2b3x: Difference between revisions

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-[[Image:2b3x.gif|left|200px]]<br />
-<applet load="2b3x" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="2b3x, resolution 2.540&Aring;" />
-'''Structure of an orthorhombic crystal form of human cytosolic aconitase (IRP1)'''<br />
-==Overview==
+==Structure of an orthorhombic crystal form of human cytosolic aconitase (IRP1)==
-Iron regulatory proteins (IRPs) control the translation of proteins, involved in iron uptake, storage and utilization by binding to specific, noncoding sequences of the corresponding mRNAs known as iron-responsive, elements (IREs). This strong interaction assures proper iron homeostasis, in animal cells under iron shortage. Conversely, under iron-replete, conditions, IRP1 binds a [4Fe-4S] cluster and functions as cytosolic, aconitase. Regulation of the balance between the two IRP1 activities is, complex, and it does not depend only on iron availability. Here, we report, the crystal structure of human IRP1 in its aconitase form. Comparison with, known structures of homologous enzymes reveals well-conserved folds and, active site environments with significantly different surface shapes and, charge distributions. The specific features of human IRP1 allow us to, propose a tentative model of an IRP1-IRE complex that agrees with a range, of previously obtained data.
+<StructureSection load='2b3x' size='340' side='right'caption='[[2b3x]], [[Resolution|resolution]] 2.54&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2b3x]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B3X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2B3X 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]] 2.54&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=2b3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b3x OCA], [https://pdbe.org/2b3x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2b3x RCSB], [https://www.ebi.ac.uk/pdbsum/2b3x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2b3x ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ACOHC_HUMAN ACOHC_HUMAN] Bifunctional iron sensor that switches between 2 activities depending on iron availability (PubMed:1946430, PubMed:1281544, PubMed:8041788). Iron deprivation, promotes its mRNA binding activity through which it regulates the expression of genes involved in iron uptake, sequestration and utilization (PubMed:1946430, PubMed:1281544, PubMed:8041788, PubMed:23891004). Binds to iron-responsive elements (IRES) in the untranslated region of target mRNAs preventing for instance the translation of ferritin and aminolevulinic acid synthase and stabilizing the transferrin receptor mRNA (PubMed:1946430, PubMed:1281544, PubMed:8041788, PubMed:23891004).<ref>PMID:1281544</ref> <ref>PMID:1946430</ref> <ref>PMID:23891004</ref> <ref>PMID:8041788</ref>   Conversely, when cellular iron levels are high, binds a 4Fe-4S cluster which precludes RNA binding activity and promotes the aconitase activity, the isomerization of citrate to isocitrate via cis-aconitate.<ref>PMID:1281544</ref> <ref>PMID:1946430</ref> <ref>PMID:8041788</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/b3/2b3x_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=2b3x ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-B3X is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with ZN, SF4 and EDO as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Aconitate_hydratase Aconitate hydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.3 4.2.1.3] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2B3X OCA].
+*[[Aconitase 3D structures|Aconitase 3D structures]]
+== References ==
-==Reference==
+<references/>
-Crystal structure of human iron regulatory protein 1 as cytosolic aconitase., Dupuy J, Volbeda A, Carpentier P, Darnault C, Moulis JM, Fontecilla-Camps JC, Structure. 2006 Jan;14(1):129-39. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16407072 16407072]
+__TOC__
-[[Category: Aconitate hydratase]]
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Dupuy, J.]]
+[[Category: Dupuy J]]
-[[Category: Fontecilla-Camps, J.C.]]
+[[Category: Fontecilla-Camps JC]]
-[[Category: Volbeda, A.]]
+[[Category: Volbeda A]]
-[[Category: EDO]]
-[[Category: SF4]]
-[[Category: ZN]]
-[[Category: irp1 ire-irp1 aconitase activity]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 20:58:09 2007''