PUMY_ARATH
ID PUMY_ARATH Reviewed; 330 AA.
AC Q84K35; Q9LPS4;
DT 23-FEB-2022, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 131.
DE RecName: Full=Pseudouridine-5'-phosphate glycosidase {ECO:0000305};
DE Short=PsiMP glycosidase {ECO:0000305};
DE EC=4.2.1.70 {ECO:0000269|PubMed:31907295};
DE AltName: Full=Pseudouridine monophosphate glycosidase {ECO:0000303|PubMed:31907295};
GN Name=PUMY {ECO:0000303|PubMed:31907295};
GN OrderedLocusNames=At1g50510 {ECO:0000312|EMBL:AEE32559.1};
GN ORFNames=F11F12.14 {ECO:0000312|EMBL:AAF87879.1};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(2000).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [4]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22223895; DOI=10.1074/mcp.m111.015131;
RA Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T.,
RA Giglione C.;
RT "Comparative large-scale characterisation of plant vs. mammal proteins
RT reveals similar and idiosyncratic N-alpha acetylation features.";
RL Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND
RP SUBCELLULAR LOCATION.
RX PubMed=31907295; DOI=10.1105/tpc.19.00639;
RA Chen M., Witte C.P.;
RT "A kinase and a glycosylase catabolize pseudouridine in the peroxisome to
RT prevent toxic pseudouridine monophosphate accumulation.";
RL Plant Cell 32:722-739(2020).
CC -!- FUNCTION: Catalyzes the reversible cleavage of pseudouridine 5'-
CC phosphate (PsiMP) to ribose 5-phosphate and uracil (PubMed:31907295).
CC Functions biologically in the cleavage direction, as part of a
CC pseudouridine degradation pathway (PubMed:31907295). Acts together with
CC the pseudouridine kinase PUKI in the peroxisome to prevent toxic
CC pseudouridine monophosphate accumulation (PubMed:31907295). Can
CC catalyze the formation of pseudouridine 5'-phosphate (reverse reaction)
CC in vitro, with a catalytic efficiency 4 times lower than the hydrolysis
CC reaction (PubMed:31907295). {ECO:0000269|PubMed:31907295}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-ribose 5-phosphate + uracil = H2O + psi-UMP;
CC Xref=Rhea:RHEA:18337, ChEBI:CHEBI:15377, ChEBI:CHEBI:17568,
CC ChEBI:CHEBI:58380, ChEBI:CHEBI:78346; EC=4.2.1.70;
CC Evidence={ECO:0000269|PubMed:31907295};
CC PhysiologicalDirection=right-to-left; Xref=Rhea:RHEA:18339;
CC Evidence={ECO:0000269|PubMed:31907295};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000250|UniProtKB:P33025};
CC Note=Binds 1 Mn(2+) ion per subunit. {ECO:0000250|UniProtKB:P33025};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=32.7 uM for pseudouridine 5'-phosphate
CC {ECO:0000269|PubMed:31907295};
CC Note=kcat is 1.41 (sec-1) with pseudouridine 5'-phosphate as
CC substrate. {ECO:0000269|PubMed:31907295};
CC -!- SUBUNIT: Homotrimer. {ECO:0000250|UniProtKB:P33025}.
CC -!- SUBCELLULAR LOCATION: Peroxisome {ECO:0000269|PubMed:31907295}.
CC -!- SIMILARITY: Belongs to the pseudouridine-5'-phosphate glycosidase
CC family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAF87879.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC012561; AAF87879.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE32559.1; -; Genomic_DNA.
DR EMBL; BT002789; AAO22617.1; -; mRNA.
DR EMBL; BT004358; AAO42352.1; -; mRNA.
DR RefSeq; NP_564574.2; NM_103934.5.
DR AlphaFoldDB; Q84K35; -.
DR SMR; Q84K35; -.
DR STRING; 3702.AT1G50510.1; -.
DR PaxDb; Q84K35; -.
DR PRIDE; Q84K35; -.
DR ProteomicsDB; 180881; -.
DR EnsemblPlants; AT1G50510.1; AT1G50510.1; AT1G50510.
DR GeneID; 841473; -.
DR Gramene; AT1G50510.1; AT1G50510.1; AT1G50510.
DR KEGG; ath:AT1G50510; -.
DR TAIR; locus:2008081; AT1G50510.
DR eggNOG; KOG3009; Eukaryota.
DR HOGENOM; CLU_012201_0_1_1; -.
DR InParanoid; Q84K35; -.
DR OMA; RKLGHRD; -.
DR OrthoDB; 406966at2759; -.
DR PhylomeDB; Q84K35; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q84K35; baseline and differential.
DR GO; GO:0005777; C:peroxisome; IDA:TAIR.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004730; F:pseudouridylate synthase activity; IEA:InterPro.
DR GO; GO:0030597; F:RNA glycosylase activity; IDA:TAIR.
DR Gene3D; 3.40.1790.10; -; 1.
DR HAMAP; MF_01876; PsiMP_glycosidase; 1.
DR InterPro; IPR022830; Indigdn_synthA-like.
DR InterPro; IPR007342; PsuG.
DR PANTHER; PTHR42909; PTHR42909; 1.
DR Pfam; PF04227; Indigoidine_A; 1.
DR SUPFAM; SSF110581; SSF110581; 1.
PE 1: Evidence at protein level;
KW Glycosidase; Hydrolase; Lyase; Manganese; Metal-binding; Peroxisome;
KW Reference proteome.
FT CHAIN 1..330
FT /note="Pseudouridine-5'-phosphate glycosidase"
FT /id="PRO_0000454668"
FT ACT_SITE 50
FT /note="Proton donor"
FT /evidence="ECO:0000250|UniProtKB:P33025"
FT ACT_SITE 185
FT /note="Nucleophile"
FT /evidence="ECO:0000250|UniProtKB:P33025"
FT BINDING 112
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P33025"
FT BINDING 132
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P33025"
FT BINDING 164
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000250|UniProtKB:P33025"
FT BINDING 166..168
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P33025"
SQ SEQUENCE 330 AA; 34800 MW; 2A30187121EC881A CRC64;
MASSLAQSRI SNLQNHLSPL EANNKLRSLV KISPQVSEAL SNGRAVVALE STIISHGMPY
PQNLQTAKEV ESIVRENGAI PATIAILNGV PCIGLSEEEL ERLASLGKSV QKTAGRDIAN
VVATRGNGAT TVSATLFFAS MVGIQVFVTG GIGGVHRHAN HSMDISSDLT ALGRTPIAVI
SAGVKSILDI PKTLEYLETQ EVYVAAYKSD EFPAFFTEKS GCKAPSRVNS PEDCARVIDA
NMKLNRQAGI LFAIPIPKHH SAAGNLIESA TQRALTEARE QNVTGNAETP FLLARVNELT
GGTSLAANIA LVKNNALIGS QIAVALSQLM
