2rkw: Difference between revisions

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-{{Seed}}
-[[Image:2rkw.jpg|left|200px]]
-<!--
+==Intermediate position of ATP on its trail to the binding pocket inside the subunit B mutant R416W of the energy converter A1Ao ATP synthase==
-The line below this paragraph, containing "STRUCTURE_2rkw", creates the "Structure Box" on the page.
+<StructureSection load='2rkw' size='340' side='right'caption='[[2rkw]], [[Resolution|resolution]] 2.81&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'>[[2rkw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanosarcina_mazei Methanosarcina mazei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RKW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RKW 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]] 2.81&#8491;</td></tr>
--->
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2rkw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rkw OCA], [https://pdbe.org/2rkw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rkw RCSB], [https://www.ebi.ac.uk/pdbsum/2rkw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rkw ProSAT]</span></td></tr>
-{{STRUCTURE_2rkw|  PDB=2rkw  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/VATB_METMA VATB_METMA] Produces ATP from ADP in the presence of a proton gradient across the membrane. The archaeal beta chain is a regulatory subunit.
+== 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/rk/2rkw_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=2rkw ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+A strategically placed tryptophan in position of Arg416 was used as an optical probe to monitor adenosine triphosphate and adenosine-diphosphate binding to subunit B of the A(1)A(O) adenosine triphosphate (ATP) synthase from Methanosarcina mazei Go1. Tryptophan fluorescence and fluorescence correlation spectroscopy gave binding constants indicating a preferred binding of ATP over ADP to the protein. The X-ray crystal structure of the R416W mutant protein in the presence of ATP was solved to 2.1 A resolution, showing the substituted Trp-residue inside the predicted adenine-binding pocket. The cocrystallized ATP molecule could be trapped in a so-called transition nucleotide-binding state. The high resolution structure shows the phosphate residues of the ATP near the P-loop region (S150-E158) and its adenine ring forms pi-pi interaction with Phe149. This transition binding position of ATP could be confirmed by tryptophan emission spectra using the subunit B mutant F149W. The trapped ATP position, similar to the one of the binding region of the antibiotic efrapeptin in F(1)F(O) ATP synthases, is discussed in light of a transition nucleotide-binding state of ATP while on its way to the final binding pocket. Finally, the inhibitory effect of efrapeptin C in ATPase activity of a reconstituted A(3)B(3)- and A(3)B(R416W)(3)-subcomplex, composed of subunit A and the B subunit mutant R416W, of the A(1)A(O) ATP synthase is shown.
-===Intermediate position of ATP on its trail to the binding pocket inside the subunit B mutant R416W of the energy converter A1Ao ATP synthase===
+Spectroscopic and crystallographic studies of the mutant R416W give insight into the nucleotide binding traits of subunit B of the A1Ao ATP synthase.,Kumar A, Manimekalai MS, Balakrishna AM, Hunke C, Weigelt S, Sewald N, Gruber G Proteins. 2009 Jun;75(4):807-19. PMID:19003877<ref>PMID:19003877</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2rkw" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_16563431}}, adds the Publication Abstract to the page
+*[[ATPase 3D structures|ATPase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 16563431 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16563431}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-RKW is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Methanosarcina_mazei Methanosarcina mazei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RKW OCA].
-==Reference==
-Crystal structure of the archaeal A1Ao ATP synthase subunit B from Methanosarcina mazei Go1: Implications of nucleotide-binding differences in the major A1Ao subunits A and B., Schafer IB, Bailer SM, Duser MG, Borsch M, Bernal RA, Stock D, Gruber G, J Mol Biol. 2006 May 5;358(3):725-40. Epub 2006 Mar 10. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16563431 16563431]
 [[Category: Methanosarcina mazei]]
-[[Category: Single protein]]
+[[Category: Balakrishna AM]]
-[[Category: Balakrishna, A M.]]
+[[Category: Gruber G]]
-[[Category: Gruber, G.]]
+[[Category: Hunke C]]
-[[Category: Hunke, C.]]
+[[Category: Kumar A]]
-[[Category: Kumar, A.]]
+[[Category: Manimekalai MSS]]
-[[Category: Manimekalai, M S.S.]]
-[[Category: Atp synthesis]]
-[[Category: Hydrogen ion transport]]
-[[Category: Hydrolase]]
-[[Category: Ion transport]]
-[[Category: Transport]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 10 12:53:01 2008''