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UDP-glycosyltransferase activity #1836

Closed gocentral closed 9 years ago

gocentral commented 20 years ago

Hi,

I need the knowledge of an enzymologist- I'm relooking at the FlyBase annotation of a set of glycosyltransferases. We have them annotated to UDP-glycosyltransferase activity ; GO:0008194. They also show homology to UDP-glucuronosyltransferases.

The current function graph doesn't connect these 2 terms:

transferase activity, transferring glycosyl groups ; GO:0016757 ; --%transferase activity, transferring hexosyl groups ; GO:0016758 ; ----%glucuronosyltransferase activity ; GO:0015020 ; EC:2.4.1.17 ; synonym:UDP-glucuronosyltransferase ----%UDP-glycosyltransferase activity ; GO:0008194

I think UDP-glycosyltransferase activity ; GO:0008194 (currently undefined) should be a parent of glucuronosyltransferase activity ; GO:0015020 and other UDP-transferase terms in this part of the graph instead.

eg:

transferase activity, transferring glycosyl groups ; GO:0016757 ; EC:2.4.-.- ; synonym:glycosyltransferase --%transferase activity, transferring hexosyl groups ; GO:0016758 ; EC:2.4.1.- ; synonym:hexosyltransferase ----%glucuronosyltransferase activity ; GO:0015020 ; EC:2.4.1.17 ; synonym:UDP-glucuronosyltransferase --%UDP-glycosyltransferase activity ; GO:0008194 ----%glucuronosyltransferase activity ; GO:0015020 ; EC:2.4.1.17 ; synonym:UDP-glucuronosyltransferase ----%UDP-galacturonosyltransferase activity ; GO:0050375 ; EC:2.4.1.75 etc..

is this correct?

UDP-glycosyltransferase activity ; GO:0008194 Catalysis of the transfer of a glycosyl group from a UTP-sugar to a small hydrophobic molecule. PMID:11846783 InterPro:IPR002213

In PMID:11846783, they say.....

The UDP-glycosyltransferases (UGTs) are a superfamily of enzymes that [snip] catalyze the addition of the glycosyl group from a nucleotide sugar to a variety of small hydrophobic molecules. The UDP-sugar may be UDP-glucuronic acid, UDP-galactose, UDP-glucose, or UDP-xylose. The best-characterized UGTs are the mammalian UDP-glucuronosyltransferases, which use UDP-glucuronic acid as sugar donor.

see also the blurb in InterPro:IPR002213

thanks, Becky

Reported by: beckyfoulger

Original Ticket: "geneontology/ontology-requests/1840":https://sourceforge.net/p/geneontology/ontology-requests/1840

gocentral commented 20 years ago

Logged In: YES user_id=482748

I queried the enzyme interest group on this to double check before I made any edits. This is what Kirill says:

> Q1: Can you tell me if all glucuronosyltransferases transfer a > glycosyl group from a UDP-sugar to an acceptor? > i.e. can glucuronosyltransferase activity ; GO:0015020 ; EC:2.4.1.17 > be made a child of UDP-glycosyltransferase activity ; >GO:0008194. The definition suggests so, but I just wanted to >double-check?

Yes (that is the definition of EC 2.4.1.17). However, instead of the IUBMB "official" name "glucuronosyltransferase", I would rather prefer to see thr term "UDP-glucuronosyltransferase" because it makes it (place in ontology) completely clear.

> Q2: There are a number of GO terms in the glycosyltransferase part of the function ontology that have in the definition: > acceptor molecule + > UDP-glucose (eg GO:0047228) > UDP-glucuronate (eg GO:0015020 and all children) > UDP-xylose (eg GO:0047517) > UDP-apiose (eg GO:0047892) > UDP-N-acetyl-galactosamine (eg GO:0008376 and all children) > UDP-N-acetyl-glucosamine (eg GO:0008375 and all children) > UDP-N-acetyl-mannosaminouronate (eg GO:0047241) > UDP-rhamose (eg GO:0047230) > UDP-galactose (eg GO:0004461) > UDP-galacturonate (eg GO:0050375) > UDP-sulfoquinovose (eg GO:0046510) > > Can all these terms (probably around 100 in total) be made children > of UDP-glycosyltransferase activity ; GO:0008194?

Yes

Kirill

so: I'll copy glucuronosyltransferase activity ; GO:0015020 and all the other glycosyltransferase activity terms which transfer from UDP-sugar (according to the GO definition) to be children of UDP-glycosyltransferase activity ; GO:0008194.

Is the text string name always the IUBMB name?

thanks Becky

Original comment by: beckyfoulger

gocentral commented 20 years ago

Original comment by: beckyfoulger

gocentral commented 20 years ago

Logged In: YES user_id=482748

There are >100 terms in the glyosyltransferase part of the tree that should have UDP-glycosyltransferase as a parent (http://www.chem.qmul.ac.uk/iubmb/enzyme/reaction/polysacc/UDPsugar.html).

I could make all of these direct children of UDP-glycosyltransferase activity ; GO:0008194. However, to make the tree easier to read, I'd like to group these terms, depending on the type of sugar group transferred, as is the case for sugar transferase GO terms at the moment.

Eg:

transferase activity, transferring glycosyl groups ; GO:0016757 --%UDP-glycosyltransferase activity ; GO:0008194 ----%acetylgalactosaminyltransferase activity ; GO:0008376 ----%acetylglucosaminyltransferase activity ; GO:0008375 ----%UDP-galactosyltransferase activity ; GO:NEW % galactosyltransferase activity ; GO:0008378 ----%UDP-glucosyltransferase activity ; GO:NEW % glucosyltransferase activity ; GO:0046527 ----%glucuronosyltransferase activity ; GO:0015020 ; EC:2.4.1.17 ----%UDP-xylosyltransferase activty ; GO:NEW % xylosyltransferase activity ; GO:0042285

eg UDP-galactosyltransferase activity Catalysis of the transfer of a galactose group from UDP-galactose to an acceptor molecule.

I'll plan to do this on Fri (17th sept).

Original comment by: beckyfoulger

gocentral commented 20 years ago

Logged In: YES user_id=482748

Done-

1/ added definition to GO:0008194: Catalysis of the transfer of a glycosyl group from a UDP-sugar to a small hydrophobic molecule. definition_reference: PMID:11846783 definition_reference: INTERPRO:IPR004224.

2/ Changed the parentage of GO:0008194 from

transferase activity, transferring hexosyl groups ; GO:0016758 --%UDP-glycosyltransferase activity ; GO:0008194 to transferase activity, transferring glycosyl groups ; GO:0016757 --%UDP-glycosyltransferase activity ; GO:0008194

3/ created 3 new terms:

transferase activity, transferring glycosyl groups ; GO:0016757 --%UDP-glycosyltransferase activity ; GO:0008194 ----%acetylgalactosaminyltransferase activity ; GO:0008376 ----%acetylglucosaminyltransferase activity ; GO:0008375 ----%UDP-galactosyltransferase activity ; GO:0035250 (NEW) % galactosyltransferase activity ; GO:0008378 ----%UDP-glucosyltransferase activity ; GO:0035251 (NEW) % glucosyltransferase activity ; GO:0046527 ----%glucuronosyltransferase activity ; GO:0015020 ; EC:2.4.1.17 ----%UDP-xylosyltransferase activty ; GO:0035252 (NEW) % xylosyltransferase activity ; GO:0042285

UDP-galactosyltransferase activity ; GO:0035250 (NEW) Catalysis of the transfer of a galactose group from UDP-galactose to an acceptor molecule. definition_reference: http://www.chem.qmul.ac.uk/iubmb/enzyme/reaction/polysacc/UDPsugar.html

UDP-glucosyltransferase activity ; GO:0035251 (NEW) Catalysis of the transfer of a glucosyl group from UDP-glucose to an acceptor molecule. definition_reference: http://www.chem.qmul.ac.uk/iubmb/enzyme/reaction/polysacc/UDPsugar.html

UDP-xylosyltransferase activty ; GO:0035252 (NEW) Catalysis of the transfer of a xylosyl group from UDP-xylose to an acceptor molecule. definition_reference: http://www.chem.qmul.ac.uk/iubmb/enzyme/reaction/polysacc/UDPsugar.html

4/ moved/copied the following terms:

COPIED the following to be is_a children of UDP-glycosyltransferase activity ; GO:0008194:

glucuronosyltransferase activity ; GO:0015020 ; EC:2.4.1.17 alpha-1,3-glucan synthase activity ; GO:0047657 ; EC:2.4.1.183 alpha-1,4-glucan-protein synthase (UDP-forming) activity ; GO:0047210 ; EC:2.4.1.112 hyaluronan synthase activity ; GO:0050501 ; EC:2.4.1.212 linamarin synthase activity ; GO:0050057 ; EC:2.4.1.63 lipid-A-disaccharide synthase activity ; GO:0008915 ; EC:2.4.1.182 lipopolysaccharide N-acetylmannosaminouronosyltransferase activity ; GO:0047241 ; EC:2.4.1.180 N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase activity ; GO:0047244 ; EC:2.4.1.187 UDP-galacturonosyltransferase activity ; GO:0050375 ; EC:2.4.1.75 UDP-sulfoquinovose:DAG sulfoquinovosyltransferase activity ; GO:0046510 acetylgalactosaminyltransferase activity ; GO:0008376 ; EC:2.4.1.-
acetylglucosaminyltransferase activity ; GO:0008375 ; EC:2.4.1.-
1,4-beta-D-xylan synthase activity ; GO:0047517 ; EC:2.4.2.24 flavone apiosyltransferase activity ; GO:0047892 ; EC:2.4.2.25 indolylacetylinositol arabinosyltransferase activity ; GO:0050409 ; EC:2.4.2.34

MOVED the following to be is_a children of UDP-galactosyltransferase activity:

1,2-diacylglycerol 3-beta-galactosyltransferase activity ; GO:0046509 ; EC:2.4.1.46 2-hydroxyacylsphingosine 1-beta-galactosyltransferase activity ; GO:0003851 ; EC:2.4.1.45 beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity ; GO:0003831 ; EC:2.4.1.38 fucosylgalactoside 3-alpha-galactosyltransferase activity ; GO:0004381 ; EC:2.4.1.37 galactogen 6-beta-galactosyltransferase activity ; GO:0047255 ; EC:2.4.1.205 galactosylxylosylprotein 3-beta-galactosyltransferase activity ; GO:0047220 ; EC:2.4.1.134 ganglioside galactosyltransferase activity ; GO:0047915 ; EC:2.4.1.62 glucosaminylgalactosylglucosylceramide beta-galactosyltransferase activity ; GO:0047275 ; EC:2.4.1.86 glycosaminoglycan galactosyltransferase activity ; GO:0047271 ; EC:2.4.1.74 indolylacetyl-myo-inositol galactosyltransferase activity ; GO:0047227 ; EC:2.4.1.156 inositol 3-alpha-galactosyltransferase activity ; GO:0047216 ; EC:2.4.1.123 lactose synthase activity ; GO:0004461 ; EC:2.4.1.22 lactosylceramide 4-alpha-galactosyltransferase activity ; GO:0050512 ; EC:2.4.1.228 lactosylceramide beta-1,3-galactosyltransferase activity ; GO:0047240 ; EC:2.4.1.179 lipopolysaccharide 3-alpha-galactosyltransferase activity ; GO:0008918 ; EC:2.4.1.44 lipopolysaccharide-1,6-galactosyltransferase activity ; GO:0008921 ; EC:2.4.1.- N-acetyllactosamine synthase activity ; GO:0003945 ; EC:2.4.1.90 N-acetyllactosaminide 3-alpha-galactosyltransferase activity ; GO:0047276 ; EC:2.4.1.87 N-acylsphingosine galactosyltransferase activity ; GO:0047263 ; EC:2.4.1.47 procollagen galactosyltransferase activity ; GO:0050211 ; EC:2.4.1.50 sn-glycerol-3-phosphate 1-galactosyltransferase activity ; GO:0047279 ; EC:2.4.1.96 sn-glycerol-3-phosphate 2-alpha-galactosyltransferase activity ; GO:0047221 ; EC:2.4.1.137 sphingosine beta-galactosyltransferase activity ; GO:0047258 ; EC:2.4.1.23 sucrose 6F-alpha-galactotransferase activity ; GO:0047235 ; EC:2.4.1.167 UDP-galactose beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity ; GO:0008499 UDP-galactose-glucosylceramide beta-1,4-galactosyltransferase activity ; GO:0008489 UDP-galactose:MGDG galactosyltransferase activity ; GO:0046481 xylosylprotein 4-beta-galactosyltransferase activity ; GO:0046525 ; EC:2.4.1.133

MOVED the following to be is_a children of UDP-glucosyltransferase activity:

1,2-diacylglycerol 3-glucosyltransferase activity ; GO:0047228 ; EC:2.4.1.157 1,2-dihydroxy-phenanthrene glycosyltransferase activity ; GO:0018718 ; EC:2.4.1.- 1,3-beta-glucan synthase activity ; GO:0003843 ; EC:2.4.1.34 13-hydroxydocosanoate 13-beta-glucosyltransferase activity ; GO:0047229 ; EC:2.4.1.158 2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one 2-D-glucosyltransferase activity ; GO:0047254 ; EC:2.4.1.202 2-coumarate O-beta-glucosyltransferase activity ; GO:0047212 ; EC:2.4.1.114 4-hydroxybenzoate 4-O-beta-D-glucosyltransferase activity ; GO:0047250 ; EC:2.4.1.194 alizarin 2-beta-glucosyltransferase activity ; GO:0047644 ; EC:2.4.1.103 alpha,alpha-trehalose-phosphate synthase (UDP-forming) activity ; GO:0003825 ; EC:2.4.1.15 anthocyanidin 3-O-glucosyltransferase activity ; GO:0047213 ; EC:2.4.1.115 arylamine glucosyltransferase activity ; GO:0047684 ; EC:2.4.1.71 cellulose synthase (UDP-forming) activity ; GO:0016760 ; EC:2.4.1.12 ceramide glucosyltransferase activity ; GO:0008120 ; EC:2.4.1.80 cinnamate beta-D-glucosyltransferase activity ; GO:0050412 ; EC:2.4.1.177 cis-p-coumarate glucosyltransferase activity ; GO:0050644 ; EC:2.4.1.209 cis-zeatin O-beta-D-glucosyltransferase activity ; GO:0050502 ; EC:2.4.1.215 coniferyl-alcohol glucosyltransferase activity ; GO:0047209 ; EC:2.4.1.111 cyanidin-3-rhamnosylglucoside 5-O-glucosyltransferase activity ; GO:0047214 ; EC:2.4.1.116 cyanohydrin beta-glucosyltransferase activity ; GO:0047792 ; EC:2.4.1.85 cytokinin 7-beta-glucosyltransferase activity ; GO:0047807 ; EC:2.4.1.118 dolichyl-phosphate beta-glucosyltransferase activity ; GO:0004581 ; EC:2.4.1.117 ecdysteroid UDP-glucosyltransferase activity ; GO:0050488 flavanone 7-O-beta-glucosyltransferase activity ; GO:0047243 ; EC:2.4.1.185 flavone 7-O-beta-glucosyltransferase activity ; GO:0047891 ; EC:2.4.1.81 flavonol 3-O-glucosyltransferase activity ; GO:0047893 ; EC:2.4.1.91 gallate 1-beta-glucosyltransferase activity ; GO:0047913 ; EC:2.4.1.136 gibberellin beta-D-glucosyltransferase activity ; GO:0047928 ; EC:2.4.1.176 glycogen (starch) synthase activity ; GO:0004373 ; EC:2.4.1.11 glycogenin glucosyltransferase activity ; GO:0008466 ; EC:2.4.1.186 hydroquinone glucosyltransferase activity ; GO:0050505 ; EC:2.4.1.218 hydroxyanthraquinone glucosyltransferase activity ; GO:0047242 ; EC:2.4.1.18 hydroxycinnamate 4-beta-glucosyltransferase activity ; GO:0047218 ; EC:2.4.1.126 hydroxymandelonitrile glucosyltransferase activity ; GO:0047239 ; EC:2.4.1.178 indole-3-acetate beta-glucosyltransferase activity ; GO:0047215 ; EC:2.4.1.121 indoxyl-UDPG glucosyltransferase activity ; GO:0050507 ; EC:2.4.1.220 isoflavone 7-O-glucosyltransferase activity ; GO:0050004 ; EC:2.4.1.170 isovitexin beta-glucosyltransferase activity ; GO:0050010 ; EC:2.4.1.106 limonoid glucosyltransferase activity ; GO:0050645 ; EC:2.4.1.210 lipopolysaccharide glucosyltransferase I activity ; GO:0008919 ; EC:2.4.1.58 lipopolysaccharide glucosyltransferase II activity ; GO:0047270 ; EC:2.4.1.73 methyl-ONN-azoxymethanol beta-D-glucosyltransferase activity ; GO:0047236 ; EC:2.4.1.171 monoterpenol beta-glucosyltransferase activity ; GO:0047219 ; EC:2.4.1.127 N-acetylglucosaminyldiphosphoundecaprenol glucosyltransferase activity ; GO:0047245 ; EC:2.4.1.188 nicotinate glucosyltransferase activity ; GO:0050139 ; EC:2.4.1.196 nuatigenin 3-beta-glucosyltransferase activity ; GO:0047248 ; EC:2.4.1.192 o-dihydroxycoumarin 7-O-glucosyltransferase activity ; GO:0047208 ; EC:2.4.1.104 phenol beta-glucosyltransferase activity ; GO:0050171 ; EC:2.4.1.3 phosphopolyprenol glucosyltransferase activity ; GO:0047272 ; EC:2.4.1.78 poly(glycerol-phosphate) alpha-glucosyltransferase activity ; GO:0047265 ; EC:2.4.1.52 poly(ribitol-phosphate) beta-glucosyltransferase activity ; GO:0047266 ; EC:2.4.1.53 pyridoxine 5'-O-beta-D-glucosyltransferase activity ; GO:0047231 ; EC:2.4.1.160 salicyl-alcohol beta-D-glucosyltransferase activity ; GO:0050274 ; EC:2.4.1.172 sarsapogenin 3-beta-glucosyltransferase activity ; GO:0047249 ; EC:2.4.1.193 scopoletin glucosyltransferase activity ; GO:0050275 ; EC:2.4.1.128 sinapate 1-glucosyltransferase activity ; GO:0050284 ; EC:2.4.1.120 sterol 3-beta-glucosyltransferase activity ; GO:0016906 ; EC:2.4.1.173 sucrose synthase activity ; GO:0016157 ; EC:2.4.1.13 sucrose-phosphate synthase activity ; GO:0046524 ; EC:2.4.1.14 thiohydroximate beta-D-glucosyltransferase activity ; GO:0047251 ; EC:2.4.1.195 trans-zeatin O-beta-D-glucosyltransferase activity ; GO:0050403 ; EC:2.4.1.203 UDP-glucose:glycoprotein glucosyltransferase activity ; GO:0003980 ; EC:2.4.1.- vitexin beta-glucosyltransferase activity ; GO:0050395 ; EC:2.4.1.105 vomilenine glucosyltransferase activity ; GO:0050506 ; EC:2.4.1.219

MOVED the following to be is_a children of UDP-xylosyltransferase activity:

dolichyl-phosphate D-xylosyltransferase activity ; GO:0047283 ; EC:2.4.2.32 flavonol-3-O-glycoside xylosyltransferase activity ; GO:0047285 ; EC:2.4.2.35 glycoprotein 2-beta-D-xylosyltransferase activity ; GO:0050513 ; EC:2.4.2.38 protein xylosyltransferase activity ; GO:0030158 ; EC:2.4.2.26 zeatin O-beta-D-xylosyltransferase activity ; GO:0050404 ; EC:2.4.2.40

Original comment by: beckyfoulger

gocentral commented 20 years ago

Original comment by: beckyfoulger