1ls9: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,330,058 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,330,058 edits
No edit summary
 
(8 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1ls9.png|left|200px]]


{{STRUCTURE_1ls9| PDB=1ls9 | SCENE= }}
==Structure of the Cytochrome c6 from the Green Alga Cladophora glomerata==
<StructureSection load='1ls9' size='340' side='right'caption='[[1ls9]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1ls9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cladophora_glomerata Cladophora glomerata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LS9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LS9 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]] 1.3&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=1ls9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ls9 OCA], [https://pdbe.org/1ls9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ls9 RCSB], [https://www.ebi.ac.uk/pdbsum/1ls9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ls9 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/CYC6_CLAGO CYC6_CLAGO]
== 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/ls/1ls9_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=1ls9 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
This is a thorough biochemical, spectroscopic, electrochemical, and structural study of a cytochrome c(6) isolated from the filamentous green alga Cladophora glomerata. The protein sequence, elucidated using chemical and mass spectrometric techniques, features 91 amino acids and the characteristic CXXCH heme-binding motif found in c-type cytochromes. The protein is monomeric in both oxidation forms, thereby putting in question a functional role for protein dimerization. Direct electrochemical measurements established, for the first time, the kinetic and thermodynamic data for the redox process in a cytochrome c(6). In particular, the quasi-reversible and diffusion-controlled redox process is accompanied by negative enthalpy and entropy changes, resulting in an E degrees ' value of 0.352 V at 298 K. The pH-dependent properties of the oxidized protein, detected by UV-visible, NMR, and direct cyclic voltammetry, indicate the presence of two acid-base equilibria occurring in the acidic (pK(a) = 4.5) and alkaline regions (pK(a) = 9.0). NMR and electronic spectra allowed the assignment of these equilibria to deprotonation of heme propionate-7 and to replacement of the axial methionine with another ligand, respectively. The 1.3 A resolution X-ray structure of the oxidized protein, revealing a fold typical for class I cytochromes, suggests that the conserved Lys60 replaces the axial methionine at pH &gt;9. The heme solvent accessibility is low, and no water molecules were found in the vicinity of the axial ligands of the heme Fe. A structure-based alignment of cytochromes c(6), and the direct comparison of their structures, indicate a substantial degree of identity between the tertiary structures and suggest patches involved in protein-protein interaction. In particular, the surface electrostatic potential of cytochromes c(6) features a hydrophobic region around the heme cofactor, and a backside surface rich in negative charges.


===Structure of the Cytochrome c6 from the Green Alga Cladophora glomerata===
Structural basis for the molecular properties of cytochrome c6.,Dikiy A, Carpentier W, Vandenberghe I, Borsari M, Safarov N, Dikaya E, Van Beeumen J, Ciurli S Biochemistry. 2002 Dec 17;41(50):14689-99. PMID:12475218<ref>PMID:12475218</ref>


{{ABSTRACT_PUBMED_12475218}}
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
</div>
==About this Structure==
<div class="pdbe-citations 1ls9" style="background-color:#fffaf0;"></div>
[[1ls9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cladophora_glomerata Cladophora glomerata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LS9 OCA].
== References ==
 
<references/>
==See Also==
__TOC__
*[[Cytochrome c|Cytochrome c]]
</StructureSection>
 
==Reference==
<ref group="xtra">PMID:012475218</ref><references group="xtra"/>
[[Category: Cladophora glomerata]]
[[Category: Cladophora glomerata]]
[[Category: Carpentier, W.]]
[[Category: Large Structures]]
[[Category: Antiparallel beta-sheet]]
[[Category: Carpentier W]]
[[Category: Cytochrome]]
[[Category: Electron transport]]
[[Category: Haem]]
[[Category: Heme]]
[[Category: Omega loop]]
[[Category: Protoporphyrin ix containing fe]]
Retrieved from "https://proteopedia.org/1ls9"