1d3w: Difference between revisions

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

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-[[Image:1d3w.gif|left|200px]]<br /><applet load="1d3w" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1d3w, resolution 1.7&Aring;" />
-'''Crystal structure of ferredoxin 1 d15e mutant from azotobacter vinelandii at 1.7 angstrom resolution.'''<br />
-==Overview==
+==Crystal structure of ferredoxin 1 d15e mutant from azotobacter vinelandii at 1.7 angstrom resolution.==
-The basis of the chemiosmotic theory is that energy from light or, respiration is used to generate a trans-membrane proton gradient. This is, largely achieved by membrane-spanning enzymes known as 'proton pumps., There is intense interest in experiments which reveal, at the molecular, level, how protons are drawn through proteins. Here we report the, mechanism, at atomic resolution, for a single long-range electron-coupled, proton transfer. In Azotobacter vinelandii ferredoxin I, reduction of a, buried iron-sulphur cluster draws in a solvent proton, whereas, re-oxidation is 'gated' by proton release to the solvent. Studies of this, 'proton-transferring module' by fast-scan protein film voltammetry, high-resolution crystallography, site-directed mutagenesis and molecular, dynamics, reveal that proton transfer is exquisitely sensitive to the, position and pK of a single amino acid. The proton is delivered through, the protein matrix by rapid penetrative excursions of the side-chain, carboxylate of a surface residue (Asp 15), whose pK shifts in response to, the electrostatic charge on the iron-sulphur cluster. Our analysis defines, the structural, dynamic and energetic requirements for proton courier, groups in redox-driven proton-pumping enzymes.
+<StructureSection load='1d3w' size='340' side='right'caption='[[1d3w]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1d3w]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D3W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D3W 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]] 1.7&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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=1d3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d3w OCA], [https://pdbe.org/1d3w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d3w RCSB], [https://www.ebi.ac.uk/pdbsum/1d3w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d3w ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/FER1_AZOVI FER1_AZOVI] Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions. This ferredoxin could play a role in regulating gene expression by interacting directly with DNA.
+== 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/d3/1d3w_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/main_output.php?pdb_ID=1d3w ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-D3W is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii] with SF4 and F3S as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1D3W OCA].
+*[[Ferredoxin 3D structures|Ferredoxin 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-Atomically defined mechanism for proton transfer to a buried redox centre in a protein., Chen K, Hirst J, Camba R, Bonagura CA, Stout CD, Burgess BK, Armstrong FA, Nature. 2000 Jun 15;405(6788):814-7. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10866206 10866206]
 [[Category: Azotobacter vinelandii]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Armstrong, F.A.]]
+[[Category: Armstrong FA]]
-[[Category: Bonagura, C.A.]]
+[[Category: Bonagura CA]]
-[[Category: Burges, B.K.]]
+[[Category: Burges BK]]
-[[Category: Camba, R.]]
+[[Category: Camba R]]
-[[Category: Chen, K.]]
+[[Category: Chen K]]
-[[Category: Hirst, J.]]
+[[Category: Hirst J]]
-[[Category: Stout, C.D.]]
+[[Category: Stout CD]]
-[[Category: F3S]]
-[[Category: SF4]]
-[[Category: beta sheet]]
-[[Category: electron transport]]
-[[Category: ferredoxin]]
-[[Category: iron-sulphur protein]]
-[[Category: protein monomer]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 12:59:44 2007''