1kqf: Difference between revisions

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OCA

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-[[Image:1kqf.gif|left|200px]]<br /><applet load="1kqf" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1kqf, resolution 1.60&Aring;" />
-'''FORMATE DEHYDROGENASE N FROM E. COLI'''<br />
-==Overview==
+==FORMATE DEHYDROGENASE N FROM E. COLI==
-The structure of the membrane protein formate dehydrogenase-N (Fdn-N), a, major component of Escherichia coli nitrate respiration, has been, determined at 1.6 angstroms. The structure demonstrates 11 redox centers, including molybdopterin-guanine dinucleotides, five [4Fe-4S] clusters, two, heme b groups, and a menaquinone analog. These redox centers are aligned, in a single chain, which extends almost 90 angstroms through the enzyme., The menaquinone reduction site associated with a possible proton pathway, was also characterized. This structure provides critical insights into the, proton motive force generation by redox loop, a common mechanism among a, wide range of respiratory enzymes.
+<StructureSection load='1kqf' size='340' side='right'caption='[[1kqf]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1kqf]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KQF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KQF 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]] 1.6&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6MO:MOLYBDENUM(VI)+ION'>6MO</scene>, <scene name='pdbligand=CDL:CARDIOLIPIN'>CDL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MGD:2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE+GUANOSINE+DINUCLEOTIDE'>MGD</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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=1kqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kqf OCA], [https://pdbe.org/1kqf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kqf RCSB], [https://www.ebi.ac.uk/pdbsum/1kqf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kqf ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/FDNG_ECOLI FDNG_ECOLI] Formate dehydrogenase allows E.coli to use formate as major electron donor during anaerobic respiration, when nitrate is used as electron acceptor. The alpha subunit FdnG contains the formate oxidation site. Electrons are transferred from formate to menaquinone in the gamma subunit (FdnI), through the 4Fe-4S clusters in the beta subunit (FdnH). Formate dehydrogenase-N is part of a system that generates proton motive force, together with the dissimilatory nitrate reductase (Nar).<ref>PMID:11884747</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/kq/1kqf_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=1kqf ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-KQF is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with 6MO, SF4, MGD, HEM and CDL as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Formate_dehydrogenase Formate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.2 1.2.1.2] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1KQF OCA].
+*[[Formate dehydrogenase 3D structures|Formate dehydrogenase 3D structures]]
+== References ==
-==Reference==
+<references/>
-Molecular basis of proton motive force generation: structure of formate dehydrogenase-N., Jormakka M, Tornroth S, Byrne B, Iwata S, Science. 2002 Mar 8;295(5561):1863-8. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11884747 11884747]
+__TOC__
+</StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Formate dehydrogenase]]
+[[Category: Large Structures]]
-[[Category: Protein complex]]
+[[Category: Byrne B]]
-[[Category: Byrne, B.]]
+[[Category: Iwata S]]
-[[Category: Iwata, S.]]
+[[Category: Jormakka M]]
-[[Category: Jormakka, M.]]
+[[Category: Tornroth S]]
-[[Category: Tornroth, S.]]
-[[Category: 6MO]]
-[[Category: CDL]]
-[[Category: HEM]]
-[[Category: MGD]]
-[[Category: SF4]]
-[[Category: anaerobic]]
-[[Category: dehydrogenase]]
-[[Category: fe4s4]]
-[[Category: formate]]
-[[Category: integral membrane protein]]
-[[Category: iron sulfur cluster]]
-[[Category: mgd]]
-[[Category: molybdenum]]
-[[Category: molybdopterin]]
-[[Category: molybdopterin guanine dinucleotide]]
-[[Category: mpt]]
-[[Category: oxidoreductase]]
-[[Category: secys]]
-[[Category: selenium]]
-[[Category: selenocysteine]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 19:38:53 2007''