1l2p: Difference between revisions

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-[[Image:1l2p.gif|left|200px]]<br />
-<applet load="1l2p" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1l2p, resolution 1.55&Aring;" />
-'''ATP Synthase b Subunit Dimerization Domain'''<br />
-==Overview==
+==ATP Synthase b Subunit Dimerization Domain==
-The b subunit of E. coli F(0)F(1)-ATPase links the peripheral F(1), subunits to the membrane-integral F(0) portion and functions as a, "stator", preventing rotation of F(1). The b subunit is present as a dimer, in ATP synthase, and residues 62-122 are required to mediate dimerization., To understand how the b subunit dimer is formed, we have studied the, structure of the isolated dimerization domain, b(62-122). Analytical, ultracentrifugation and solution small-angle X-ray scattering (SAXS), indicate that the b(62-122) dimer is extremely elongated, with a, frictional ratio of 1.60, a maximal dimension of 95 A, and a radius of, gyration of 27 A, values that are consistent with an alpha-helical, coiled-coil structure. The crystal structure of b(62-122) has been solved, and refined to 1.55 A. The protein crystallized as an isolated, monomeric, alpha helix with a length of 90 A. Combining the crystal structure of, monomeric b(62-122) with SAXS data from the dimer in solution, we have, constructed a model for the b(62-122) dimer in which the two helices form, a coiled coil with a right-handed superhelical twist. Analysis of b, sequences from E. coli and other prokaryotes indicates conservation of an, undecad repeat, which is characteristic of a right-handed coiled coil and, consistent with our structural model. Mutation of residue Arg-83, which, interrupts the undecad pattern, to alanine markedly stabilized the dimer, as expected for the proposed two-stranded, right-handed coiled-coil, structure.
+<StructureSection load='1l2p' size='340' side='right'caption='[[1l2p]], [[Resolution|resolution]] 1.55&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1l2p]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. The December 2005 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''ATP Synthase''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2005_12 10.2210/rcsb_pdb/mom_2005_12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L2P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1L2P 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]] 1.55&#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=1l2p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l2p OCA], [https://pdbe.org/1l2p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1l2p RCSB], [https://www.ebi.ac.uk/pdbsum/1l2p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1l2p ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ATPF_ECOLI ATPF_ECOLI] F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation (By similarity).<ref>PMID:1682301</ref>   Component of the F(0) channel, it forms part of the peripheral stalk, linking F(1) to F(0) (By similarity).<ref>PMID:1682301</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/l2/1l2p_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=1l2p ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-L2P is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. The following page contains interesting information on the relation of 1L2P with [[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb72_1.html ATP Synthase]]. Active as [http://en.wikipedia.org/wiki/Iron-chelate-transporting_ATPase Iron-chelate-transporting ATPase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.3.34 3.6.3.34] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1L2P OCA].
+*[[ATPase 3D structures|ATPase 3D structures]]
+== References ==
-==Reference==
+<references/>
-The "second stalk" of Escherichia coli ATP synthase: structure of the isolated dimerization domain., Del Rizzo PA, Bi Y, Dunn SD, Shilton BH, Biochemistry. 2002 May 28;41(21):6875-84. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12022893 12022893]
+__TOC__
+</StructureSection>
 [[Category: ATP Synthase]]
 [[Category: Escherichia coli]]
-[[Category: Iron-chelate-transporting ATPase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: RCSB PDB Molecule of the Month]]
-[[Category: Bi, Y.]]
+[[Category: Bi Y]]
-[[Category: Dunn, S.D.]]
+[[Category: Del Rizzo PA]]
-[[Category: Rizzo, P.A.Del.]]
+[[Category: Dunn SD]]
-[[Category: Shilton, B.H.]]
+[[Category: Shilton BH]]
-[[Category: alpha helix]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 18 09:03:09 2007''