1i6d: Difference between revisions
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< | ==SOLUTION STRUCTURE OF THE FUNCTIONAL DOMAIN OF PARACOCCUS DENITRIFICANS CYTOCHROME C552 IN THE REDUCED STATE== | ||
<StructureSection load='1i6d' size='340' side='right'caption='[[1i6d]]' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1i6d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Paracoccus_denitrificans Paracoccus denitrificans]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1I6D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1I6D FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR, 20 models</td></tr> | |||
-- | <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'>[https://proteopedia.org/fgij/fg.htm?mol=1i6d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1i6d OCA], [https://pdbe.org/1i6d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1i6d RCSB], [https://www.ebi.ac.uk/pdbsum/1i6d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1i6d ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/CY552_PARDE CY552_PARDE] | |||
== 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/i6/1i6d_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1i6d ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
A soluble and fully functional 10.5 kDa fragment of the 18.2 kDa membrane-bound cytochrome c(552) from Paracoccus denitrificans has been heterologously expressed and (13)C/(15)N-labeled to study the structural features of this protein in both redox states. Well-resolved solution structures of both the reduced and oxidized states have been determined using high-resolution heteronuclear NMR. The overall protein topology consists of two long terminal helices and three shorter helices surrounding the heme moiety. No significant redox-induced structural differences have been observed. (15)N relaxation rates and heteronuclear NOE values were determined at 500 and 600 MHz. Several residues located around the heme moiety display increased backbone mobility in both oxidation states, while helices I, III, and V as well as the two concatenated beta-turns between Leu30 and Arg36 apparently form a less flexible domain within the protein structure. Major redox-state-dependent differences of the internal backbone mobility on the picosecond-nanosecond time scale were not evident. Hydrogen exchange experiments demonstrated that the slow-exchanging amide proton resonances mainly belong to the helices and beta-turns, corresponding to the regions with high order parameters in the dynamics data. Despite this correlation, the backbone amide protons of the oxidized cytochrome c(552) exchange considerably faster with the solvent compared to the reduced protein. Using both differential scanning calorimetry as well as temperature-dependent NMR spectroscopy, a significant difference in the thermostabilities of the two redox states has been observed, with transition temperatures of 349.9 K (76.8 degrees C) for reduced and 307.5 K (34.4 degrees C) for oxidized cytochrome c(552). These results suggest a clearly distinct backbone stability between the two oxidation states. | |||
Solution structure and dynamics of the functional domain of Paracoccus denitrificans cytochrome c(552) in both redox states.,Reincke B, Perez C, Pristovsek P, Lucke C, Ludwig C, Lohr F, Rogov VV, Ludwig B, Ruterjans H Biochemistry. 2001 Oct 16;40(41):12312-20. PMID:11591150<ref>PMID:11591150</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1i6d" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Cytochrome c nitrite reductase|Cytochrome c nitrite reductase]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Large Structures]] | ||
== | |||
< | |||
[[Category: Paracoccus denitrificans]] | [[Category: Paracoccus denitrificans]] | ||
[[Category: Loehr | [[Category: Loehr F]] | ||
[[Category: Ludwig | [[Category: Ludwig B]] | ||
[[Category: Ludwig | [[Category: Ludwig C]] | ||
[[Category: Luecke | [[Category: Luecke C]] | ||
[[Category: Perez | [[Category: Perez C]] | ||
[[Category: Pristovsek | [[Category: Pristovsek P]] | ||
[[Category: Reincke | [[Category: Reincke B]] | ||
[[Category: Rogov | [[Category: Rogov VV]] | ||
[[Category: Rueterjans | [[Category: Rueterjans H]] | ||
Latest revision as of 07:36, 17 October 2024
SOLUTION STRUCTURE OF THE FUNCTIONAL DOMAIN OF PARACOCCUS DENITRIFICANS CYTOCHROME C552 IN THE REDUCED STATESOLUTION STRUCTURE OF THE FUNCTIONAL DOMAIN OF PARACOCCUS DENITRIFICANS CYTOCHROME C552 IN THE REDUCED STATE
Structural highlights
FunctionEvolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedA soluble and fully functional 10.5 kDa fragment of the 18.2 kDa membrane-bound cytochrome c(552) from Paracoccus denitrificans has been heterologously expressed and (13)C/(15)N-labeled to study the structural features of this protein in both redox states. Well-resolved solution structures of both the reduced and oxidized states have been determined using high-resolution heteronuclear NMR. The overall protein topology consists of two long terminal helices and three shorter helices surrounding the heme moiety. No significant redox-induced structural differences have been observed. (15)N relaxation rates and heteronuclear NOE values were determined at 500 and 600 MHz. Several residues located around the heme moiety display increased backbone mobility in both oxidation states, while helices I, III, and V as well as the two concatenated beta-turns between Leu30 and Arg36 apparently form a less flexible domain within the protein structure. Major redox-state-dependent differences of the internal backbone mobility on the picosecond-nanosecond time scale were not evident. Hydrogen exchange experiments demonstrated that the slow-exchanging amide proton resonances mainly belong to the helices and beta-turns, corresponding to the regions with high order parameters in the dynamics data. Despite this correlation, the backbone amide protons of the oxidized cytochrome c(552) exchange considerably faster with the solvent compared to the reduced protein. Using both differential scanning calorimetry as well as temperature-dependent NMR spectroscopy, a significant difference in the thermostabilities of the two redox states has been observed, with transition temperatures of 349.9 K (76.8 degrees C) for reduced and 307.5 K (34.4 degrees C) for oxidized cytochrome c(552). These results suggest a clearly distinct backbone stability between the two oxidation states. Solution structure and dynamics of the functional domain of Paracoccus denitrificans cytochrome c(552) in both redox states.,Reincke B, Perez C, Pristovsek P, Lucke C, Ludwig C, Lohr F, Rogov VV, Ludwig B, Ruterjans H Biochemistry. 2001 Oct 16;40(41):12312-20. PMID:11591150[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences |
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