2d2f: Difference between revisions

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-[[Image:2d2f.gif|left|200px]]<br /><applet load="2d2f" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="2d2f, resolution 1.90&Aring;" />
-'''Crystal structure of atypical cytoplasmic ABC-ATPase SufC from Thermus thermophilus HB8'''<br />
-==Overview==
+==Crystal structure of atypical cytoplasmic ABC-ATPase SufC from Thermus thermophilus HB8==
-SufC, a cytoplasmic ABC-ATPase, is one of the most conserved Suf proteins., SufC forms a stable complex with SufB and SufD, and the SufBCD complex, interacts with other Suf proteins in the Fe-S cluster assembly. We have, determined the crystal structure of SufC from Thermus thermophilus HB8 in, nucleotide-free and ADP-Mg-bound states at 1.7A and 1.9A resolution, respectively. The overall architecture of the SufC structure is similar to, other ABC ATPases structures, but there are several specific motifs in, SufC. Three residues following the end of the Walker B motif form a novel, 3(10) helix which is not observed in other ABC ATPases. Due to the novel, 3(10) helix, a conserved glutamate residue involved in ATP hydrolysis is, flipped out. Although this unusual conformation is unfavorable for ATP, hydrolysis, salt-bridges formed by conserved residues and a strong, hydrogen-bonding network around the novel 3(10) helix suggest that the, novel 3(10) helix of SufC is a rigid conserved motif. Compared to other, ABC-ATPase structures, a significant displacement occurs at a linker, region between the ABC alpha/beta domain and the alpha-helical domain. The, linker conformation is stabilized by a hydrophobic interaction between, conserved residues around the Q loop. The molecular surfaces of SufC and, the C-terminal helices of SufD (PDB code: 1VH4) suggest that the unusual, linker conformation conserved among SufC proteins is probably suitable for, interacting with SufB and SufD.
+<StructureSection load='2d2f' size='340' side='right'caption='[[2d2f]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[2d2f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D2F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D2F FirstGlance]. <br>
-D2F is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus] with <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=ADP:'>ADP</scene> and <scene name='pdbligand=GOL:'>GOL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D2F OCA].
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-==Reference==
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2d2f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d2f OCA], [https://pdbe.org/2d2f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d2f RCSB], [https://www.ebi.ac.uk/pdbsum/2d2f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d2f ProSAT], [https://www.topsan.org/Proteins/RSGI/2d2f TOPSAN]</span></td></tr>
-Crystal structure of atypical cytoplasmic ABC-ATPase SufC from Thermus thermophilus HB8., Watanabe S, Kita A, Miki K, J Mol Biol. 2005 Nov 11;353(5):1043-54. Epub 2005 Sep 23. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16216272 16216272]
+</table>
-[[Category: Single protein]]
+== Function ==
-[[Category: Thermus thermophilus]]
+[https://www.uniprot.org/uniprot/Q5SH92_THET8 Q5SH92_THET8]
-[[Category: Kita, A.]]
+== Evolutionary Conservation ==
-[[Category: Miki, K.]]
+[[Image:Consurf_key_small.gif|200px|right]]
-[[Category: RSGI, RIKEN.Structural.Genomics/Proteomics.Initiative.]]
+Check<jmol>
-[[Category: Watanabe, S.]]
+  <jmolCheckbox>
-[[Category: ADP]]
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d2/2d2f_consurf.spt"</scriptWhenChecked>
-[[Category: GOL]]
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-[[Category: MG]]
+    <text>to colour the structure by Evolutionary Conservation</text>
-[[Category: 310-helix]]
+  </jmolCheckbox>
-[[Category: abc-atpase]]
+</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=2d2f ConSurf].
-[[Category: riken structural genomics/proteomics initiative]]
+<div style="clear:both"></div>
-[[Category: rsgi]]
+__TOC__
-[[Category: structural genomics]]
+</StructureSection>
-[[Category: suf protein]]
+[[Category: Large Structures]]
+[[Category: Thermus thermophilus HB8]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 18:53:33 2008''
+[[Category: Kita A]]
+[[Category: Miki K]]
+[[Category: Watanabe S]]