This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

Sandbox Reserved 1501

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 16:56, 10 January 2019

This Sandbox is Reserved from 06/12/2018, through 30/06/2019 for use in the course "Structural Biology" taught by Bruno Kieffer at the University of Strasbourg, ESBS. This reservation includes Sandbox Reserved 1480 through Sandbox Reserved 1543.

To get started:

Click the edit this page tab at the top. Save the page after each step, then edit it again.
Click the 3D button (when editing, above the wikitext box) to insert Jmol.
show the Scene authoring tools, create a molecular scene, and save it. Copy the green link into the page.
Add a description of your scene. Use the buttons above the wikitext box for bold, italics, links, headlines, etc.

More help: Help:Editing

Encoded in the Saccharomyces cerevisiae (strain ATCC 204508 / S288c) gene CYB2 the protein Flavocytochrome b(2)

It is an Oxidoreductase categorized according to IUB as EC: 1.1.2.3.

1 Function
2 Reaction
3 Relevance
4 Structural highlights

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 step of the bacterial lactate metabolic pathway.

Reaction

Similar oxidants that can be used to perform the reaction in vitro are ferricyanide, phenozine methosulfate and quinone [experiment first performed 1963 by Nygaard, later in 1966 described by Symons and Burgoyne]^[1]. The Yeasts L-Lactate Dehydrogenase can be inhibited by heavy metals, oxygen, glycerate, oxalate, malate, phenylpyruvate and fatty acids [Nygaard 1963]^[2]. The Enzyme shows a specificity for L-lactate but none for the D-isomer or -hydroxybutyrate.

Relevance

While the function of cytochrome b2 is to couple L-lactate dehydrogenation to cytochrome c reduction; the mutant ARG289LYS is changing the kinetics of the reactions. It is rising the K_i of several components in comparison to the wild-type, while k_cat and K_M are also changed by a factor of 10. It changes also the induction by L-lactate. R289K-b(2) eing a component of the mitochondrial inter membrane space

Structural highlights

Global Symmetry Cyclic - C4 Global Stoichiometry Homotetramer A4

Flavocytochrome b(2) is a tetrameric enzyme [Jacq and Lederer, 1972]. 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 FM3- (FlavinMonoNucleotide),

https://www.wikiwand.com/de/Flavinmononukleotid

as well as one in with the iron complexed in the tetrapyrrole ring interacts with heme b(2-) cofactor [Risler and Groudinsky, 1973].

https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:60344

The amino acid sequence in the heme binding region was first determined by Guidard et al. (1974).

For every subunit the crystallized preparation analysis determined a molecular weight of the chain of 36 kD [Appleby and Morton] and the chain of 21 kD [Jacq and Lederer, 1974].

Arginin 289 to Lysine

http://www.worthington-biochem.com/yldhs/

This is a sample scene created with SAT to by Group, and another to make of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

References

↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644

Retrieved from "http://52.214.119.220/wiki/index.php/Sandbox_Reserved_1501"

@@ Line 1: / Line 1: @@
 {{Sandbox_Reserved_ESBS}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE -->
 <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.
-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.
 Encoded in the ''Saccharomyces cerevisiae'' (strain ATCC 204508 / S288c) gene CYB2 the protein Flavocytochrome b(2)
 It is an Oxidoreductase categorized according to IUB as EC: 1.1.2.3.
@@ Line 15: / Line 12: @@
 [[Image:Reaction1.JPG|center|x150px]]
-Similar oxidants that can be used to perform the reaction in vitro are ferricyanide, phenozine methosulfate and quinone [experiment first performed 1963 by Nygaard, later in 1966 described by Symons and Burgoyne].
+Similar oxidants that can be used to perform the reaction in vitro are ferricyanide, phenozine methosulfate and quinone [experiment first performed 1963 by Nygaard, later in 1966 described by Symons and Burgoyne]<ref>DOI 10.1002/ijch.201300024</ref>.
-The Yeasts L-Lactate Dehydrogenase can be inhibited by heavy metals, oxygen, glycerate, oxalate, malate, phenylpyruvate and fatty acids [Nygaard 1963].
+The Yeasts L-Lactate Dehydrogenase can be inhibited by heavy metals, oxygen, glycerate, oxalate, malate, phenylpyruvate and fatty acids [Nygaard 1963]<ref>PMID:21638687</ref>.
 The Enzyme shows a specificity for L-lactate but none for the D-isomer or -hydroxybutyrate.

Sandbox Reserved 1501

From Proteopedia

Revision as of 16:56, 10 January 2019

Contents

Function

Reaction

Relevance

Structural highlights

References

Views

Personal tools

Navigation

Search

Toolbox