1i6d

From Proteopedia

(Difference between revisions)

Current revision

SOLUTION STRUCTURE OF THE FUNCTIONAL DOMAIN OF PARACOCCUS DENITRIFICANS CYTOCHROME C552 IN THE REDUCED STATE

Structural highlights

1i6d is a 1 chain structure with sequence from Paracoccus denitrificans. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR, 20 models
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CY552_PARDE

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Reincke B, Perez C, Pristovsek P, Lucke C, Ludwig C, Lohr F, Rogov VV, Ludwig B, Ruterjans H. Solution structure and dynamics of the functional domain of Paracoccus denitrificans cytochrome c(552) in both redox states. Biochemistry. 2001 Oct 16;40(41):12312-20. PMID:11591150

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1i6d"

@@ Line 1: / Line 1: @@
 ==SOLUTION STRUCTURE OF THE FUNCTIONAL DOMAIN OF PARACOCCUS DENITRIFICANS CYTOCHROME C552 IN THE REDUCED STATE==
-<StructureSection load='1i6d' size='340' side='right'caption='[[1i6d]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='1i6d' size='340' side='right'caption='[[1i6d]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1i6d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_17741 Atcc 17741]. 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>
+<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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEC:HEME+C'>HEC</scene></td></tr>
+</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1i6e|1i6e]], [[1ql3|1ql3]], [[1ql4|1ql4]], [[1c7m|1c7m]]</div></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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CYCM ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266 ATCC 17741])</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]]
@@ Line 14: / Line 15: @@
   <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/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 35: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 17741]]
 [[Category: Large Structures]]
-[[Category: Loehr, F]]
+[[Category: Paracoccus denitrificans]]
-[[Category: Ludwig, B]]
+[[Category: Loehr F]]
-[[Category: Ludwig, C]]
+[[Category: Ludwig B]]
-[[Category: Luecke, C]]
+[[Category: Ludwig C]]
-[[Category: Perez, C]]
+[[Category: Luecke C]]
-[[Category: Pristovsek, P]]
+[[Category: Perez C]]
-[[Category: Reincke, B]]
+[[Category: Pristovsek P]]
-[[Category: Rogov, V V]]
+[[Category: Reincke B]]
-[[Category: Rueterjans, H]]
+[[Category: Rogov VV]]
-[[Category: Cytochrome c552]]
+[[Category: Rueterjans H]]
-[[Category: Electron transport]]
-[[Category: Heme]]
-[[Category: Isotope enrichment {13c/15n}]]
-[[Category: Nmr spectroscopy]]
-[[Category: Redox state]]
-[[Category: Solution structure]]

1i6d

From Proteopedia

Current revision

SOLUTION STRUCTURE OF THE FUNCTIONAL DOMAIN OF PARACOCCUS DENITRIFICANS CYTOCHROME C552 IN THE REDUCED STATE

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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