1rhc: Difference between revisions

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-[[Image:1rhc.jpg|left|200px]]<br /><applet load="1rhc" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="1rhc, resolution 1.80&Aring;" />
-'''F420-dependent secondary alcohol dehydrogenase in complex with an F420-acetone adduct'''<br />
-==Overview==
+==F420-dependent secondary alcohol dehydrogenase in complex with an F420-acetone adduct==
-F(420)-dependent secondary alcohol dehydrogenase (Adf) from methanogenic archaea is a member of the growing bacterial luciferase family which are all TIM barrel enzymes, most of which with an unusual nonprolyl cis peptide bond. We report here on the crystal structure of Adf from Methanoculleus thermophilicus at 1.8 A resolution in complex with a F(420)-acetone adduct. The knowledge of the F(420) binding mode in Adf provides the molecular basis for modeling F(420) and FMN into the other enzymes of the family. A nonprolyl cis peptide bond was identified as an essential part of a bulge that serves as backstop at the Re-face of F(420) to keep it in a bent conformation. The acetone moiety of the F(420)-acetone adduct is positioned at the Si-face of F(420) deeply buried inside the protein. Isopropanol can be reliably modeled and a hydrogen transfer mechanism postulated. His39 and Glu108 can be identified as key players for binding of the acetone or isopropanol oxygens and for catalysis.
+<StructureSection load='1rhc' size='340' side='right'caption='[[1rhc]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1rhc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanoculleus_thermophilus Methanoculleus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RHC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RHC 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]] 1.8&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACN:ACETONE'>ACN</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=F42:COENZYME+F420'>F42</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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=1rhc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rhc OCA], [https://pdbe.org/1rhc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rhc RCSB], [https://www.ebi.ac.uk/pdbsum/1rhc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rhc ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/O93734_9EURY O93734_9EURY]
+== 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/rh/1rhc_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=1rhc ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-RHC is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Methanoculleus_thermophilus Methanoculleus thermophilus] with <scene name='pdbligand=CL:'>CL</scene>, <scene name='pdbligand=K:'>K</scene>, <scene name='pdbligand=F42:'>F42</scene> and <scene name='pdbligand=ACN:'>ACN</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RHC OCA].
+*[[Alcohol dehydrogenase 3D structures|Alcohol dehydrogenase 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-Coenzyme binding in F420-dependent secondary alcohol dehydrogenase, a member of the bacterial luciferase family., Aufhammer SW, Warkentin E, Berk H, Shima S, Thauer RK, Ermler U, Structure. 2004 Mar;12(3):361-70. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15016352 15016352]
+[[Category: Large Structures]]
 [[Category: Methanoculleus thermophilus]]
-[[Category: Single protein]]
+[[Category: Aufhammer SW]]
-[[Category: Aufhammer, S W.]]
+[[Category: Berk H]]
-[[Category: Berk, H.]]
+[[Category: Ermler U]]
-[[Category: Ermler, U.]]
+[[Category: Shima S]]
-[[Category: Shima, S.]]
+[[Category: Thauer RK]]
-[[Category: Thauer, R K.]]
+[[Category: Warkentin E]]
-[[Category: Warkentin, E.]]
-[[Category: ACN]]
-[[Category: CL]]
-[[Category: F42]]
-[[Category: K]]
-[[Category: (alpha]]
-[[Category: beta)8 barrel]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:50:56 2008''