3i4l: Difference between revisions

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-[[Image:3i4l.png|left|200px]]
-{{STRUCTURE_3i4l|  PDB=3i4l  |  SCENE=  }}
+==Structural characterization for the nucleotide binding ability of subunit A with AMP-PNP of the A1AO ATP synthase==
+<StructureSection load='3i4l' size='340' side='right'caption='[[3i4l]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3i4l]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I4L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3I4L FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></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=3i4l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i4l OCA], [https://pdbe.org/3i4l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3i4l RCSB], [https://www.ebi.ac.uk/pdbsum/3i4l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3i4l ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/VATA_PYRHO VATA_PYRHO] Produces ATP from ADP in the presence of a proton gradient across the membrane. The archaeal alpha chain is a catalytic 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/i4/3i4l_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=3i4l ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The crystal structures of the nucleotide-empty (A(E)), 5'-adenylyl-beta,gamma-imidodiphosphate (A(PNP))-bound, and ADP (A(DP))-bound forms of the catalytic A subunit of the energy producer A(1)A(O) ATP synthase from Pyrococcus horikoshii OT3 have been solved at 2.47 A and 2.4 A resolutions. The structures provide novel features of nucleotide binding and depict the residues involved in the catalysis of the A subunit. In the A(E) form, the phosphate analog SO(4)(2-) binds, via a water molecule, to the phosphate binding loop (P-loop) residue Ser238, which is also involved in the phosphate binding of ADP and 5'-adenylyl-beta,gamma-imidodiphosphate. Together with amino acids Gly234 and Phe236, the serine residue stabilizes the arched P-loop conformation of subunit A, as shown by the 2.4-A structure of the mutant protein S238A in which the P-loop flips into a relaxed state, comparable to the one in catalytic beta subunits of F(1)F(O) ATP synthases. Superposition of the existing P-loop structures of ATPases emphasizes the unique P-loop in subunit A, which is also discussed in the light of an evolutionary P-loop switch in related A(1)A(O) ATP synthases, F(1)F(O) ATP synthases, and vacuolar ATPases and implicates diverse catalytic mechanisms inside these biological motors.
-===Structural characterization for the nucleotide binding ability of subunit A with AMP-PNP of the A1AO ATP synthase===
+Nucleotide binding states of subunit A of the A-ATP synthase and the implication of P-loop switch in evolution.,Kumar A, Manimekalai MS, Balakrishna AM, Jeyakanthan J, Gruber G J Mol Biol. 2010 Feb 19;396(2):301-20. Epub 2009 Nov 26. PMID:19944110<ref>PMID:19944110</ref>
-{{ABSTRACT_PUBMED_19944110}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 3i4l" style="background-color:#fffaf0;"></div>
-[[3i4l]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I4L OCA].
 ==See Also==
-*[[ATP synthase|ATP synthase]]
+*[[ATPase 3D structures|ATPase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:019944110</ref><ref group="xtra">PMID:016627940</ref><references group="xtra"/>
+__TOC__
-[[Category: Pyrococcus horikoshii]]
+</StructureSection>
-[[Category: Balakrishna, A M.]]
+[[Category: Large Structures]]
-[[Category: Gruber, G.]]
+[[Category: Pyrococcus horikoshii OT3]]
-[[Category: Jeyakanthan, J.]]
+[[Category: Balakrishna AM]]
-[[Category: Kumar, A.]]
+[[Category: Gruber G]]
-[[Category: Manimekalai, S M.S.]]
+[[Category: Jeyakanthan J]]
-[[Category: Hydrolase]]
+[[Category: Kumar A]]
+[[Category: Manimekalai SMS]]