1lm3: Difference between revisions

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New page: left|200px<br /><applet load="1lm3" size="450" color="white" frame="true" align="right" spinBox="true" caption="1lm3, resolution 2.7Å" /> '''A Multi-generation An...
 
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[[Image:1lm3.gif|left|200px]]<br /><applet load="1lm3" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1lm3, resolution 2.7&Aring;" />
'''A Multi-generation Analysis of Cytochrome b562 Redox Variants: Evolutionary Strategies for Modulating Redox Potential Revealed Using a Library Approach'''<br />


==Overview==
==A Multi-generation Analysis of Cytochrome b562 Redox Variants: Evolutionary Strategies for Modulating Redox Potential Revealed Using a Library Approach==
The redox potential of cytochromes sets the energy yield possible in, metabolism and is also a key determinant of the rate at which redox, reactions proceed. Here, the heme protein, cytochrome b(562), is used to, study the in vitro evolution of redox potential within a library of, variants containing the same structural archetype, the four-helix bundle., Multisite variations in the active site of cytochrome b(562) were, introduced. A library of variants containing random mutations in place of, R98 and R106 was created, and the redox potentials of a statistical, sampling of this library were measured. This procedure was carried out for, both the low- and high-potential variants of a previously studied, F61X/F65X, first-generation library [Springs, S. L., Bass, S. E., and, McLendon, G. L. (2000) Biochemistry 39, 6075]. The second-generation, library reported here has a range of redox potentials which is greater, than 40% (160 mV) of the known accessible potential among cytochromes with, identical axial ligands (but different folds) and exceeds the range, exhibited phylogenetically by the cytochrome c' family which internally, maintains the same axial ligation and fold. A statistical analysis of the, libraries examined reveals that the redox potential of WT cyt b(562) is, found at the high-potential extremum of the distribution, indicating that, this protein apparently evolved to differentially stabilize the reduced, protein. The 2.7 A crystal structure of F61I/F65Y/R106L (low-potential, variant of the second-generation library) was solved and is compared to, the wild-type structure and the 2.2 A resolution structure of the, F61I/F65Y variant (low-potential variant of the first-generation library)., The structures indicate that charge-dipole effects are responsible for, shifting the redox equilibrium toward the oxidized state in both the, F61I/F65Y and F61I/F65Y/R106L variants. Specifically, a new protein dipole, is introduced into the heme microenvironment as a result of the F65Y, mutation, two new internal water molecules (one in hydrogen-bonding, distance of Y65) are found, and in the case of F61I/F65Y/R106L (DeltaE(m), = 158 mV vs NHE), increased solvent exposure of the heme as a result of, the R106L substitution is identified.
<StructureSection load='1lm3' size='340' side='right'caption='[[1lm3]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1lm3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LM3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LM3 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]] 2.7&#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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=1lm3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lm3 OCA], [https://pdbe.org/1lm3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lm3 RCSB], [https://www.ebi.ac.uk/pdbsum/1lm3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lm3 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/C562_ECOLX C562_ECOLX] Electron-transport protein of unknown function.
== 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/lm/1lm3_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=1lm3 ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1LM3 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with MG and HEM as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1LM3 OCA].
*[[Cytochrome b5 3D structures|Cytochrome b5 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
A multigeneration analysis of cytochrome b(562) redox variants: evolutionary strategies for modulating redox potential revealed using a library approach., Springs SL, Bass SE, Bowman G, Nodelman I, Schutt CE, McLendon GL, Biochemistry. 2002 Apr 2;41(13):4321-8. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11914078 11914078]
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Bass, S.E.]]
[[Category: Bass SE]]
[[Category: Bowman, G.]]
[[Category: Bowman G]]
[[Category: McLendon, G.L.]]
[[Category: McLendon GL]]
[[Category: Nodelman, I.]]
[[Category: Nodelman I]]
[[Category: Schutt, C.E.]]
[[Category: Schutt CE]]
[[Category: Springs, S.L.]]
[[Category: Springs SL]]
[[Category: HEM]]
[[Category: MG]]
[[Category: cytochrome]]
[[Category: four helix bundle]]
[[Category: heme-binding]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 20:40:12 2007''

Latest revision as of 10:34, 14 February 2024

A Multi-generation Analysis of Cytochrome b562 Redox Variants: Evolutionary Strategies for Modulating Redox Potential Revealed Using a Library ApproachA Multi-generation Analysis of Cytochrome b562 Redox Variants: Evolutionary Strategies for Modulating Redox Potential Revealed Using a Library Approach

Structural highlights

1lm3 is a 2 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.7Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

C562_ECOLX Electron-transport protein of unknown function.

Evolutionary Conservation

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

See Also

1lm3, resolution 2.70Å

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