PUKI_ARATH
ID PUKI_ARATH Reviewed; 378 AA.
AC Q94AT3; Q8LFL6;
DT 23-FEB-2022, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 140.
DE RecName: Full=Pseudouridine kinase {ECO:0000303|PubMed:31907295};
DE EC=2.7.1.83 {ECO:0000269|PubMed:31907295, ECO:0000269|PubMed:33290549};
GN Name=PUKI {ECO:0000303|PubMed:31907295};
GN OrderedLocusNames=At1g49350 {ECO:0000312|Araport:AT1G49350};
GN ORFNames=F13F21.22 {ECO:0000312|EMBL:AEE32421.1};
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 NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
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).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.08 ANGSTROMS) IN COMPLEX WITH PSEUDOURIDINE; ATP
RP AND MAGNESIUM IONS, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES,
RP SUBUNIT, AND MUTAGENESIS OF ILE-10; ASP-12; THR-26; ASN-137; GLU-160;
RP LYS-166; THR-298; VAL-303; LEU-306; ASP-311 AND VAL-342.
RX PubMed=33290549; DOI=10.1093/nar/gkaa1144;
RA Kim S.H., Witte C.P., Rhee S.;
RT "Structural basis for the substrate specificity and catalytic features of
RT pseudouridine kinase from Arabidopsis thaliana.";
RL Nucleic Acids Res. 49:491-503(2021).
CC -!- FUNCTION: Catalyzes the phosphorylation of pseudouridine to
CC pseudouridine 5'-phosphate (PsiMP) (PubMed:31907295). Catalyzes the
CC first step in a pseudouridine degradation pathway (PubMed:31907295).
CC Acts together with the pseudouridine 5'-phosphate glycosidase PUMY in
CC the peroxisome to prevent toxic pseudouridine monophosphate
CC accumulation (PubMed:31907295). {ECO:0000269|PubMed:31907295}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + pseudouridine = ADP + H(+) + psi-UMP;
CC Xref=Rhea:RHEA:22448, ChEBI:CHEBI:15378, ChEBI:CHEBI:17802,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:58380, ChEBI:CHEBI:456216;
CC EC=2.7.1.83; Evidence={ECO:0000269|PubMed:31907295,
CC ECO:0000269|PubMed:33290549};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:22449;
CC Evidence={ECO:0000269|PubMed:31907295, ECO:0000269|PubMed:33290549};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=4.4 uM for pseudouridine {ECO:0000269|PubMed:31907295};
CC KM=39.6 uM for pseudouridine {ECO:0000269|PubMed:33290549};
CC KM=762 uM for ATP {ECO:0000269|PubMed:33290549};
CC Note=kcat is 0.23 (sec-1) with pseudouridine as substrate
CC (PubMed:31907295). kcat is 5.28 (sec-1) with pseudouridine as
CC substrate (PubMed:33290549). kcat is 5.80 (sec-1) with ATP as
CC substrate (PubMed:33290549). {ECO:0000269|PubMed:31907295,
CC ECO:0000269|PubMed:33290549};
CC -!- SUBUNIT: Forms homodimers. {ECO:0000269|PubMed:33290549}.
CC -!- SUBCELLULAR LOCATION: Peroxisome {ECO:0000269|PubMed:31907295}.
CC -!- SIMILARITY: Belongs to the carbohydrate kinase PfkB family.
CC {ECO:0000305}.
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DR EMBL; CP002684; AEE32421.1; -; Genomic_DNA.
DR EMBL; AY045816; AAK76490.1; -; mRNA.
DR EMBL; AY142514; AAN13115.1; -; mRNA.
DR EMBL; AY084771; AAM61339.1; -; mRNA.
DR RefSeq; NP_564543.1; NM_103825.6.
DR PDB; 7C1X; X-ray; 2.39 A; A/B=1-378.
DR PDB; 7C1Y; X-ray; 2.08 A; A/B=1-378.
DR PDB; 7C1Z; X-ray; 2.10 A; A/B=1-378.
DR PDBsum; 7C1X; -.
DR PDBsum; 7C1Y; -.
DR PDBsum; 7C1Z; -.
DR AlphaFoldDB; Q94AT3; -.
DR SMR; Q94AT3; -.
DR STRING; 3702.AT1G49350.1; -.
DR PaxDb; Q94AT3; -.
DR PRIDE; Q94AT3; -.
DR ProteomicsDB; 176749; -.
DR EnsemblPlants; AT1G49350.1; AT1G49350.1; AT1G49350.
DR GeneID; 841358; -.
DR Gramene; AT1G49350.1; AT1G49350.1; AT1G49350.
DR KEGG; ath:AT1G49350; -.
DR Araport; AT1G49350; -.
DR TAIR; locus:2010187; AT1G49350.
DR eggNOG; KOG3009; Eukaryota.
DR HOGENOM; CLU_038991_0_0_1; -.
DR InParanoid; Q94AT3; -.
DR OMA; GHIMNLM; -.
DR OrthoDB; 918144at2759; -.
DR PhylomeDB; Q94AT3; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q94AT3; baseline and differential.
DR GO; GO:0005777; C:peroxisome; IDA:TAIR.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016301; F:kinase activity; IDA:TAIR.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0016773; F:phosphotransferase activity, alcohol group as acceptor; IEA:InterPro.
DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW.
DR Gene3D; 3.40.1190.20; -; 1.
DR InterPro; IPR002173; Carboh/pur_kinase_PfkB_CS.
DR InterPro; IPR011611; PfkB_dom.
DR InterPro; IPR002139; Ribo/fructo_kinase.
DR InterPro; IPR029056; Ribokinase-like.
DR Pfam; PF00294; PfkB; 2.
DR PRINTS; PR00990; RIBOKINASE.
DR SUPFAM; SSF53613; SSF53613; 1.
DR PROSITE; PS00583; PFKB_KINASES_1; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Kinase; Magnesium; Metal-binding;
KW Nucleotide-binding; Peroxisome; Reference proteome; Transferase.
FT CHAIN 1..378
FT /note="Pseudouridine kinase"
FT /id="PRO_0000454667"
FT BINDING 12
FT /ligand="pseudouridine"
FT /ligand_id="ChEBI:CHEBI:17802"
FT /evidence="ECO:0000269|PubMed:33290549,
FT ECO:0007744|PDB:7C1Y"
FT BINDING 26
FT /ligand="pseudouridine"
FT /ligand_id="ChEBI:CHEBI:17802"
FT /evidence="ECO:0000269|PubMed:33290549,
FT ECO:0007744|PDB:7C1Y"
FT BINDING 37..41
FT /ligand="pseudouridine"
FT /ligand_id="ChEBI:CHEBI:17802"
FT /evidence="ECO:0000269|PubMed:33290549,
FT ECO:0007744|PDB:7C1Y"
FT BINDING 38
FT /ligand="pseudouridine"
FT /ligand_id="ChEBI:CHEBI:17802"
FT /evidence="ECO:0000269|PubMed:33290549,
FT ECO:0007744|PDB:7C1Y"
FT BINDING 137
FT /ligand="pseudouridine"
FT /ligand_id="ChEBI:CHEBI:17802"
FT /evidence="ECO:0000269|PubMed:33290549,
FT ECO:0007744|PDB:7C1Y"
FT BINDING 166
FT /ligand="pseudouridine"
FT /ligand_id="ChEBI:CHEBI:17802"
FT /evidence="ECO:0000269|PubMed:33290549,
FT ECO:0007744|PDB:7C1Y"
FT BINDING 181
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:33290549,
FT ECO:0007744|PDB:7C1Z"
FT BINDING 237
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:33290549,
FT ECO:0007744|PDB:7C1Y, ECO:0007744|PDB:7C1Z"
FT BINDING 237
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:33290549,
FT ECO:0007744|PDB:7C1Z"
FT BINDING 239
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:33290549,
FT ECO:0007744|PDB:7C1Y, ECO:0007744|PDB:7C1Z"
FT BINDING 242
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:33290549,
FT ECO:0007744|PDB:7C1Y, ECO:0007744|PDB:7C1Z"
FT BINDING 298
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:33290549,
FT ECO:0007744|PDB:7C1Y, ECO:0007744|PDB:7C1Z"
FT BINDING 306
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:33290549,
FT ECO:0007744|PDB:7C1Z"
FT BINDING 310
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:33290549,
FT ECO:0007744|PDB:7C1Y, ECO:0007744|PDB:7C1Z"
FT BINDING 311
FT /ligand="pseudouridine"
FT /ligand_id="ChEBI:CHEBI:17802"
FT /evidence="ECO:0000269|PubMed:33290549,
FT ECO:0007744|PDB:7C1Y"
FT MUTAGEN 10
FT /note="I->A: Reduces kinase activity 2-fold."
FT /evidence="ECO:0000269|PubMed:33290549"
FT MUTAGEN 12
FT /note="D->A: Reduces kinase activity 171-fold."
FT /evidence="ECO:0000269|PubMed:33290549"
FT MUTAGEN 12
FT /note="D->N: Reduces kinase activity 66-fold."
FT /evidence="ECO:0000269|PubMed:33290549"
FT MUTAGEN 26
FT /note="T->A: Reduces kinase activity 8-fold."
FT /evidence="ECO:0000269|PubMed:33290549"
FT MUTAGEN 26
FT /note="T->S: Reduces kinase activity 2-fold."
FT /evidence="ECO:0000269|PubMed:33290549"
FT MUTAGEN 26
FT /note="T->V: Reduces kinase activity 13-fold."
FT /evidence="ECO:0000269|PubMed:33290549"
FT MUTAGEN 137
FT /note="N->A: Reduces kinase activity 39-fold."
FT /evidence="ECO:0000269|PubMed:33290549"
FT MUTAGEN 160
FT /note="E->A: Reduces kinase activity 214-fold."
FT /evidence="ECO:0000269|PubMed:33290549"
FT MUTAGEN 160
FT /note="E->Q: Reduces kinase activity 50-fold."
FT /evidence="ECO:0000269|PubMed:33290549"
FT MUTAGEN 166
FT /note="K->A: Reduces kinase activity 6-fold."
FT /evidence="ECO:0000269|PubMed:33290549"
FT MUTAGEN 298
FT /note="T->A: Reduces kinase activity 2-fold."
FT /evidence="ECO:0000269|PubMed:33290549"
FT MUTAGEN 298
FT /note="T->V: No effect on kinase activity."
FT /evidence="ECO:0000269|PubMed:33290549"
FT MUTAGEN 303
FT /note="V->A: Reduces kinase activity 3-fold."
FT /evidence="ECO:0000269|PubMed:33290549"
FT MUTAGEN 306
FT /note="L->A: Reduces kinase activity 4-fold."
FT /evidence="ECO:0000269|PubMed:33290549"
FT MUTAGEN 311
FT /note="D->A: Reduces kinase activity 171-fold."
FT /evidence="ECO:0000269|PubMed:33290549"
FT MUTAGEN 342
FT /note="V->A: Reduces kinase activity 5-fold."
FT /evidence="ECO:0000269|PubMed:33290549"
FT CONFLICT 130
FT /note="R -> P (in Ref. 4; AAM61339)"
FT /evidence="ECO:0000305"
FT CONFLICT 288..289
FT /note="Missing (in Ref. 4; AAM61339)"
FT /evidence="ECO:0000305"
FT CONFLICT 366
FT /note="N -> H (in Ref. 4; AAM61339)"
FT /evidence="ECO:0000305"
FT STRAND 4..7
FT /evidence="ECO:0007829|PDB:7C1Y"
FT STRAND 10..19
FT /evidence="ECO:0007829|PDB:7C1Y"
FT STRAND 25..36
FT /evidence="ECO:0007829|PDB:7C1Y"
FT HELIX 38..48
FT /evidence="ECO:0007829|PDB:7C1Y"
FT STRAND 54..62
FT /evidence="ECO:0007829|PDB:7C1Y"
FT HELIX 63..69
FT /evidence="ECO:0007829|PDB:7C1Y"
FT STRAND 79..82
FT /evidence="ECO:0007829|PDB:7C1Y"
FT STRAND 89..94
FT /evidence="ECO:0007829|PDB:7C1Y"
FT STRAND 98..106
FT /evidence="ECO:0007829|PDB:7C1Y"
FT HELIX 108..113
FT /evidence="ECO:0007829|PDB:7C1Y"
FT HELIX 116..120
FT /evidence="ECO:0007829|PDB:7C1Y"
FT HELIX 123..127
FT /evidence="ECO:0007829|PDB:7C1Y"
FT STRAND 132..135
FT /evidence="ECO:0007829|PDB:7C1Y"
FT HELIX 140..152
FT /evidence="ECO:0007829|PDB:7C1Y"
FT STRAND 157..160
FT /evidence="ECO:0007829|PDB:7C1Y"
FT HELIX 166..172
FT /evidence="ECO:0007829|PDB:7C1Y"
FT HELIX 174..176
FT /evidence="ECO:0007829|PDB:7C1Y"
FT STRAND 178..180
FT /evidence="ECO:0007829|PDB:7C1Y"
FT HELIX 184..195
FT /evidence="ECO:0007829|PDB:7C1Y"
FT HELIX 212..228
FT /evidence="ECO:0007829|PDB:7C1Y"
FT STRAND 233..237
FT /evidence="ECO:0007829|PDB:7C1Y"
FT HELIX 239..241
FT /evidence="ECO:0007829|PDB:7C1Y"
FT STRAND 243..249
FT /evidence="ECO:0007829|PDB:7C1Y"
FT HELIX 251..253
FT /evidence="ECO:0007829|PDB:7C1Y"
FT HELIX 266..274
FT /evidence="ECO:0007829|PDB:7C1Y"
FT STRAND 292..296
FT /evidence="ECO:0007829|PDB:7C1Y"
FT HELIX 309..322
FT /evidence="ECO:0007829|PDB:7C1Y"
FT HELIX 327..342
FT /evidence="ECO:0007829|PDB:7C1Y"
FT STRAND 344..348
FT /evidence="ECO:0007829|PDB:7C1Y"
FT HELIX 354..367
FT /evidence="ECO:0007829|PDB:7C1Y"
FT STRAND 369..371
FT /evidence="ECO:0007829|PDB:7C1Y"
SQ SEQUENCE 378 AA; 40320 MW; 02BA190FFF214EAC CRC64;
MEPVIIGALI LDVHAKPSTT PISGTTVPGQ VLFAPGGVAR NVADCIFKLG ITPFMIGTLG
LDGPANVLLK EWKLSMKGIL RREDISTPIV SLVYDTNGEV AAGVAGVDAV ENFLTPEWIQ
RFEYNISSAR LLMVDANLSS LALEASCKLA AESSVPVWFE PVSVTKSQRI ASIAKYVTIV
SPNQDELIAM ANALCAKNLF HPFRSDENKL SIEDMFRALK PAILVLLKNG VKVVIVTLGS
NGALLCSKGN PKKALNIDRK FLRSGEVFKR VQSVCSPNRF SELGSNRSPS LFAMHFPTIP
AKVKKLTGAG DCLVGGTVAS LSDGLDLIQS LAVGIASAKA AVESDDNVPP EFKLDLISGD
AELVYNGAKM LMVHQSML
