Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

transketolase activity GO:0004802 xref updates #29091

Closed
6 tasks done
sjm41 opened this issue Oct 23, 2024 · 0 comments
Closed
6 tasks done

transketolase activity GO:0004802 xref updates #29091

sjm41 opened this issue Oct 23, 2024 · 0 comments
Assignees

Comments

@sjm41
Copy link
Contributor

sjm41 commented Oct 23, 2024

id: GO:0004802
name: transketolase activity
namespace: molecular_function
def: "Catalysis of the reversible transfer of a 2-carbon ketol group (CH2OH-CO-) from a ketose phosphate donor to an aldose phosphate acceptor." [GOC:fmc, RHEA:10508]
synonym: "fructose 6-phosphate:D-glyceraldehyde-3-phosphate glycolaldehydetransferase activity" NARROW [GOC:fmc, GOC:mah]
synonym: "glycoaldehyde transferase activity" RELATED [EC:2.2.1.1]
synonym: "glycolaldehydetransferase activity" RELATED [EC:2.2.1.1]
synonym: "sedoheptulose-7-phosphate:D-glyceraldehyde-3-phosphate glycolaldehydetransferase activity" NARROW [EC:2.2.1.1]
xref: EC:2.2.1.1
xref: MetaCyc:1TRANSKETO-RXN
xref: RHEA:10508
is_a: GO:0016744 ! transketolase or transaldolase activity

The GO def here is correctly broad.
E.g. the EC:2.2.1.1 says:
Reaction: D-glyceraldehyde 3-phosphate + D-sedoheptulose 7-phosphate = aldehydo-D-ribose 5-phosphate + D-xylulose 5-phosphate
Comment: Wide specificity for both reactants, e.g. converts hydroxypyruvate and R-CHO into CO2 and R-CHOH-CO-CH2OH.

And RHEA maps EC:2.2.1.1 to two distinct RHEAs:

RHEA:10508 (40,468 proteins in UniProtKB)
D-glyceraldehyde 3-phosphate + D-sedoheptulose 7-phosphate = aldehydo-D-ribose 5-phosphate + D-xylulose 5-phosphate
=> this is the first reaction catalysed by the TKT enzyme in the Pentose Phosphate Pathway (e.g. see https://reactome.org/PathwayBrowser/#/R-HSA-71336&SEL=R-HSA-71324)

RHEA:27626 (0 proteins in UniProtKB)
D-erythrose 4-phosphate + D-xylulose 5-phosphate = β-D-fructose 6-phosphate + D-glyceraldehyde 3-phosphate
=> this is the second reaction catalysed by the TKT enzyme in the Pentose Phosphate Pathway (e.g. see https://reactome.org/PathwayBrowser/#/R-HSA-71336&SEL=R-HSA-71335)

So, actions here:

  • Make EC:2.2.1.1 exactMatch
  • Use EC in def xref instead of RHEA
  • Make RHEA:10508 narrowMatch
  • Add RHEA:27626 as narrowMatch
  • Make MetaCyc:1TRANSKETO-RXN narrowMatch
  • Add MetaCyc:2TRANSKETO-RXN as narrowMatch
@sjm41 sjm41 self-assigned this Oct 23, 2024
@sjm41 sjm41 closed this as completed in f7fa39a Oct 24, 2024
sjm41 added a commit that referenced this issue Oct 24, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
Development

No branches or pull requests

1 participant