3vym: Difference between revisions
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==Dimeric Hydrogenobacter thermophilus cytochrome c552== | ==Dimeric Hydrogenobacter thermophilus cytochrome c552== | ||
<StructureSection load='3vym' size='340' side='right' caption='[[3vym]], [[Resolution|resolution]] 2.00Å' scene=''> | <StructureSection load='3vym' size='340' side='right'caption='[[3vym]], [[Resolution|resolution]] 2.00Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3vym]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3vym]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Hydrogenobacter_thermophilus_TK-6 Hydrogenobacter thermophilus TK-6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VYM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VYM FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEC:HEME+C'>HEC</scene></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3vym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vym OCA], [https://pdbe.org/3vym PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vym RCSB], [https://www.ebi.ac.uk/pdbsum/3vym PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vym ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/CY552_HYDTT CY552_HYDTT] Reacts with hydrogenase. | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 3vym" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[ | *[[Cytochrome c nitrite reductase|Cytochrome c nitrite reductase]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Hydrogenobacter thermophilus | [[Category: Hydrogenobacter thermophilus TK-6]] | ||
[[Category: Hayashi | [[Category: Large Structures]] | ||
[[Category: Higuchi | [[Category: Hayashi Y]] | ||
[[Category: Hirota | [[Category: Higuchi Y]] | ||
[[Category: Komori | [[Category: Hirota S]] | ||
[[Category: Nagao | [[Category: Komori H]] | ||
[[Category: Osuka | [[Category: Nagao S]] | ||
[[Category: Osuka H]] | |||
Latest revision as of 11:13, 9 October 2024
Dimeric Hydrogenobacter thermophilus cytochrome c552Dimeric Hydrogenobacter thermophilus cytochrome c552
Structural highlights
FunctionCY552_HYDTT Reacts with hydrogenase. Publication Abstract from PubMedOxidized horse cytochrome c (cyt c) has been shown to oligomerize by domain swapping its C-terminal helix successively. We show that the structural and thermodynamic properties of dimeric Hydrogenobacter thermophilus (HT) cytochrome c(552) (cyt c(552)) and dimeric horse cyt c are different, although both proteins belong to the cyt c superfamily. Optical absorption and circular dichroism spectra of oxidized dimeric HT cyt c(552) were identical to the corresponding spectra of its monomer. Dimeric HT cyt c(552) exhibited a domain-swapped structure, where the N-terminal alpha-helix together with the heme was exchanged between protomers. Since a relatively strong H-bond network was formed at the loop around the heme-coordinating Met, the C-terminal alpha-helix did not dissociate from the rest of the protein in dimeric HT cyt c(552). The packing of the amino acid residues important for thermostability in monomeric HT cyt c(552) were maintained in its dimer, and thus, dimeric HT cyt c(552) exhibited high thermostability. Although the midpoint redox potential shifted from 240 +/- 2 to 213 +/- 2 mV by dimerization, it was maintained relatively high. Ethanol has been shown to decrease both the activation enthalpy and activation entropy for the dissociation of the dimer to monomers from 140 +/- 9 to 110 +/- 5 kcal/mol and 310 +/- 30 to 270 +/- 20 cal/(mol.K), respectively. Enthalpy change for the dissociation of the dimer to monomers was positive (14 +/- 2 kcal/mol per protomer unit). These results give new insights into factors governing the swapping region and thermodynamic properties of domain swapping. Domain Swapping of the Heme and N-Terminal alpha-Helix in Hydrogenobacter thermophilus Cytochrome c(552) Dimer.,Hayashi Y, Nagao S, Osuka H, Komori H, Higuchi Y, Hirota S Biochemistry. 2012 Oct 18. PMID:23035813[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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