-Catalan C, Bergner A, Huber R, Hopfner KP, Schlott B, Guhrs KH, Bode W, Nat Struct Biol. 1998 Oct;5(10):917-23. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9783753 9783753]
 [[Category: Homo sapiens]]
-[[Category: Plasmin]]
+[[Category: Large Structures]]
-[[Category: Protein complex]]
+[[Category: Staphylococcus phage 42D m]]
-[[Category: Bergner, A.]]
+[[Category: Bergner A]]
-[[Category: Bode, W.]]
+[[Category: Bode W]]
-[[Category: Fernandez-Catalan, C.]]
+[[Category: Fernandez-Catalan C]]
-[[Category: Guehrs, K.]]
+[[Category: Guehrs K]]
-[[Category: Hopfner, K.]]
+[[Category: Hopfner K]]
-[[Category: Huber, R.]]
+[[Category: Huber R]]
-[[Category: Parry, M A.A.]]
+[[Category: Parry MAA]]
-[[Category: Schlott, B.]]
+[[Category: Schlott B]]
-[[Category: Cofactor]]
-[[Category: Fibrinolysis]]
-[[Category: Plasmin]]
-[[Category: Serine proteinase]]
-[[Category: Staphylokinase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 19:44:31 2008''