PCO5_ARATH
ID PCO5_ARATH Reviewed; 242 AA.
AC Q9LXT4;
DT 01-APR-2015, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 131.
DE RecName: Full=Plant cysteine oxidase 5 {ECO:0000303|PubMed:24599061};
DE Short=AtPCO5 {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=PCO5 {ECO:0000303|PubMed:24599061};
GN OrderedLocusNames=At3g58670 {ECO:0000312|Araport:AT3G58670};
GN ORFNames=T20N10.20 {ECO:0000312|EMBL:CAB88284.1};
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=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(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, 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, 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 [7]
RP X-RAY CRYSTALLOGRAPHY (2.50 ANGSTROMS) OF 1-242 IN COMPLEX WITH IRON IONS,
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, AND MUTAGENESIS OF HIS-164;
RP ASP-176; TYR-182 AND CYS-190.
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 [8]
RP X-RAY CRYSTALLOGRAPHY (1.91 ANGSTROMS) IN COMPLEX WITH IRON IONS, FUNCTION,
RP AND CATALYTIC ACTIVITY.
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: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:29848548,
CC PubMed:33207269, PubMed:32868422). Acts as an oxygen sensor that
CC controls the stability of ERF-VII proteins, which are stabilized in
CC flooding-induced hypoxia, and regulate transcriptional adaptation to
CC these adverse conditions (Probable) (PubMed:29848548).
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:33207269};
CC Note=Binds 1 Fe(2+) cation per subunit. {ECO:0000269|PubMed:33207269};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.16 mM for CGGAIISDFIPPPR peptide {ECO:0000269|PubMed:29848548};
CC Vmax=16.1 umol/min/mg enzyme with CGGAIISDFIPPPR peptide as substrate
CC {ECO:0000269|PubMed:29848548};
CC Note=kcat is 7.9 sec(-1) with CGGAIISDFIPPPR peptide as substrate.
CC {ECO:0000269|PubMed:29848548};
CC pH dependence:
CC Optimum pH is 9.0 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 -!- SIMILARITY: Belongs to the cysteine dioxygenase family. {ECO:0000305}.
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DR EMBL; AL353032; CAB88284.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE79813.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE79814.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE79815.1; -; Genomic_DNA.
DR EMBL; AY050940; AAK93617.1; -; mRNA.
DR EMBL; AY142515; AAN13116.1; -; mRNA.
DR EMBL; AY084662; AAM61224.1; -; mRNA.
DR PIR; T49150; T49150.
DR RefSeq; NP_001078310.1; NM_001084841.2.
DR RefSeq; NP_001190128.1; NM_001203199.1.
DR RefSeq; NP_191426.1; NM_115729.4.
DR PDB; 6SBP; X-ray; 1.91 A; A=1-242.
DR PDB; 7CHI; X-ray; 2.50 A; A=1-242.
DR PDBsum; 6SBP; -.
DR PDBsum; 7CHI; -.
DR AlphaFoldDB; Q9LXT4; -.
DR SMR; Q9LXT4; -.
DR IntAct; Q9LXT4; 1.
DR STRING; 3702.AT3G58670.3; -.
DR PaxDb; Q9LXT4; -.
DR PRIDE; Q9LXT4; -.
DR ProteomicsDB; 236371; -.
DR EnsemblPlants; AT3G58670.1; AT3G58670.1; AT3G58670.
DR EnsemblPlants; AT3G58670.2; AT3G58670.2; AT3G58670.
DR EnsemblPlants; AT3G58670.3; AT3G58670.3; AT3G58670.
DR GeneID; 825036; -.
DR Gramene; AT3G58670.1; AT3G58670.1; AT3G58670.
DR Gramene; AT3G58670.2; AT3G58670.2; AT3G58670.
DR Gramene; AT3G58670.3; AT3G58670.3; AT3G58670.
DR KEGG; ath:AT3G58670; -.
DR Araport; AT3G58670; -.
DR TAIR; locus:2098984; AT3G58670.
DR eggNOG; KOG4281; Eukaryota.
DR HOGENOM; CLU_061320_3_2_1; -.
DR InParanoid; Q9LXT4; -.
DR OMA; RCIWGKL; -.
DR OrthoDB; 929927at2759; -.
DR PhylomeDB; Q9LXT4; -.
DR SABIO-RK; Q9LXT4; -.
DR PRO; PR:Q9LXT4; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9LXT4; baseline and differential.
DR Genevisible; Q9LXT4; 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; Cytoplasm; Iron; Metal-binding; Nucleus; Oxidoreductase;
KW Reference proteome.
FT CHAIN 1..242
FT /note="Plant cysteine oxidase 5"
FT /id="PRO_0000432453"
FT BINDING 98
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:33207269,
FT ECO:0007744|PDB:7CHI"
FT BINDING 100
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:33207269,
FT ECO:0007744|PDB:7CHI"
FT BINDING 164
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:33207269,
FT ECO:0007744|PDB:7CHI"
FT MUTAGEN 164
FT /note="H->A: Abolishes catalytic activity."
FT /evidence="ECO:0000269|PubMed:33207269"
FT MUTAGEN 176
FT /note="D->A: Strongly reduces catalytic activity."
FT /evidence="ECO:0000269|PubMed:33207269"
FT MUTAGEN 182
FT /note="Y->F: Reduces catalytic activity."
FT /evidence="ECO:0000269|PubMed:33207269"
FT MUTAGEN 190
FT /note="C->A: No effect on catalytic activity."
FT /evidence="ECO:0000269|PubMed:33207269"
FT HELIX 4..15
FT /evidence="ECO:0007829|PDB:6SBP"
FT STRAND 20..22
FT /evidence="ECO:0007829|PDB:6SBP"
FT HELIX 24..34
FT /evidence="ECO:0007829|PDB:6SBP"
FT HELIX 39..42
FT /evidence="ECO:0007829|PDB:6SBP"
FT HELIX 45..48
FT /evidence="ECO:0007829|PDB:6SBP"
FT TURN 49..52
FT /evidence="ECO:0007829|PDB:6SBP"
FT STRAND 71..78
FT /evidence="ECO:0007829|PDB:6SBP"
FT STRAND 83..89
FT /evidence="ECO:0007829|PDB:6SBP"
FT STRAND 94..98
FT /evidence="ECO:0007829|PDB:6SBP"
FT STRAND 104..122
FT /evidence="ECO:0007829|PDB:6SBP"
FT HELIX 124..126
FT /evidence="ECO:0007829|PDB:6SBP"
FT TURN 127..129
FT /evidence="ECO:0007829|PDB:6SBP"
FT STRAND 136..149
FT /evidence="ECO:0007829|PDB:6SBP"
FT STRAND 153..155
FT /evidence="ECO:0007829|PDB:6SBP"
FT STRAND 157..160
FT /evidence="ECO:0007829|PDB:6SBP"
FT STRAND 162..180
FT /evidence="ECO:0007829|PDB:6SBP"
FT TURN 184..187
FT /evidence="ECO:0007829|PDB:6SBP"
FT STRAND 192..195
FT /evidence="ECO:0007829|PDB:6SBP"
FT HELIX 208..210
FT /evidence="ECO:0007829|PDB:7CHI"
FT STRAND 215..222
FT /evidence="ECO:0007829|PDB:6SBP"
FT STRAND 230..233
FT /evidence="ECO:0007829|PDB:6SBP"
SQ SEQUENCE 242 AA; 27223 MW; AFF81F770EB5F623 CRC64;
MPYFIQRLFN TCKSSLSPNG PVSEEALDKV RNVLEKIKPS DVGLEQEAQL VRNWPGPGNE
RNGNHHSLPA IKYLQLHECD SFSIGIFCMP PGSIIPLHNH PGMTVLSKLV YGSMHVKSYD
WAEPDQSELD DPLQARPAKL VKDIDMTSPS PATTLYPTTG GNIHCFKAIT HCAIFDILSP
PYSSTHGRHC NYFRKSPMLD LPGEIEVMNG EVISNVTWLE EYQPPDNFVI WRVPYRGPVI
RK
