2gtf: Difference between revisions

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-[[Image:2gtf.jpg|left|200px]]
-<!--
+==Crystal structure of nitrophorin 2 complex with pyrimidine==
-The line below this paragraph, containing "STRUCTURE_2gtf", creates the "Structure Box" on the page.
+<StructureSection load='2gtf' size='340' side='right'caption='[[2gtf]], [[Resolution|resolution]] 1.40&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'>[[2gtf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodnius_prolixus Rhodnius prolixus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GTF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GTF 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]] 1.4&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=P1R:PYRIMIDINE'>P1R</scene></td></tr>
-{{STRUCTURE_2gtf|  PDB=2gtf  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2gtf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gtf OCA], [https://pdbe.org/2gtf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gtf RCSB], [https://www.ebi.ac.uk/pdbsum/2gtf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gtf ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NP2_RHOPR NP2_RHOPR] Heme-based protein that deliver nitric oxide gas (NO) to the victim while feeding, resulting in vasodilation and inhibition of platelet aggregation. Also bind tightly to histamine, which is released by the host to induce wound healing (By similarity).  Specifically inhibits factor IXa-catalyzed activation of factor X in the presence of calcium and phospholipids irrespective of the presence or absence of factor VIIIa.
+== 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/gt/2gtf_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=2gtf ConSurf].
+<div style="clear:both"></div>
-'''Crystal structure of nitrophorin 2 complex with pyrimidine'''
+==See Also==
+*[[Nitrophorin|Nitrophorin]]
+__TOC__
-==Overview==
+</StructureSection>
-Nitrophorin 2 (NP2) (also known as prolixin-S) is a salivary protein that transports nitric oxide, binds histamine, and acts as an anticoagulant during blood feeding by the insect Rhodnius prolixus. The 2.0-A crystal structure of NP2 reveals an eight-stranded antiparallel beta-barrel containing a ferric heme coordinated through His(57), similar to the structures of NP1 and NP4. All four Rhodnius nitrophorins transport NO and sequester histamine through heme binding, but only NP2 acts as an anticoagulant. Here, we demonstrate that recombinant NP2, but not recombinant NP1 or NP4, is a potent anticoagulant; recombinant NP3 also displays minor activity. Comparison of the nitrophorin structures suggests that a surface region near the C terminus and the loops between beta strands B-C and E-F is responsible for the anticoagulant activity. NP2 also displays larger NO association rates and smaller dissociation rates than NP1 and NP4, which may result from a more open and more hydrophobic distal pocket, allowing more rapid solvent reorganization on ligand binding. The NP2 protein core differs from NP1 and NP4 in that buried Glu(53), which allows for larger NO release rates when deprotonated, hydrogen bonds to invariant Tyr(81). Surprisingly, this tyrosine lies on the protein surface in NP1 and NP4.
+[[Category: Large Structures]]
-==About this Structure==
-GTF is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Rhodnius_prolixus Rhodnius prolixus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GTF OCA].
-==Reference==
-The crystal structure of nitrophorin 2. A trifunctional antihemostatic protein from the saliva of Rhodnius prolixus., Andersen JF, Montfort WR, J Biol Chem. 2000 Sep 29;275(39):30496-503. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10884386 10884386]
 [[Category: Rhodnius prolixus]]
-[[Category: Single protein]]
+[[Category: Montfort WR]]
-[[Category: Montfort, W R.]]
+[[Category: Weichsel A]]
-[[Category: Weichsel, A.]]
-[[Category: Beta barrel]]
-[[Category: Ferric heme]]
-[[Category: Lipocalin]]
-[[Category: Pyrimidine]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 05:30:49 2008''