1fvx: Difference between revisions

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 <StructureSection load='1fvx' size='340' side='right'caption='[[1fvx]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1fvx]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"clostridium_rubrum"_ng_and_vaughn_1963 "clostridium rubrum" ng and vaughn 1963]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FVX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1FVX FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1fvx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_beijerinckii Clostridium beijerinckii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FVX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FVX FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1fvx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fvx OCA], [http://pdbe.org/1fvx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1fvx RCSB], [http://www.ebi.ac.uk/pdbsum/1fvx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1fvx ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</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=1fvx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fvx OCA], [https://pdbe.org/1fvx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fvx RCSB], [https://www.ebi.ac.uk/pdbsum/1fvx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fvx ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/FLAV_CLOBE FLAV_CLOBE]] Low-potential electron donor to a number of redox enzymes.
+[https://www.uniprot.org/uniprot/FLAV_CLOBE FLAV_CLOBE] Low-potential electron donor to a number of redox enzymes.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
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 </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=1fvx ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-X-ray analyses of wild-type and mutant flavodoxins from Clostridium beijerinckii show that the conformation of the peptide Gly57-Asp58, in a bend near the isoalloxazine ring of FMN, is correlated with the oxidation state of the FMN prosthetic group. The Gly-Asp peptide may adopt any of three conformations: trans O-up, in which the carbonyl oxygen of Gly57 (O57) points toward the flavin ring; trans O-down, in which O57 points away from the flavin; and cis O-down. Interconversions among these conformers that are linked to oxidation-reduction of the flavin can modulate the redox potentials of bound FMN. In the semiquinone and reduced forms of the protein, the Gly57-Asp58 peptide adopts the trans O-up conformation and accepts a hydrogen bond from the flavin N5H [Smith, W. W., Burnett, R. M., Darling, G. D., &amp; Ludwig, M. L. (1977) J. Mol. Biol. 117, 195-225; Ludwig, M. L., &amp; Luschinsky, C. L. (1992) in Chemistry and Biochemistry of Flavoenzymes III (Muller, F., Ed.) pp 427-466, CRC Press, Boca Raton, FL]. Analyses reported in this paper confirm that, in crystals of wild-type oxidized C. beijerinckii flavodoxin, the Gly57-Asp58 peptide adopts the O-down orientation and isomerizes to the cis conformation. This cis form is preferentially stabilized in the crystals by intermolecular hydrogen bonding to Asn137. Structures for the mutant Asn137Ala indicate that a mixture of all three conformers, mostly O-down, exists in oxidized C. beijerinckii flavodoxin in the absence of intermolecular hydrogen bonds. Redox potentials have been manipulated by substitutions that alter the conformational energies of the bend at 56M-G-D-E. The mutation Asp58Pro was constructed to study a case where energies for cis-trans conversion would be different from that of wild type. Intermolecular interactions with Asn137 are precluded in the crystal, yet Gly57-Pro58 is cis, and O-down, when the flavin is oxidized. Reduction of the flavin induces rearrangement to the trans O-up conformation. Redox potential shifts reflect the altered energies associated with the peptide rearrangement; E(ox/sq) decreases by approximately 60 mV (1.3 kcal/mol). Further, the results of mutation of Gly57 agree with predictions that a side chain at residue 57 should make addition of the first electron more difficult, by raising the energy of the O-up conformer that forms when the flavin is reduced to its semiquinone state. The ox/sq potentials in the mutants Gly57Ala, Gly57Asn, and Gly57Asp are all decreased by approximately 60 mV (1.3 kcal/mol). Introduction of the beta-branched threonine side chain at position 57 has much larger effects on the conformations and potentials. The Thr57-Asp58 peptide adopts a trans O-down conformation when the flavin is oxidized; upon reduction to the semiquinone, the 57-58 peptide rotates to a trans O-up conformation resembling that found in the wild-type protein. Changes in FMN-protein interactions and in conformational equilibria in G57T combine to decrease the redox potential for the ox/sq equilibrium by 180 mV (+4.0 kcal/mol) and to increase the sq/hq potential by 80 mV (-1.7 kcal/mol). A thermodynamic scheme is introduced as a framework for rationalizing the properties of wild-type flavodoxin and the effects of the mutations.
-Control of oxidation-reduction potentials in flavodoxin from Clostridium beijerinckii: the role of conformation changes.,Ludwig ML, Pattridge KA, Metzger AL, Dixon MM, Eren M, Feng Y, Swenson RP Biochemistry. 1997 Feb 11;36(6):1259-80. PMID:9063874<ref>PMID:9063874</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1fvx" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[Flavodoxin 3D structures|Flavodoxin 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Clostridium rubrum ng and vaughn 1963]]
+[[Category: Clostridium beijerinckii]]
 [[Category: Large Structures]]
-[[Category: Dixon, M M]]
+[[Category: Dixon MM]]
-[[Category: Eren, M]]
+[[Category: Eren M]]
-[[Category: Feng, Y]]
+[[Category: Feng Y]]
-[[Category: Ludwig, M L]]
+[[Category: Ludwig ML]]
-[[Category: Metzger, A L]]
+[[Category: Metzger AL]]
-[[Category: Pattridge, K A]]
+[[Category: Pattridge KA]]
-[[Category: Swenson, R]]
+[[Category: Swenson R]]
-[[Category: Electron transport]]
-[[Category: Flavoprotein]]
-[[Category: Fmn]]