2vkr: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,613 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,613 edits
No edit summary
 
(13 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{Seed}}
[[Image:2vkr.png|left|200px]]


<!--
==3Fe-4S, 4Fe-4S plus Zn Acidianus ambivalens ferredoxin==
The line below this paragraph, containing "STRUCTURE_2vkr", creates the "Structure Box" on the page.
<StructureSection load='2vkr' size='340' side='right'caption='[[2vkr]], [[Resolution|resolution]] 2.01&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[2vkr]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Acidianus_ambivalens Acidianus ambivalens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VKR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VKR FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.01&#8491;</td></tr>
-->
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
{{STRUCTURE_2vkr|  PDB=2vkr  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vkr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vkr OCA], [https://pdbe.org/2vkr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vkr RCSB], [https://www.ebi.ac.uk/pdbsum/2vkr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vkr ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/FER_ACIAM FER_ACIAM] Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions. The 3Fe-4S cluster is reduced by a flavoprotein with NADH oxidase activity from the same organism.
== 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/vk/2vkr_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=2vkr ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Detailed structural models of di-cluster seven-iron ferredoxins constitute a valuable resource for folding and stability studies relating the metal cofactors' role in protein stability. The here reported, hemihedric twinned crystal structure at 2.0 A resolution from Acidianus ambivalens ferredoxin, shows an integral 103 residues, physiologically relevant native form composed by a N-terminal extension comprising a His/Asp Zn(2+) site and the ferredoxin (betaalphabeta)(2) core, which harbours intact clusters I and II, a [3Fe-4S](1+/0) and a [4Fe-4S](2+/1+) centres. This is in contrast with the previously available ferredoxin structure from Sulfolofus tokodai, which was obtained from an artificial oxidative conversion with two [3Fe-4S](1+/0) centres and poor definition around cluster II.


===3FE-4S, 4FE-4S PLUS ZN ACIDIANUS AMBIVALENS FERREDOXIN===
Crystallographic analysis of the intact metal centres [3Fe-4S](1+/0) and [4Fe-4S](2+/1+) in a Zn(2+) -containing ferredoxin.,Frazao C, Aragao D, Coelho R, Leal SS, Gomes CM, Teixeira M, Carrondo MA FEBS Lett. 2008 Mar 5;582(5):763-7. Epub 2008 Feb 5. PMID:18258200<ref>PMID:18258200</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2vkr" style="background-color:#fffaf0;"></div>


<!--
==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_18258200}}, adds the Publication Abstract to the page
*[[Ferredoxin 3D structures|Ferredoxin 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 18258200 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_18258200}}
__TOC__
 
</StructureSection>
==About this Structure==
2VKR is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Acidianus_ambivalens Acidianus ambivalens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VKR OCA].
 
==Reference==
Crystallographic analysis of the intact metal centres [3Fe-4S](1+/0) and [4Fe-4S](2+/1+) in a Zn(2+)-containing ferredoxin., Frazao C, Aragao D, Coelho R, Leal SS, Gomes CM, Teixeira M, Carrondo MA, FEBS Lett. 2008 Mar 5;582(5):763-7. Epub 2008 Feb 5. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18258200 18258200]
 
A spectroscopic study of the temperature induced modifications on ferredoxin folding and iron-sulfur moieties., Todorovic S, Leal SS, Salgueiro CA, Zebger I, Hildebrandt P, Murgida DH, Gomes CM, Biochemistry. 2007 Sep 18;46(37):10733-8. Epub 2007 Aug 16. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17696500 17696500]
 
Natural domain design: enhanced thermal stability of a zinc-lacking ferredoxin isoform shows that a hydrophobic core efficiently replaces the structural metal site., Rocha R, Leal SS, Teixeira VH, Regalla M, Huber H, Baptista AM, Soares CM, Gomes CM, Biochemistry. 2006 Aug 29;45(34):10376-84. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16922514 16922514]
 
A seven-iron ferredoxin from the thermoacidophilic archaeon Desulfurolobus ambivalens., Teixeira M, Batista R, Campos AP, Gomes C, Mendes J, Pacheco I, Anemuller S, Hagen WR, Eur J Biochem. 1995 Jan 15;227(1-2):322-7. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/7851403 7851403]
[[Category: Acidianus ambivalens]]
[[Category: Acidianus ambivalens]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Aragao, D.]]
[[Category: Aragao D]]
[[Category: Carrondo, M A.]]
[[Category: Carrondo MA]]
[[Category: Coelho, R.]]
[[Category: Coelho R]]
[[Category: Frazao, C.]]
[[Category: Frazao C]]
[[Category: Gomes, C M.]]
[[Category: Gomes CM]]
[[Category: Leal, S S.]]
[[Category: Leal SS]]
[[Category: Teixeira, M.]]
[[Category: Teixeira M]]
[[Category: 3fe-4]]
[[Category: 4fe-4]]
[[Category: Electron transport]]
[[Category: Ferredoxin]]
[[Category: Hemihedric twinnig]]
[[Category: Iron]]
[[Category: Iron-sulfur]]
[[Category: Iron-sulfur protein]]
[[Category: Metal-binding]]
[[Category: Methylation]]
[[Category: Protein folding]]
[[Category: Thermophile]]
[[Category: Thermostable protein]]
[[Category: Transport]]
[[Category: Zinc]]
[[Category: Zn center]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 05:19:45 2008''
Retrieved from "https://proteopedia.org/2vkr"