2i6r: Difference between revisions

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-[[Image:2i6r.jpg|left|200px]]<br /><applet load="2i6r" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="2i6r, resolution 2.51&Aring;" />
-'''Crystal structure of E. coli HypE, a hydrogenase maturation protein'''<br />
-==Overview==
+==Crystal structure of E. coli HypE, a hydrogenase maturation protein==
-Hydrogenases are enzymes involved in hydrogen metabolism, utilizing H2 as, an electron source. [NiFe] hydrogenases are heterodimeric Fe-S proteins, with a large subunit containing the reaction centre involving Fe and Ni, metal ions and a small subunit containing one or more Fe-S clusters., Maturation of the [NiFe]-hydrogenase involves assembly of, non-proteinaceous ligands on the large subunit by accessory proteins, encoded by the hyp operon. HypE is an essential accessory protein and, participates in the synthesis of two cyano groups found in the large, subunit. We report the crystal structure of Escherichia coli HypE at 2.0 A, resolution. HypE exhibits fold similar to PurM and ThiL and forms dimers., The C-terminal catalytically-essential Cys336 is internalized at the dimer, interface between the N- and C-terminal domains. A mechanism for, dehydration of the thiocarbamate to the thiocyanate is proposed, involving, Asp83 and Glu272. The interactions of HypE and HypF were characterized in, detail by surface plasmon resonance and isothermal titration calorimetry, revealing a Kd for their association of approximately 400 nM. The, stoichiometry and molecular weights of the complex were verified by size, exclusion chromatography and gel scanning densitometry. These experiments, reveal that HypE and HypF associate to form a stoichiometric, hetero-oligomeric complex predominantly consisting of a [EF]2, heterotetramer which exists in a dynamic equilibrium with the EF, heterodimer. The surface plasmon resonance results indicate that a, conformational change occurs upon heterodimerization which facilitates, formation of a productive complex as part of the carbamate transfer, reaction.
+<StructureSection load='2i6r' size='340' side='right'caption='[[2i6r]], [[Resolution|resolution]] 2.51&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2i6r]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_O157:H7 Escherichia coli O157:H7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I6R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2I6R 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]] 2.51&#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=2i6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i6r OCA], [https://pdbe.org/2i6r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2i6r RCSB], [https://www.ebi.ac.uk/pdbsum/2i6r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2i6r ProSAT], [https://www.topsan.org/Proteins/BSGI/2i6r TOPSAN]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/HYPE_ECOLI HYPE_ECOLI] Involved in the maturation of [NiFe] hydrogenases. Along with HypF, it catalyzes the synthesis of the CN ligands of the active site iron of [NiFe]-hydrogenases. HypE catalyzes the ATP-dependent dehydration of the carboxamido group attached to its C-terminal cysteine to a cyano group (PubMed:12586941, PubMed:15291820). The cyano group is then transferred from HypE to the HypC-HypD complex or the HybG-HypD complex (PubMed:15504408).<ref>PMID:12586941</ref> <ref>PMID:15291820</ref> <ref>PMID:15504408</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/i6/2i6r_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=2i6r ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-I6R is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_o157:h7 Escherichia coli o157:h7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I6R OCA].
+*[[HypA%2C HypB%2C HypC%2C HypD%2C HypE and HypF 3D structures|HypA%2C HypB%2C HypC%2C HypD%2C HypE and HypF 3D structures]]
+== References ==
-==Reference==
+<references/>
-Structure of [NiFe]-Hydrogenase Maturation Protein HypE from Escherichia coli and its Interaction with HypF., Rangarajan ES, Asinas A, Proteau A, Munger C, Baardsnes J, Iannuzzi P, Matte A, Cygler M, J Bacteriol. 2007 Dec 7;. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=18065529 18065529]
+__TOC__
-[[Category: Escherichia coli o157:h7]]
+</StructureSection>
-[[Category: Single protein]]
+[[Category: Escherichia coli O157:H7]]
-[[Category: BSGI, Montreal-Kingston.Bacterial.Structural.Genomics.Initiative.]]
+[[Category: Large Structures]]
-[[Category: Cygler, M.]]
+[[Category: Cygler M]]
-[[Category: Iannuzzi, P.]]
+[[Category: Iannuzzi P]]
-[[Category: Matte, A.]]
+[[Category: Matte A]]
-[[Category: Proteau, A.]]
+[[Category: Proteau A]]
-[[Category: Rangarajan, E.S.]]
+[[Category: Rangarajan ES]]
-[[Category: bsgi]]
-[[Category: hydrogenase maturation protein]]
-[[Category: hype]]
-[[Category: montreal-kingston bacterial structural genomics initiative]]
-[[Category: structural genomics]]
-[[Category: unknown function]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 13 08:17:35 2008''