1m2d: Difference between revisions

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:1m2d.gif|left|200px]]<br /><applet load="1m2d" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1m2d, resolution 1.05&Aring;" />
-'''Crystal structure at 1.05 Angstroms resolution of the Cys59Ser variant of the thioredoxin-like [2Fe-2S] ferredoxin from Aquifex aeolicus'''<br />
-==Overview==
+==Crystal structure at 1.05 Angstroms resolution of the Cys59Ser variant of the thioredoxin-like [2Fe-2S] ferredoxin from Aquifex aeolicus==
-The [2Fe-2S] ferredoxin (Fd4) from Aquifex aeolicus adopts a, thioredoxin-like polypeptide fold that is distinct from other [2Fe-2S], ferredoxins. Crystal structures of the Cys-55 --&gt; Ser (C55S) and Cys-59, --&gt; Ser (C59S) variants of this protein have been determined to 1.25 A and, 1.05 A resolution, respectively, whereas the resolution of the wild type, (WT) has been extended to 1.5 A. The improved WT structure provides a, detailed description of the [2Fe-2S] cluster, including two features that, have not been noted previously in any [2Fe-2S] cluster-containing protein, namely, pronounced distortions in the cysteine coordination to the cluster, and a Calpha-H-Sgamma hydrogen bond between cluster ligands Cys-55 and, Cys-9. These features may contribute to the unusual electronic and, magnetic properties of the [2Fe-2S] clusters in WT and variants of this, ferredoxin. The structures of the two variants of Fd4, in which single, cysteine ligands to the [2Fe-2S] cluster are replaced by serine, establish, the metric details of serine-ligated Fe-S active sites with unprecedented, accuracy. Both the cluster and its surrounding protein matrix change in, subtle ways to accommodate this ligand substitution, particularly in terms, of distortions of the Fe(2)S(2) inorganic core from planarity and, displacements of the polypeptide chain. These high resolution structures, illustrate how the interactions between polypeptide chains and Fe-S active, sites reflect combinations of flexibility and rigidity on the part of both, partners; these themes are also evident in more complex systems, as, exemplified by changes associated with serine ligation of the nitrogenase, P cluster.
+<StructureSection load='1m2d' size='340' side='right'caption='[[1m2d]], [[Resolution|resolution]] 1.05&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1m2d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M2D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M2D 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]] 1.05&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</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=1m2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m2d OCA], [https://pdbe.org/1m2d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m2d RCSB], [https://www.ebi.ac.uk/pdbsum/1m2d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m2d ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/FER2_AQUAE FER2_AQUAE] Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions.
+== 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/m2/1m2d_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=1m2d ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-M2D is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus] with FES as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1M2D OCA].
+*[[Ferredoxin 3D structures|Ferredoxin 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-High resolution crystal structures of the wild type and Cys-55--&gt;Ser and Cys-59--&gt;Ser variants of the thioredoxin-like [2Fe-2S] ferredoxin from Aquifex aeolicus., Yeh AP, Ambroggio XI, Andrade SL, Einsle O, Chatelet C, Meyer J, Rees DC, J Biol Chem. 2002 Sep 13;277(37):34499-507. Epub 2002 Jun 27. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12089152 12089152]
 [[Category: Aquifex aeolicus]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Ambroggio, X.I.]]
+[[Category: Ambroggio XI]]
-[[Category: Andrade, S.L.A.]]
+[[Category: Andrade SLA]]
-[[Category: Chatelet, C.]]
+[[Category: Chatelet C]]
-[[Category: Einsle, O.]]
+[[Category: Einsle O]]
-[[Category: Meyer, J.]]
+[[Category: Meyer J]]
-[[Category: Rees, D.C.]]
+[[Category: Rees DC]]
-[[Category: Yeh, A.P.]]
+[[Category: Yeh AP]]
-[[Category: FES]]
-[[Category: [2fe-2s] cluster]]
-[[Category: cys59ser variant]]
-[[Category: ferredoxin]]
-[[Category: thioredoxin-like fold]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 21:05:09 2007''