2gba: Difference between revisions

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New page: left|200px<br /><applet load="2gba" size="450" color="white" frame="true" align="right" spinBox="true" caption="2gba, resolution 0.92Å" /> '''Reduced Cu(I) form a...
 
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[[Image:2gba.gif|left|200px]]<br /><applet load="2gba" size="450" color="white" frame="true" align="right" spinBox="true"
caption="2gba, resolution 0.92&Aring;" />
'''Reduced Cu(I) form at pH 4 of P52G mutant of amicyanin'''<br />


==Overview==
==Reduced Cu(I) form at pH 4 of P52G mutant of amicyanin==
Amicyanin is a type I copper protein that is the natural electron acceptor, for the quinoprotein methylamine dehydrogenase (MADH). The conversion of, Proline52 of amicyanin to a glycine does not alter the physical and, spectroscopic properties of the copper binding site, but it does alter the, rate of electron transfer (ET) from MADH. The values of electronic, coupling (H(AB)) and reorganization energy (lambda) that are associated, with the true ET reaction from the reduced O-quinol tryptophan, tryptophylquinone (TTQ) of MADH to oxidized amicyanin are significantly, altered as a consequence of the P52G mutation. The experimentally, determined H(AB) increases from 12 to 78 cm(-1), and lambda increases from, 2.3 to 2.8 eV. The rate and salt-dependence of the proton transfer-gated, ET reaction from N-quinol MADH to amicyanin are also changed by the P52G, mutation. Kinetic data suggests that a new common reaction step has become, rate-limiting for both the true and gated ET reactions that occur from, different redox forms of MADH. A comparison of the crystal structures of, P52G amicyanin with those of native amicyanin free and in complex with, MADH provided clues as to the basis for the change in ET parameters. The, mutation results in the loss of three carbons from Pro52 and the movement, of the neighboring residue Met51. This reduces the number of hydrophobic, interactions with MADH in the complex and perturbs the protein-protein, interface. A model is proposed for the ET reaction with P52G amicyanin in, which the most stable conformation of the protein-protein complex with, MADH is not optimal for ET. A new preceding kinetic step is introduced, prior to true ET that requires P52G amicyanin to switch from this, redox-inactive stable complex to a redox-active unstable complex. Thus, the ET reaction of P52G amicyanin is no longer a true ET but one that is, conformationally gated by the reorientation of the proteins within the ET, protein complex. This same reaction step now also gates the ET from, N-quinol MADH, which is normally rate-limited by a proton transfer.
<StructureSection load='2gba' size='340' side='right'caption='[[2gba]], [[Resolution|resolution]] 0.92&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[2gba]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Paracoccus_denitrificans Paracoccus denitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GBA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GBA FirstGlance]. <br>
2GBA is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Paracoccus_denitrificans Paracoccus denitrificans] with CU1 as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2GBA OCA].
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 0.92&#8491;</td></tr>
 
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU1:COPPER+(I)+ION'>CU1</scene></td></tr>
==Reference==
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2gba FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gba OCA], [https://pdbe.org/2gba PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gba RCSB], [https://www.ebi.ac.uk/pdbsum/2gba PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gba ProSAT]</span></td></tr>
Site-directed mutagenesis of proline 52 to glycine in amicyanin converts a true electron transfer reaction into one that is conformationally gated., Ma JK, Carrell CJ, Mathews FS, Davidson VL, Biochemistry. 2006 Jul 11;45(27):8284-93. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16819827 16819827]
</table>
== Function ==
[https://www.uniprot.org/uniprot/AMCY_PARDE AMCY_PARDE] Primary acceptor of electrons from methylamine dehydrogenase. Passes those electrons on either a soluble cytochrome c or to pseudoazurin.
== 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/gb/2gba_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=2gba ConSurf].
<div style="clear:both"></div>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Paracoccus denitrificans]]
[[Category: Paracoccus denitrificans]]
[[Category: Single protein]]
[[Category: Carrell CJ]]
[[Category: Carrell, C.J.]]
[[Category: Davidson VL]]
[[Category: Davidson, V.L.]]
[[Category: Ma JK]]
[[Category: Ma, J.K.]]
[[Category: Mathews FS]]
[[Category: Mathews, F.S.]]
[[Category: CU1]]
[[Category: beta-sandwich]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 11:05:37 2007''

Latest revision as of 12:27, 14 February 2024

Reduced Cu(I) form at pH 4 of P52G mutant of amicyaninReduced Cu(I) form at pH 4 of P52G mutant of amicyanin

Structural highlights

2gba is a 1 chain structure with sequence from Paracoccus denitrificans. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 0.92Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

AMCY_PARDE Primary acceptor of electrons from methylamine dehydrogenase. Passes those electrons on either a soluble cytochrome c or to pseudoazurin.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

2gba, resolution 0.92Å

Drag the structure with the mouse to rotate

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

OCA
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