2bh4

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[[Image:2bh4.gif|left|200px]]<br /><applet load="2bh4" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2bh4, resolution 1.55&Aring;" />
 
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'''X-RAY STRUCTURE OF THE M100K VARIANT OF FERRIC CYT C-550 FROM PARACOCCUS VERSUTUS DETERMINED AT 100 K.'''<br />
 
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==Overview==
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==X-ray structure of the M100K variant of ferric cyt c-550 from Paracoccus versutus determined at 100 K.==
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The structure of cytochrome c-550 from the nonphotosynthetic bacteria, Paraccocus versutus has been solved by X-ray crystallography to 1.90 A, resolution, and reveals a high structural homology to other bacterial, cytochromes c(2). The effect of replacing the axial heme-iron methionine, ligand with a lysine residue on protein structure and unfolding has been, assessed using the M100K variant. From X-ray structures at 1.95 and 1.55 A, resolution it became clear that the amino group of the lysine side chain, coordinates to the heme-iron. Structural differences compared to the, wild-type protein are confined to the lysine ligand loop connecting, helices four and five. In the heme cavity an additional water molecule is, found which participates in an H-bonding interaction with the lysine, ligand. Under cryo-conditions extra electron density in the lysine ligand, loop is revealed, leading to residues K97 to T101 being modeled with a, double main-chain conformation. Upon unfolding, dissociation of the lysine, ligand from the heme-iron is shown to be pH dependent, with NMR data, consistent with the occurrence of a ligand exchange mechanism similar to, that seen for the wild-type protein.
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<StructureSection load='2bh4' size='340' side='right'caption='[[2bh4]], [[Resolution|resolution]] 1.55&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2bh4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Paracoccus_versutus Paracoccus versutus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BH4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BH4 FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.55&#8491;</td></tr>
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<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>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2bh4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bh4 OCA], [https://pdbe.org/2bh4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bh4 RCSB], [https://www.ebi.ac.uk/pdbsum/2bh4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bh4 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/CY550_PARVE CY550_PARVE]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bh/2bh4_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2bh4 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The structure of cytochrome c-550 from the nonphotosynthetic bacteria Paraccocus versutus has been solved by X-ray crystallography to 1.90 A resolution, and reveals a high structural homology to other bacterial cytochromes c(2). The effect of replacing the axial heme-iron methionine ligand with a lysine residue on protein structure and unfolding has been assessed using the M100K variant. From X-ray structures at 1.95 and 1.55 A resolution it became clear that the amino group of the lysine side chain coordinates to the heme-iron. Structural differences compared to the wild-type protein are confined to the lysine ligand loop connecting helices four and five. In the heme cavity an additional water molecule is found which participates in an H-bonding interaction with the lysine ligand. Under cryo-conditions extra electron density in the lysine ligand loop is revealed, leading to residues K97 to T101 being modeled with a double main-chain conformation. Upon unfolding, dissociation of the lysine ligand from the heme-iron is shown to be pH dependent, with NMR data consistent with the occurrence of a ligand exchange mechanism similar to that seen for the wild-type protein.
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==About this Structure==
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The effect of replacing the axial methionine ligand with a lysine residue in cytochrome c-550 from Paracoccus versutus assessed by X-ray crystallography and unfolding.,Worrall JA, van Roon AM, Ubbink M, Canters GW FEBS J. 2005 May;272(10):2441-55. PMID:15885094<ref>PMID:15885094</ref>
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2BH4 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Paracoccus_versutus Paracoccus versutus] with <scene name='pdbligand=HEC:'>HEC</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Known structural/functional Site: <scene name='pdbsite=AC1:Hec+Binding+Site+For+Chain+X'>AC1</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BH4 OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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The effect of replacing the axial methionine ligand with a lysine residue in cytochrome c-550 from Paracoccus versutus assessed by X-ray crystallography and unfolding., Worrall JA, van Roon AM, Ubbink M, Canters GW, FEBS J. 2005 May;272(10):2441-55. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15885094 15885094]
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</div>
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[[Category: Paracoccus versutus]]
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<div class="pdbe-citations 2bh4" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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[[Category: Canters, G.W.]]
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[[Category: Roon, A.M.M.Van.]]
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[[Category: Ubbink, M.]]
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[[Category: Worrall, J.A.R.]]
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[[Category: HEC]]
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[[Category: axial ligand]]
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[[Category: c-type cytochrome]]
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[[Category: electron transfer]]
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[[Category: heme]]
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[[Category: pyrrolidone carboxylic acid]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Feb 3 10:23:59 2008''
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==See Also==
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*[[Cytochrome C 3D structures|Cytochrome C 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Paracoccus versutus]]
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[[Category: Canters GW]]
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[[Category: Ubbink M]]
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[[Category: Van Roon A-MM]]
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[[Category: Worrall JAR]]

Current revision

X-ray structure of the M100K variant of ferric cyt c-550 from Paracoccus versutus determined at 100 K.

PDB ID 2bh4

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