Electron transport: Difference between revisions

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==Working Group==
==Working Group==


David Hill dph@informatics.jax.org<br>
David Hill dph at informatics.jax.org<br>
Jim Hu jimhu@tamu.edu<br>
Jim Hu jimhu at tamu.edu<br>
Debby Siegele siegele@mail.bio.tamu.edu<br>
Debby Siegele siegele at mail.bio.tamu.edu<br>
Michelle Gwinn-Giglio mgiglio@som.umaryland.edu<br>
Michelle Gwinn-Giglio mgiglio at som.umaryland.edu<br>
Ingrid Keseler keseler@ai.sri.com<br>
Ingrid Keseler keseler at ai.sri.com<br>
Jen Deegan jdeegan@ebi.ac.uk<br>
Jen Deegan jdeegan at ebi.ac.uk<br>


[[Progress]]


* Jen is contacting Jim Hu to try to arrange a skype call to clear up some relationship problems under electron transport. 12/12/07
[[Changes committed on 25th March, 2008]]


* Meeting will be on Tuesday Dec 18, 9 AM Central Time.


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[[http://spreadsheets.google.com/ccc?key=pt9OZIJ8pTRYeq9fKTo5iLw&hl=en_GB&pli=1 Spreadsheet of relationships]]
====Discussion Points====
* GO: 0006118 electron transport
and children
* GO:0006133 : 5,10-methylenetetrahydrofolate oxidation
* GO:0019646 : aerobic electron transport
* GO:0019645 : anaerobic electron transport
* GO:0000044 : ascorbate stabilization
* GO:0042773 : ATP synthesis coupled electron transport
* GO:0010478 : chlororespiration
* GO:0006127 : glycerophosphate shuttle
* GO:0043490 : malate-aspartate shuttle
* GO:0006123 : mitochondrial electron transport, cytochrome c to oxygen (ok?)
* GO:0006120 : mitochondrial electron transport, NADH to ubiquinone (ok?)
* GO:0006121 : mitochondrial electron transport, succinate to ubiquinone (ok?)
* GO:0006122 : mitochondrial electron transport, ubiquinol to cytochrome c (ok?)
* GO:0006138 : NADH-O2 electron transport(ok?)
* GO:0009767 : photosynthetic electron transport (ok?)
* GO:0030965 : plasma membrane electron transport, NADH to quinone
* GO:0009766 : primary charge separation
* GO:0006136 : succinate-O2 electron transport
* GO:0006125 : thioredoxin pathway
* GO:0006137 : ubiquinone-8-O2 electron transport(ok?)




while we're at it:  
[[Category:Ontology]]
* NADH dehydrogenase complex (plastoquinone) (sensu Cyanobacteria)
[[Category:Function-Process]]
* NADH dehydrogenase complex (quinone) (sensu Bacteria)
* NADH dehydrogenase complex (ubiquinone) (sensu Bacteria)
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====Emails====
Hi Harold,
 
Do you know if all cytochrome P450 proteins are involved in electron transport?
 
I wonder if those mappings are always correct:
http://www.ebi.ac.uk/interpro/IEntry?ac=IPR001128
 
Thanks
Pascale
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In I nutshell,  and based on our def, yes.
 
Cytochome P450s are a large group of monooxygenase enzymes  that metabolize of toxic hydrocarbons. They use NADPH coenzyme. Oxygen is a substrate.    Some are  enzymes are located in the endoplasmic reticulum as well as in the  the mitochondrial membrane. So the ones in the mitochondria might be considered to be involved in THE electron transport if  you are referring to the one that makes ATP.  So, unless the definition of electron transport is really broad, I wonder if it would not be fair to classify all of them as being invovled in that process.
SO, notice that  our def is very broad: :*GO:0006118: **The transport of electrons from an electron donor to an electron acceptor.
 
*It has a child,
GO term:     *NADH-O2 electron transport*
GO id:    *GO:0006138*
 
 
SO I would say any CYP450 is involved in GO:0006138.
 
 
Harold
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But, remember how we've have been trying to clean that up?
 
see
http://sourceforge.net/tracker/index.php?func=detail&aid=1226172&group_id=36855&atid=440764
there was also this really fun item:
http://sourceforge.net/tracker/index.php?func=detail&aid=1332197&group_id=36855&atid=440764
but that was rather for function.
 
The problem is that this used to cover all electron transfer reactions, including all oxidoreductases. I just wonder if that's the case for some cytochrome P450s. Also, electron transport is a child of 'generation of precursor metabolites and energy'. It's possible that many children of 'electron transport' dont belong there.
If that parent is correct, then  'electron transport' as you describe it above should not be a child. Also, GO:6120 to 6023 should be children of 'ATP synthesis coupled electron transport'??
 
Seems like some work is needed here... Should I open a SF item?
 
Thanks for your input,
 
Pascale
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Yes, most definitely, tt seems obvious that the standing definition of "electron transport" is too broad.  The Oxford Dictionary of Biochemistry (aka, the bible), has this for an entry
 
Electron transport:
1. respiratory electron transport: the process by which pairs of electrons derived from intermediates of the tricarboxcylic acid cycle and other substraes flows down the respiratory chain to dioxygen, the ultimate electron acceptor in respiration.
2. photosynthetic elecron transport: the process by which pairs of electrons are trasported from water to NADP+ in the light phase of photosynthesis during noncyclic photophosphorylation.
 
Also, I still object to the actual term "electron transport", since it is not has if the same electron is passed down the chain. However, the term is historical in context, so we need to keep the convention.
 
So, some CYP450's could be annotated using def. 1; not all
 
It is clear that electron transport uses oxidation/reduction at each of it's steps.
The way ET is defined in the GO now is almost meaningless
 
A definite SF item
 
hjd
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Hi Jen and Pascale,
 
Is this really transport? According to Harold it's not. The electrons don't really get transported anywhere. People just call it that.
 
David 
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Hi David,
 
Transport for me is transmembrane transport, which this isn't. But this also happens in membranes, and I know a fair bit about both, so I'd be happy to take the ball, quietly rename it, and then run with it.
 
Jen

Latest revision as of 09:29, 12 April 2019

Working Group

David Hill dph at informatics.jax.org
Jim Hu jimhu at tamu.edu
Debby Siegele siegele at mail.bio.tamu.edu
Michelle Gwinn-Giglio mgiglio at som.umaryland.edu
Ingrid Keseler keseler at ai.sri.com
Jen Deegan jdeegan at ebi.ac.uk

Progress

Changes committed on 25th March, 2008


[Spreadsheet of relationships]