2c1d: Difference between revisions

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[[Image:2c1d.gif|left|200px]]<br />
<applet load="2c1d" size="450" color="white" frame="true" align="right" spinBox="true"
caption="2c1d, resolution 1.92&Aring;" />
'''CRYSTAL STRUCTURE OF SOXXA FROM P. PANTOTROPHUS'''<br />


==Overview==
==Crystal structure of SoxXA from P. pantotrophus==
The sulfur-oxidizing enzyme system (Sox) of the chemotroph Paracoccus, pantotrophus is composed of several proteins, which together oxidize, hydrogen sulfide, sulfur, thiosulfate or sulfite and transfers the gained, electrons to the respiratory chain. The hetero-dimeric cytochrome c, complex SoxXA functions as heme enzyme and links covalently the sulfur, substrate to the thiol of the cysteine-138 residue of the SoxY protein of, the SoxYZ complex. Here, we report the crystal structure of the c-type, cytochrome complex SoxXA. The structure could be solved by molecular, replacement and refined to a resolution of 1.9A identifying the axial, heme-iron coordination involving an unusual Cys-251 thiolate of heme2., Distance measurements between the three heme groups provide deeper insight, into ... [[http://ispc.weizmann.ac.il/pmbin/getpm?16297640 (full description)]]
<StructureSection load='2c1d' size='340' side='right'caption='[[2c1d]], [[Resolution|resolution]] 1.92&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2c1d]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Paracoccus_denitrificans Paracoccus denitrificans] and [https://en.wikipedia.org/wiki/Paracoccus_pantotrophus Paracoccus pantotrophus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C1D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C1D 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]] 1.92&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSS:S-MERCAPTOCYSTEINE'>CSS</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=2c1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c1d OCA], [https://pdbe.org/2c1d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c1d RCSB], [https://www.ebi.ac.uk/pdbsum/2c1d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c1d ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q9LCV0_PARDE Q9LCV0_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/c1/2c1d_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=2c1d ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The sulfur-oxidizing enzyme system (Sox) of the chemotroph Paracoccus pantotrophus is composed of several proteins, which together oxidize hydrogen sulfide, sulfur, thiosulfate or sulfite and transfers the gained electrons to the respiratory chain. The hetero-dimeric cytochrome c complex SoxXA functions as heme enzyme and links covalently the sulfur substrate to the thiol of the cysteine-138 residue of the SoxY protein of the SoxYZ complex. Here, we report the crystal structure of the c-type cytochrome complex SoxXA. The structure could be solved by molecular replacement and refined to a resolution of 1.9A identifying the axial heme-iron coordination involving an unusual Cys-251 thiolate of heme2. Distance measurements between the three heme groups provide deeper insight into the electron transport inside SoxXA and merge in a better understanding of the initial step of the aerobic sulfur oxidation process in chemotrophic bacteria.


==About this Structure==
Structure of the cytochrome complex SoxXA of Paracoccus pantotrophus, a heme enzyme initiating chemotrophic sulfur oxidation.,Dambe T, Quentmeier A, Rother D, Friedrich C, Scheidig AJ J Struct Biol. 2005 Dec;152(3):229-34. Epub 2005 Nov 2. PMID:16297640<ref>PMID:16297640</ref>
2C1D is a [[http://en.wikipedia.org/wiki/Protein_complex Protein complex]] structure of sequences from [[http://en.wikipedia.org/wiki/Paracoccus_denitrificans Paracoccus denitrificans]] and [[http://en.wikipedia.org/wiki/Paracoccus_pantotrophus Paracoccus pantotrophus]] with ZN and HEC as [[http://en.wikipedia.org/wiki/ligands ligands]]. Structure known Active Site: AC1. Full crystallographic information is available from [[http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2C1D OCA]].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Structure of the cytochrome complex SoxXA of Paracoccus pantotrophus, a heme enzyme initiating chemotrophic sulfur oxidation., Dambe T, Quentmeier A, Rother D, Friedrich C, Scheidig AJ, J Struct Biol. 2005 Dec;152(3):229-34. Epub 2005 Nov 2. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16297640 16297640]
</div>
<div class="pdbe-citations 2c1d" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Paracoccus denitrificans]]
[[Category: Paracoccus denitrificans]]
[[Category: Paracoccus pantotrophus]]
[[Category: Paracoccus pantotrophus]]
[[Category: Protein complex]]
[[Category: Dambe T]]
[[Category: Dambe, T.]]
[[Category: Friedrich C]]
[[Category: Friedrich, C.]]
[[Category: Quentmeier A]]
[[Category: Quentmeier, A.]]
[[Category: Rother D]]
[[Category: Rother, D.]]
[[Category: Scheidig AJ]]
[[Category: Scheidig, A.J.]]
[[Category: HEC]]
[[Category: ZN]]
[[Category: cytochrome-c-type]]
[[Category: oxidoreductase]]
[[Category: sulfur oxidation]]
 
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Retrieved from "https://proteopedia.org/2c1d"