2x4m

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (10:21, 9 May 2024) (edit) (undo)
 
(7 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2x4m.png|left|200px]]
 
-
<!--
+
==Yersinia Pestis Plasminogen Activator Pla==
-
The line below this paragraph, containing "STRUCTURE_2x4m", creates the "Structure Box" on the page.
+
<StructureSection load='2x4m' size='340' side='right'caption='[[2x4m]], [[Resolution|resolution]] 2.55&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'>[[2x4m]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Yersinia_pestis Yersinia pestis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2X4M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2X4M 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]] 2.55&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C8E:(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE'>C8E</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-
{{STRUCTURE_2x4m| PDB=2x4m | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2x4m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2x4m OCA], [https://pdbe.org/2x4m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2x4m RCSB], [https://www.ebi.ac.uk/pdbsum/2x4m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2x4m ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/COLY_YERPE COLY_YERPE] Seems to play an essential role in plague transmission by mediating flea blockage in a temperature-dependent fashion. Fibrinolytic activity prevails at 37 degrees Celsius whereas coagulase expression predominates at lower temperatures (<30 degrees Celsius). Activates plasminogen by cleaving it.
 +
== 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/x4/2x4m_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=2x4m ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
The plasminogen activator Pla from Yersinia pestis is an outer membrane protease (omptin) that is important for the virulence of plague. Here, we present the high-resolution crystal structure of wild-type, enzymatically active Pla at 1.9 A. The structure shows a water molecule located between active site residues D84 and H208, which likely corresponds to the nucleophilic water. A number of other water molecules are present in the active site, linking residues important for enzymatic activity. The R211 sidechain in loop L4 is close to the nucleophilic water and possibly involved in the stabilization of the oxyanion intermediate. Subtle conformational changes of H208 result from the binding of lipopolysaccharide to the outside of the barrel, explaining the unusual dependence of omptins on lipopolysaccharide for activity. The Pla structure suggests a model for the interaction with plasminogen substrate and provides a more detailed understanding of the catalytic mechanism of omptin proteases.
-
===Yersinia Pestis Plasminogen Activator Pla===
+
An active site water network in the plasminogen activator pla from Yersinia pestis.,Eren E, Murphy M, Goguen J, van den Berg B Structure. 2010 Jul 14;18(7):809-18. PMID:20637417<ref>PMID:20637417</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 2x4m" style="background-color:#fffaf0;"></div>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_20637417}}, adds the Publication Abstract to the page
+
*[[Plasminogen activator|Plasminogen activator]]
-
(as it appears on PubMed at http://www.pubmed.gov), where 20637417 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_20637417}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
[[Category: Large Structures]]
-
[[2x4m]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Yersinia_pestis Yersinia pestis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2X4M OCA].
+
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:020637417</ref><references group="xtra"/>
+
-
[[Category: Plasminogen activator Pla]]
+
[[Category: Yersinia pestis]]
[[Category: Yersinia pestis]]
-
[[Category: Berg, B Van Den.]]
+
[[Category: Eren E]]
-
[[Category: Eren, E.]]
+
[[Category: Goguen J]]
-
[[Category: Goguen, J.]]
+
[[Category: Murphy M]]
-
[[Category: Murphy, M.]]
+
[[Category: Van den Berg B]]
-
[[Category: Aspartyl protease]]
+
-
[[Category: Cell outer membrane]]
+
-
[[Category: Hydrolase]]
+
-
[[Category: Omptin]]
+
-
[[Category: Protease]]
+
-
[[Category: Transmembrane]]
+

Current revision

Yersinia Pestis Plasminogen Activator Pla

PDB ID 2x4m

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2x4m"
Personal tools