3p63: Difference between revisions

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-{{STRUCTURE_3p63|  PDB=3p63  |  SCENE=  }}
+==Structure of M. laminosus Ferredoxin with a shorter L1,2 loop==
-===Structure of M. laminosus Ferredoxin with a shorter L1,2 loop===
+<StructureSection load='3p63' size='340' side='right' caption='[[3p63]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
-{{ABSTRACT_PUBMED_21266547}}
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3p63]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mastigocladus_laminosus Mastigocladus laminosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3P63 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3P63 FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene></td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1frk|1frk]], [[1qt9|1qt9]], [[4fxc|4fxc]], [[1off|1off]], [[1a70|1a70]]</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">petF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83541 Mastigocladus laminosus])</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3p63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3p63 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3p63 RCSB], [http://www.ebi.ac.uk/pdbsum/3p63 PDBsum]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Regulation of protein function via cracking, or local unfolding and refolding of substructures, is becoming a widely recognized mechanism of functional control. Oftentimes, cracking events are localized to secondary and tertiary structure interactions between domains that control the optimal position for catalysis and/or the formation of protein complexes. Small changes in free energy associated with ligand binding, phosphorylation, etc., can tip the balance and provide a regulatory functional switch. However, understanding the factors controlling function in single-domain proteins is still a significant challenge to structural biologists. We investigated the functional landscape of a single-domain plant-type ferredoxin protein and the effect of a distal loop on the electron-transfer center. We find the global stability and structure are minimally perturbed with mutation, whereas the functional properties are altered. Specifically, truncating the L1,2 loop does not lead to large-scale changes in the structure, determined via X-ray crystallography. Further, the overall thermal stability of the protein is only marginally perturbed by the mutation. However, even though the mutation is distal to the iron-sulfur cluster ( approximately 20 A), it leads to a significant change in the redox potential of the iron-sulfur cluster (57 mV). Structure-based all-atom simulations indicate correlated dynamical changes between the surface-exposed loop and the iron-sulfur cluster-binding region. Our results suggest intrinsic communication channels within the ferredoxin fold, composed of many short-range interactions, lead to the propagation of long-range signals. Accordingly, protein interface interactions that involve L1,2 could potentially signal functional changes in distal regions, similar to what is observed in other allosteric systems.
-==Function==
+Allostery in the ferredoxin protein motif does not involve a conformational switch.,Nechushtai R, Lammert H, Michaeli D, Eisenberg-Domovich Y, Zuris JA, Luca MA, Capraro DT, Fish A, Shimshon O, Roy M, Schug A, Whitford PC, Livnah O, Onuchic JN, Jennings PA Proc Natl Acad Sci U S A. 2011 Jan 25. PMID:21266547<ref>PMID:21266547</ref>
-[[http://www.uniprot.org/uniprot/FER_MASLA FER_MASLA]] Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[3p63]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mastigocladus_laminosus Mastigocladus laminosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3P63 OCA].
+</div>
 ==See Also==
 *[[Ferredoxin|Ferredoxin]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:021266547</ref><references group="xtra"/><references/>
+__TOC__
+</StructureSection>
 [[Category: Mastigocladus laminosus]]
-[[Category: Eisenberg-Domovich, Y.]]
+[[Category: Eisenberg-Domovich, Y]]
-[[Category: Livnah, O.]]
+[[Category: Livnah, O]]
-[[Category: Michaeli, D.]]
+[[Category: Michaeli, D]]
-[[Category: Nechushtai, R.]]
+[[Category: Nechushtai, R]]
-[[Category: 2 loop into a beta-turn]]
+[[Category: Loop into a beta-turn]]
 [[Category: Beta-grasp fold]]
 [[Category: Concerting the l1]]