Sandbox Reserved 1501: Difference between revisions

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{{Sandbox_Reserved_ESBS}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE -->
{{Sandbox_Reserved_ESBS}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE -->
==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='1qcw' size='340' side='right' caption='Caption for this structure' scene=''>
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.


== Function ==
The oxidoreductase Flavocytochrome b(2) (Arg289Lys mutant), categorized as EC: 1.1.2.3 according to IUB, is encoded in the ''Saccharomyces cerevisiae'' (strain ATCC 204508 / S288c) gene ''CYB2''.


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==Function==
Flavocytochrome b(2) (Arg289Lys mutant) from ''Saccharomyces cerevisiae'' is an oxidoreductase that couples dehydrogenation of L-lactate to cytochrome c reduction by electron transfer. It is one reaction of the bacterial lactate metabolic pathway localized in the mitochondrial intermembrane space.


== Disease ==
==Reaction==


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Flavocytochrome b(2) catalyzes dehydrogenation of L-lactate and the coupled cytochrome c reduction.
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Similar oxidants that can be used to perform the reaction ''in vitro'' are ferricyanide, phenazine methosulfate and quinone (experiment first performed 1963 by Nygaard<ref name="aaa">PMID: 14480786</ref>, later in 1966 described by Symons and Burgoyne<ref>DOI: 10.1016/0076-6879(66)09064-5</ref>).
The yeasts L-lactate dehydrogenase can be inhibited by heavy metals, oxygen, glycerate, oxalate, malate, phenylpyruvate and fatty acids (Nygaard, 1963<ref name="aaa"/>).
The enzyme shows a specificity for L-lactate but none for the D-isomer or α-hydroxybutyrate.
[[Image:Reaction1.JPG|center|x150px]]
==Structure highlight==
<!-- Global Symmetry Cyclic - C4-->
<!-- Global Stoichiometry Homotetramer  A4 -->


Flavocytochrome b(2) is a tetrameric enzyme (Jacq and Lederer, 1972 and 1974<ref>PMID: 4336855</ref>,<ref>PMID: 4152980</ref>). Each of the four identical subunits is composed by one single polypeptide chain.
Each subunit contains a binding site for the selectively non-covalently binding of the cofactor FMN(3-) (Flavinmononucleotide), as well as one in with the iron complexed in the tetrapyrrole ring interacts with heme b(2-) cofactor (Risler and Groudinsky, 1973<ref>PMID: 4575975 </ref>). 


== Relevance ==
<!--https://www.wikiwand.com/de/Flavinmononukleotid-->
<!-- https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:60344-->


== Structural highlights ==
The amino acid sequence in the heme binding region was first determined by Guidard ''et al'', 1974<ref>PMID: 4210211</ref>.
For every subunit of the wild type protein form, the crystallized preparation analysis determined a molecular weight of the α-chain of 36 kD (Appleby and Morton, 1959<ref>PMID: 13638255</ref>) and the β-chain of 21 kD (Jacq and Lederer, 1974<ref>PMID: 4152980</ref>).
The sulfite adduct recombinant enzyme produced when expressed in ''E. coli'' was also crystallized (Tegoni and Cambillau, 1994<ref name="bob">PMID: 8003966</ref>) so key active site residues could be identified and comparisons with the mutant protein can be made.
The Arg289 of the ''E. coli'' wild type sulfite adduct can adopt two different conformations, in one of which its side chain is stacked against Arg376, that directly interacts with the substrate, while in the second one the Arg289 side chain points towards the active site.
The mutation changes that Arg289 into a Lysine becoming R289K-b(2). The mutant ARG289LYS can still be found in both conformations but it is now changing the kinetics of the reactions (Tegoni and Cambillau, 1994<ref name="bob"/>).
It is rising the K<sub>i</sub> of several components in comparison to the wild type, while k<sub>cat</sub> and K<sub>M</sub> are also changed by a factor of 10.
It changes also the induction by L-lactate. Patterns of inhibition by pyruvate and oxalate are altered and the enzyme stops being inhibited by substrate excess.
The mutation has altered the flavin reduction, the first step of the catalytic cycle. It is shown that the mutation enhances the stability of both enzyme-substrate-complex and the transition state, as well as in ligand binding to the active site when the flavin is in the semiquinone state. The first electron transfer step, from the reduced flavin to heme, is not affected by the mutation, but it indeed affects the second electron transfer from flavin semiquinone to heme b(2).
The resolution through X-ray crystal structure R289K-b(2) has been determined to 2,75 Å.


This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.
<!--{{multiple image
| width = 80
| image1 = Flav.png
| caption1 = Flavinmononucleotide
| image2 = Hfdbtg.JPG
| caption2 = heme b(2) cofactor
}}-->
 
{|style="margin: 0 auto;"
| [[Image:Flav.png|thumb|right|x250px|Flavinmononucleotide]]
| [[Image:Hfdbtg.JPG|thumb|right|x250px|Heme b(2)]]
|}
 
<!--
{{Gallery
|right
|height=400
|lines=1
|align= center
|Image:Flav.png|thumb|Flavinmononucleotide
|Image:Hfdbtg.JPG|thumb|heme b(2) cofactor
}}-->


</StructureSection>
</StructureSection>
== References ==
== References ==
<references/>
<references/>-->
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