2c1d

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of SoxXA from P. pantotrophus

Structural highlights

2c1d is a 8 chain structure with sequence from Paracoccus denitrificans and Paracoccus pantotrophus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.92Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SOXA_PARPN C-type diheme cytochrome, which is part of the SoxAX cytochrome complex involved in sulfur oxidation. The SoxAX complex catalyzes the formation of a heterodisulfide bond between the conserved cysteine residue on a sulfur carrier SoxYZ complex subunit SoxY and thiosulfate or other inorganic sulfur substrates. This leads to the liberation of two electrons, which may be transferred from the SoxAX complex to another cytochrome c that then channels them into the respiratory electron transport chain. Some electrons may be used for reductive CO(2) fixation.^[1] ^[2] ^[3]

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

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.

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^[4]

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

References

↑ Friedrich CG, Quentmeier A, Bardischewsky F, Rother D, Kraft R, Kostka S, Prinz H. Novel genes coding for lithotrophic sulfur oxidation of Paracoccus pantotrophus GB17. J Bacteriol. 2000 Sep;182(17):4677-87. PMID:10940005
↑ Dambe T, Quentmeier A, Rother D, Friedrich C, Scheidig AJ. Structure of the cytochrome complex SoxXA of Paracoccus pantotrophus, a heme enzyme initiating chemotrophic sulfur oxidation. J Struct Biol. 2005 Dec;152(3):229-34. Epub 2005 Nov 2. PMID:16297640 doi:10.1016/j.jsb.2005.09.002
↑ Reijerse EJ, Sommerhalter M, Hellwig P, Quentmeier A, Rother D, Laurich C, Bothe E, Lubitz W, Friedrich CG. The unusal redox centers of SoxXA, a novel c-type heme-enzyme essential for chemotrophic sulfur-oxidation of Paracoccus pantotrophus. Biochemistry. 2007 Jul 3;46(26):7804-10. Epub 2007 Jun 5. PMID:17547421 doi:http://dx.doi.org/10.1021/bi7003526
↑ Dambe T, Quentmeier A, Rother D, Friedrich C, Scheidig AJ. Structure of the cytochrome complex SoxXA of Paracoccus pantotrophus, a heme enzyme initiating chemotrophic sulfur oxidation. J Struct Biol. 2005 Dec;152(3):229-34. Epub 2005 Nov 2. PMID:16297640 doi:10.1016/j.jsb.2005.09.002

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2c1d"

@@ Line 1: / Line 1: @@
-==CRYSTAL STRUCTURE OF SOXXA FROM P. PANTOTROPHUS==
-<StructureSection load='2c1d' size='340' side='right' caption='[[2c1d]], [[Resolution|resolution]] 1.92&Aring;' scene=''>
+==Crystal structure of SoxXA from P. pantotrophus==
+<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 [http://en.wikipedia.org/wiki/Paracoccus_denitrificans Paracoccus denitrificans] and [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2C1D FirstGlance]. <br>
+<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><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><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><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSS:S-MERCAPTOCYSTEINE'>CSS</scene></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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2c1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c1d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2c1d RCSB], [http://www.ebi.ac.uk/pdbsum/2c1d PDBsum]</span></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>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SOXA_PARPN SOXA_PARPN] C-type diheme cytochrome, which is part of the SoxAX cytochrome complex involved in sulfur oxidation. The SoxAX complex catalyzes the formation of a heterodisulfide bond between the conserved cysteine residue on a sulfur carrier SoxYZ complex subunit SoxY and thiosulfate or other inorganic sulfur substrates. This leads to the liberation of two electrons, which may be transferred from the SoxAX complex to another cytochrome c that then channels them into the respiratory electron transport chain. Some electrons may be used for reductive CO(2) fixation.<ref>PMID:10940005</ref> <ref>PMID:16297640</ref> <ref>PMID:17547421</ref>
 == 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>
+    <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/initialview01.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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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;">
@@ Line 25: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2c1d" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Paracoccus denitrificans]]
 [[Category: Paracoccus pantotrophus]]
-[[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, A J.]]
+[[Category: Scheidig AJ]]
-[[Category: Cytochrome-c-type]]
-[[Category: Oxidoreductase]]
-[[Category: Sulfur oxidation]]

2c1d

From Proteopedia

Current revision

Crystal structure of SoxXA from P. pantotrophus

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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