PCO4_ARATH
ID PCO4_ARATH Reviewed; 241 AA.
AC Q9SJI9; Q0WUD4;
DT 01-APR-2015, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2002, sequence version 2.
DT 03-AUG-2022, entry version 134.
DE RecName: Full=Plant cysteine oxidase 4 {ECO:0000303|PubMed:24599061};
DE Short=AtPCO4 {ECO:0000303|PubMed:33207269};
DE EC=1.13.11.20 {ECO:0000269|PubMed:29848548, ECO:0000269|PubMed:32868422, ECO:0000269|PubMed:33207269, ECO:0000305|PubMed:24599061};
GN Name=PCO4 {ECO:0000303|PubMed:24599061};
GN OrderedLocusNames=At2g42670 {ECO:0000312|Araport:AT2G42670};
GN ORFNames=F14N22.6 {ECO:0000312|EMBL:AAM15389.1};
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=10617197; DOI=10.1038/45471;
RA Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL Nature 402:761-768(1999).
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] (ISOFORM 1).
RA Shinn P., Chen H., Kim C.J., Ecker J.R.;
RT "Arabidopsis ORF clones.";
RL Submitted (FEB-2006) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, GENE FAMILY, NOMENCLATURE, AND SUBCELLULAR
RP LOCATION.
RX PubMed=24599061; DOI=10.1038/ncomms4425;
RA Weits D.A., Giuntoli B., Kosmacz M., Parlanti S., Hubberten H.M.,
RA Riegler H., Hoefgen R., Perata P., van Dongen J.T., Licausi F.;
RT "Plant cysteine oxidases control the oxygen-dependent branch of the N-end-
RT rule pathway.";
RL Nat. Commun. 5:3425-3425(2014).
RN [6]
RP FUNCTION.
RX PubMed=28332493; DOI=10.1038/ncomms14690;
RA White M.D., Klecker M., Hopkinson R.J., Weits D.A., Mueller C., Naumann C.,
RA O'Neill R., Wickens J., Yang J., Brooks-Bartlett J.C., Garman E.F.,
RA Grossmann T.N., Dissmeyer N., Flashman E.;
RT "Plant cysteine oxidases are dioxygenases that directly enable arginyl
RT transferase-catalysed arginylation of N-end rule targets.";
RL Nat. Commun. 8:14690-14690(2017).
RN [7]
RP FUNCTION, CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=29848548; DOI=10.1074/jbc.ra118.003496;
RA White M.D., Kamps J.J.A.G., East S., Taylor Kearney L.J., Flashman E.;
RT "The plant cysteine oxidases from Arabidopsis thaliana are kinetically
RT tailored to act as oxygen sensors.";
RL J. Biol. Chem. 293:11786-11795(2018).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.44 ANGSTROMS) OF 1-241 IN COMPLEX WITH IRON IONS,
RP FUNCTION, CATALYTIC ACTIVITY, AND COFACTOR.
RX PubMed=33207269; DOI=10.1016/j.jsb.2020.107663;
RA Chen Z., Guo Q., Wu G., Wen J., Liao S., Xu C.;
RT "Molecular basis for cysteine oxidation by plant cysteine oxidases from
RT Arabidopsis thaliana.";
RL J. Struct. Biol. 213:107663-107663(2020).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (1.24 ANGSTROMS) IN COMPLEX WITH IRON IONS, FUNCTION,
RP CATALYTIC ACTIVITY, COFACTOR, AND MUTAGENESIS OF SER-107; HIS-164; ASP-176;
RP TYR-182 AND CYS-190.
RX PubMed=32868422; DOI=10.1073/pnas.2000206117;
RA White M.D., Dalle Carbonare L., Lavilla Puerta M., Iacopino S., Edwards M.,
RA Dunne K., Pires E., Levy C., McDonough M.A., Licausi F., Flashman E.;
RT "Structures of Arabidopsis thaliana oxygen-sensing plant cysteine oxidases
RT 4 and 5 enable targeted manipulation of their activity.";
RL Proc. Natl. Acad. Sci. U.S.A. 117:23140-23147(2020).
CC -!- FUNCTION: Catalyzes the oxidation of N-terminal cysteine residues (N-
CC Cys), thus preparing the protein for N-end rule pathway-mediated
CC proteasomal degradation, upstream of the N-end rule enzymes ATE1, ATE2
CC and PRT6 (Probable) (PubMed:28332493, PubMed:29848548, PubMed:33207269,
CC PubMed:32868422). Controls the preparation of the group VII ethylene
CC response factor (ERF-VII) proteins for degradation via the 26S
CC proteasome N-end rule pathway (Probable) (PubMed:28332493,
CC PubMed:29848548, PubMed:33207269, PubMed:32868422). Acts as an oxygen
CC sensor that controls the stability of ERF-VII proteins, which are
CC stabilized in flooding-induced hypoxia, and regulate transcriptional
CC adaptation to these adverse conditions (PubMed:28332493,
CC PubMed:29848548). {ECO:0000269|PubMed:28332493,
CC ECO:0000269|PubMed:29848548, ECO:0000269|PubMed:32868422,
CC ECO:0000269|PubMed:33207269, ECO:0000305|PubMed:24599061}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-cysteine + O2 = 3-sulfino-L-alanine + H(+);
CC Xref=Rhea:RHEA:20441, ChEBI:CHEBI:15378, ChEBI:CHEBI:15379,
CC ChEBI:CHEBI:35235, ChEBI:CHEBI:61085; EC=1.13.11.20;
CC Evidence={ECO:0000269|PubMed:29848548, ECO:0000269|PubMed:32868422,
CC ECO:0000269|PubMed:33207269, ECO:0000305|PubMed:24599061};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:20442;
CC Evidence={ECO:0000269|PubMed:29848548, ECO:0000269|PubMed:32868422,
CC ECO:0000269|PubMed:33207269, ECO:0000305|PubMed:24599061};
CC -!- COFACTOR:
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
CC Evidence={ECO:0000269|PubMed:32868422, ECO:0000269|PubMed:33207269};
CC Note=Binds 1 Fe(2+) cation per subunit. {ECO:0000269|PubMed:32868422,
CC ECO:0000269|PubMed:33207269};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.69 mM for CGGAIISDFIPPPR peptide {ECO:0000269|PubMed:29848548};
CC Vmax=63.4 umol/min/mg enzyme with CGGAIISDFIPPPR peptide as substrate
CC {ECO:0000269|PubMed:29848548};
CC Note=kcat is 31 sec(-1) with CGGAIISDFIPPPR peptide as substrate.
CC {ECO:0000269|PubMed:29848548};
CC pH dependence:
CC Optimum pH is 8.5 with CGGAIISDFIPPPR peptide as substrate.
CC {ECO:0000269|PubMed:29848548};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305|PubMed:24599061}. Cytoplasm
CC {ECO:0000305|PubMed:24599061}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q9SJI9-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9SJI9-2; Sequence=VSP_057519;
CC -!- SIMILARITY: Belongs to the cysteine dioxygenase family. {ECO:0000305}.
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DR EMBL; AC006931; AAD21739.2; -; Genomic_DNA.
DR EMBL; AC007087; AAM15389.1; -; Genomic_DNA.
DR EMBL; CP002685; AEC10153.1; -; Genomic_DNA.
DR EMBL; CP002685; AEC10154.1; -; Genomic_DNA.
DR EMBL; BT024622; ABD43020.1; -; mRNA.
DR EMBL; AK227227; BAE99264.1; -; mRNA.
DR PIR; G84856; G84856.
DR RefSeq; NP_001078042.1; NM_001084573.2. [Q9SJI9-2]
DR RefSeq; NP_565980.1; NM_129828.3. [Q9SJI9-1]
DR PDB; 6S0P; X-ray; 1.24 A; A=1-241.
DR PDB; 6S7E; X-ray; 1.82 A; A=1-241.
DR PDB; 7CHJ; X-ray; 2.44 A; A/B=1-241.
DR PDBsum; 6S0P; -.
DR PDBsum; 6S7E; -.
DR PDBsum; 7CHJ; -.
DR AlphaFoldDB; Q9SJI9; -.
DR SMR; Q9SJI9; -.
DR STRING; 3702.AT2G42670.2; -.
DR iPTMnet; Q9SJI9; -.
DR PaxDb; Q9SJI9; -.
DR PRIDE; Q9SJI9; -.
DR ProteomicsDB; 236383; -. [Q9SJI9-1]
DR EnsemblPlants; AT2G42670.1; AT2G42670.1; AT2G42670. [Q9SJI9-1]
DR EnsemblPlants; AT2G42670.2; AT2G42670.2; AT2G42670. [Q9SJI9-2]
DR GeneID; 818867; -.
DR Gramene; AT2G42670.1; AT2G42670.1; AT2G42670. [Q9SJI9-1]
DR Gramene; AT2G42670.2; AT2G42670.2; AT2G42670. [Q9SJI9-2]
DR KEGG; ath:AT2G42670; -.
DR Araport; AT2G42670; -.
DR TAIR; locus:2041524; AT2G42670.
DR eggNOG; KOG4281; Eukaryota.
DR HOGENOM; CLU_061320_3_2_1; -.
DR OMA; RSSEVAW; -.
DR PhylomeDB; Q9SJI9; -.
DR SABIO-RK; Q9SJI9; -.
DR PRO; PR:Q9SJI9; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; Q9SJI9; baseline and differential.
DR Genevisible; Q9SJI9; AT.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0017172; F:cysteine dioxygenase activity; IEA:UniProtKB-EC.
DR GO; GO:0005506; F:iron ion binding; IDA:UniProtKB.
DR GO; GO:0071456; P:cellular response to hypoxia; IDA:UniProtKB.
DR GO; GO:0070483; P:detection of hypoxia; IDA:UniProtKB.
DR GO; GO:0018171; P:peptidyl-cysteine oxidation; IDA:UniProtKB.
DR Gene3D; 2.60.120.10; -; 1.
DR InterPro; IPR012864; PCO/ADO.
DR InterPro; IPR014710; RmlC-like_jellyroll.
DR InterPro; IPR011051; RmlC_Cupin_sf.
DR PANTHER; PTHR22966; PTHR22966; 1.
DR Pfam; PF07847; PCO_ADO; 1.
DR SUPFAM; SSF51182; SSF51182; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Alternative splicing; Cytoplasm; Iron; Metal-binding;
KW Nucleus; Oxidoreductase; Reference proteome.
FT CHAIN 1..241
FT /note="Plant cysteine oxidase 4"
FT /id="PRO_0000432452"
FT REGION 44..66
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 52..66
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 98
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:32868422,
FT ECO:0000269|PubMed:33207269, ECO:0007744|PDB:6S7E,
FT ECO:0007744|PDB:7CHJ"
FT BINDING 100
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:32868422,
FT ECO:0000269|PubMed:33207269, ECO:0007744|PDB:6S7E,
FT ECO:0007744|PDB:7CHJ"
FT BINDING 164
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:32868422,
FT ECO:0000269|PubMed:33207269, ECO:0007744|PDB:6S7E,
FT ECO:0007744|PDB:7CHJ"
FT VAR_SEQ 134
FT /note="Q -> QE (in isoform 2)"
FT /id="VSP_057519"
FT MUTAGEN 107
FT /note="S->A: No effect on catalytic activity."
FT /evidence="ECO:0000269|PubMed:32868422"
FT MUTAGEN 164
FT /note="H->D: Abolishes catalytic activity."
FT /evidence="ECO:0000269|PubMed:32868422"
FT MUTAGEN 176
FT /note="D->N: Almost abolishes catalytic activity."
FT /evidence="ECO:0000269|PubMed:32868422"
FT MUTAGEN 182
FT /note="Y->F: Reduces catalytic activity 2-fold."
FT /evidence="ECO:0000269|PubMed:32868422"
FT MUTAGEN 190
FT /note="C->A: No effect on catalytic activity."
FT /evidence="ECO:0000269|PubMed:32868422"
FT HELIX 4..16
FT /evidence="ECO:0007829|PDB:6S0P"
FT STRAND 17..20
FT /evidence="ECO:0007829|PDB:6S0P"
FT HELIX 24..34
FT /evidence="ECO:0007829|PDB:6S0P"
FT HELIX 39..41
FT /evidence="ECO:0007829|PDB:6S0P"
FT HELIX 45..48
FT /evidence="ECO:0007829|PDB:6S0P"
FT HELIX 49..51
FT /evidence="ECO:0007829|PDB:6S0P"
FT STRAND 71..78
FT /evidence="ECO:0007829|PDB:6S0P"
FT STRAND 83..89
FT /evidence="ECO:0007829|PDB:6S0P"
FT STRAND 94..98
FT /evidence="ECO:0007829|PDB:6S0P"
FT STRAND 104..123
FT /evidence="ECO:0007829|PDB:6S0P"
FT STRAND 136..147
FT /evidence="ECO:0007829|PDB:6S0P"
FT STRAND 153..155
FT /evidence="ECO:0007829|PDB:6S0P"
FT STRAND 157..160
FT /evidence="ECO:0007829|PDB:6S0P"
FT STRAND 162..181
FT /evidence="ECO:0007829|PDB:6S0P"
FT TURN 184..187
FT /evidence="ECO:0007829|PDB:6S7E"
FT STRAND 192..195
FT /evidence="ECO:0007829|PDB:6S0P"
FT STRAND 199..201
FT /evidence="ECO:0007829|PDB:6S0P"
FT STRAND 205..207
FT /evidence="ECO:0007829|PDB:6S0P"
FT STRAND 210..212
FT /evidence="ECO:0007829|PDB:6S0P"
FT STRAND 214..220
FT /evidence="ECO:0007829|PDB:6S0P"
FT STRAND 229..232
FT /evidence="ECO:0007829|PDB:6S0P"
SQ SEQUENCE 241 AA; 27183 MW; 360BBB2A26F77190 CRC64;
MPYFAQRLYN TCKASFSSDG PITEDALEKV RNVLEKIKPS DVGIEQDAQL ARSRSGPLNE
RNGSNQSPPA IKYLHLHECD SFSIGIFCMP PSSMIPLHNH PGMTVLSKLV YGSMHVKSYD
WLEPQLTEPE DPSQARPAKL VKDTEMTAQS PVTTLYPKSG GNIHCFKAIT HCAILDILAP
PYSSEHDRHC TYFRKSRRED LPGELEVDGE VVTDVTWLEE FQPPDDFVIR RIPYRGPVIR
T
