A2-33

PDB links

Hi! Thanks for your edit to the {{Infobox enzyme}} template. Definitely an improvement. Concerning your edit to {{PBB/3043}} that you subsequently undid, I also thought this was a very useful edit and I had thoughts of doing something similar. What was the problem of the URLs? If we can find a good solution, we could modify the {{GNF_Protein_box}} template so that up to date PBD links could be applied to all Gene Wiki articles. Your links were based on the human UniProt accession number. An even better solution would be to link to the HomoloGene accession number so that structures of orthologs would also be included, but unfortunately it does not appear that the external structure databases support this type of query. Boghog (talk) 21:15, 20 January 2012 (UTC)

Hi, thanks for your message. I really like the enzyme browser that I've modified the link for. It would be good to modify the infobox for pfam similarly to go to PDBe's browser ebi.ac.uk/pdbe-srv/PDBeXplore/pfam/?pfam= but the template is protected so I can't edit it.

Yes the problem with PBB/3043 was the links. I can get a search term encoded in the URL at PDBe, but not from the RCSB site, and I want to be fair to both. RCSBs search results have some kind of session ID as the URL and I've no idea how to code the search in the link from wikipedia. (though the Pfam infobox manages it) Would be excellent to apply that to all the Genewiki articles if we can sort out the search URL to have uptodate PDB info from the different PDB sites. Uniprot ID isn't ideal, but until there's a homologene search I guess its better than a long list of four letter codes. I'll do some digging and see if I can work out the RCSB's URL issue.

A2-33 (talk) 21:48, 20 January 2012 (UTC)

Hi, sorry not 100% what input you want to provide for RCSB, if it is Pfam IDs that would work like this: http://www.rcsb.org/pdb/search/smartSubquery.do?smartSearchSubtype=PfamIdQuery&pfamID=PF00104 . Let me know what else you need... --Andreas (talk) 00:53, 21 January 2012 (UTC)

Thanks, what is the format for a UniProt ID? A2-33 (talk) 00:59, 21 January 2012 (UTC)

Would http://www.rcsb.org/pdb/search/smartSubquery.do?smartSearchSubtype=UpAccessionIdQuery&accessionIdList=P50225 work for you? --Andreas (talk) 05:25, 21 January 2012 (UTC)

(edit conflict) To query the RCSB PDB for structures by UniProt accession number, the following works, but it is somewhat verbose:

• http://www.rcsb.org/pdb/search/smart.do?smartComparator=and&smartSearchSubtype_0=UpAccessionIdQuery&target=Current&accessionIdList_0=P68871

This returns all the structures for a given protein from one organism (in this example, human). Even better search would be based on the HomoloGene accession number (e.g., HomoloGene: 68066) that would return structures for the human protein plus homologs in other species (e.g., mouse, rat, etc.), but unfortunately the RCSB PDB does not seem to support that type of query. The pfam query is appropriate for the {{Infobox protein family}} template but too broad for the {{GNF_Protein_box}}. Boghog (talk) 06:01, 21 January 2012 (UTC)

Thanks Andreas, your link is more compact. I have included it in the {{PBB/3043}} template (see diff). Boghog (talk) 06:11, 21 January 2012 (UTC)

Couple of things about that: You could request human and mouse hits by providing the correct uniprot IDs for both. Homologene (or Ensembl Compara) cross links is an interesting comment, but probably not easy to implement. There is also a sequence clustering available as part of rcsb pdb. Here you can see sequence neighbours for one of the sulfotransferases. With a bit of scripting those could be retrieved via this URL but I guess this might be getting too technically advanced for WP...? --Andreas (talk) 06:32, 21 January 2012 (UTC)

Thanks for pointing out that UniProt IDs can be concatenated in RCSB PDB queries. It would be possible to create a WP template that would return a list of UniProt IDs using a HomoloGene ID as an argument (similar to {{Pfam2PDBsum}} which by the way is now depreciated since it is now possible to directly query PDBsum with Pfam IDs). However even after restricting the list to those that include a human ortholog, the size of such a template is likely to be enormous and may exceed WP limits. Another disadvantage is someone would need to maintain the template. I will try to create such a template and see how it works. Boghog (talk) 11:48, 21 January 2012 (UTC)

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Incorrect PDB structures

Hey there. I checked in to the source of ProteinBoxBot's inaccuracies regarding PDB structures. It seems that it was pulling the info from Ensembl, which did indeed have a very outdated structure for the protein you pointed out. I've corrected it to retrieve the structures from rcsb instead, which should be as up-to-date as possible. Please let me know if you note any further inaccuracies, and thanks for your help. Pleiotrope (talk) 20:51, 12 March 2012 (UTC)

Hi there. There is a lot of discussion about this on the GNFProteinBox page. We have a new server implemented to provide data for addition to the box. Can you also have a look at the discussion and check the server mentioned e.g http://wwwdev.ebi.ac.uk/pdbe-apps/jsonizer/mappings/Q01524/. The discussion also decided on adding images for "best structure" which the server provides. Let me know if this requires any changes. I am assuming that you will have to change of bot to accomodate these changes. A2-25 (talk) 20:08, 13 March 2012 (UTC)

Thanks for the changes, glad the bot is now pulling uptodate infomation. As A2-25 says, there has been much discussion about the best way to handle PDB data in the PBB boxes which I'm sure you've seen. Hope the bot is able to accomodate the forthcoming improvements.A2-33 (talk) 21:28, 14 March 2012 (UTC)

Ways to improve Eric Newton (art critic)

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Cobalamin adenosyltransferase

Thanks for your edit to this page (with respect its presence in humans). I am a complete novice where this enzyme in concerned and where I have seen discussion to its presence in humans I have not been able to find good references, or indications of the cells/organs in which it occurs.

Are you aware of any research that might allow a fuller more understandable article content concerning humans, or allow us to explicitly state this it is present in humans? — Preceding unsigned comment added by Leopardtail (talk • contribs) 11:48, 11 March 2014 (UTC)

Hi Leopardtail.

Looking at the literature, many papers seem to take it for granted that the enzyme is present in humans. See for instance the MMAB page, which is specifically for the human enzyme, from where you'll find a good number of links, eg to the Uniprot entry with lots of useful references, including to the crystal structure. I deleted the line from the Cob(I)yrinic acid a,c-diamide adenosyltransferase saying that the enzyme wasn't found in eukaryotes as I'd added a structure image of the human enzyme. The review article from Appl. Microbiol. Biotechnol. which Boghog added (currently reference 2) and refs therein might also be useful. It says "Cells from all domains of life synthesize ACA enzymes" and the enzyme is mitochondrial in eukaryotes. The interpro page [1] however says that synthesis (of AdoCbl) is unique to certain prokaryotes, which seems to contradict the literature, unless the sentence is badly written and its referring to cobalamin synthesis. I'll contact Interpro and ask them to clarify. Hope that helps A2-33 (talk) 19:07, 11 March 2014 (UTC)

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