DCUP1_ARATH
ID DCUP1_ARATH Reviewed; 418 AA.
AC Q93ZB6; Q9LKB1;
DT 26-MAY-2009, integrated into UniProtKB/Swiss-Prot.
DT 26-MAY-2009, sequence version 2.
DT 03-AUG-2022, entry version 130.
DE RecName: Full=Uroporphyrinogen decarboxylase 1, chloroplastic;
DE Short=UPD1;
DE Short=URO-D1;
DE EC=4.1.1.37;
DE Flags: Precursor;
GN Name=HEME1; OrderedLocusNames=At3g14930; ORFNames=K15M2.7;
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=10907853; DOI=10.1093/dnares/7.3.217;
RA Kaneko T., Katoh T., Sato S., Nakamura Y., Asamizu E., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 3. II. Sequence
RT features of the 4,251,695 bp regions covered by 90 P1, TAC and BAC
RT clones.";
RL DNA Res. 7:217-221(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] (ISOFORM 1).
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] (ISOFORM 2).
RC STRAIN=cv. Columbia;
RX PubMed=14993207; DOI=10.1101/gr.1515604;
RA Castelli V., Aury J.-M., Jaillon O., Wincker P., Clepet C., Menard M.,
RA Cruaud C., Quetier F., Scarpelli C., Schaechter V., Temple G., Caboche M.,
RA Weissenbach J., Salanoubat M.;
RT "Whole genome sequence comparisons and 'full-length' cDNA sequences: a
RT combined approach to evaluate and improve Arabidopsis genome annotation.";
RL Genome Res. 14:406-413(2004).
RN [5]
RP IDENTIFICATION.
RX PubMed=12777052; DOI=10.1023/a:1023005504702;
RA Lange B.M., Ghassemian M.;
RT "Genome organization in Arabidopsis thaliana: a survey for genes involved
RT in isoprenoid and chlorophyll metabolism.";
RL Plant Mol. Biol. 51:925-948(2003).
RN [6]
RP INDUCTION BY LIGHT.
RX PubMed=15326282; DOI=10.1104/pp.104.042408;
RA Matsumoto F., Obayashi T., Sasaki-Sekimoto Y., Ohta H., Takamiya K.,
RA Masuda T.;
RT "Gene expression profiling of the tetrapyrrole metabolic pathway in
RT Arabidopsis with a mini-array system.";
RL Plant Physiol. 135:2379-2391(2004).
CC -!- FUNCTION: Catalyzes the decarboxylation of four acetate groups of
CC uroporphyrinogen-III to yield coproporphyrinogen-III. {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=4 H(+) + uroporphyrinogen III = 4 CO2 + coproporphyrinogen
CC III; Xref=Rhea:RHEA:19865, ChEBI:CHEBI:15378, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:57308, ChEBI:CHEBI:57309; EC=4.1.1.37;
CC -!- PATHWAY: Porphyrin-containing compound metabolism; protoporphyrin-IX
CC biosynthesis; coproporphyrinogen-III from 5-aminolevulinate: step 4/4.
CC -!- PATHWAY: Porphyrin-containing compound metabolism; chlorophyll
CC biosynthesis.
CC -!- SUBUNIT: Homodimer. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast {ECO:0000305}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q93ZB6-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q93ZB6-2; Sequence=VSP_037402;
CC -!- INDUCTION: Up-regulated by light. Not regulated by circadian rhythm.
CC {ECO:0000269|PubMed:15326282}.
CC -!- MISCELLANEOUS: [Isoform 2]: May be due to a competing acceptor splice
CC site. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the uroporphyrinogen decarboxylase family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BX824686; Type=Miscellaneous discrepancy; Note=Sequencing errors.; Evidence={ECO:0000305};
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AP000370; BAA97056.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE75589.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE75590.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE75591.1; -; Genomic_DNA.
DR EMBL; AY057663; AAL15294.1; -; mRNA.
DR EMBL; AY136476; AAM97141.1; -; mRNA.
DR EMBL; BT008826; AAP68265.1; -; mRNA.
DR EMBL; BX824686; -; NOT_ANNOTATED_CDS; mRNA.
DR RefSeq; NP_566495.1; NM_112355.3. [Q93ZB6-1]
DR RefSeq; NP_850587.1; NM_180256.2. [Q93ZB6-1]
DR RefSeq; NP_974316.1; NM_202587.1. [Q93ZB6-2]
DR AlphaFoldDB; Q93ZB6; -.
DR SMR; Q93ZB6; -.
DR BioGRID; 6056; 5.
DR STRING; 3702.AT3G14930.2; -.
DR MetOSite; Q93ZB6; -.
DR PaxDb; Q93ZB6; -.
DR PRIDE; Q93ZB6; -.
DR ProteomicsDB; 224608; -. [Q93ZB6-1]
DR EnsemblPlants; AT3G14930.1; AT3G14930.1; AT3G14930. [Q93ZB6-1]
DR EnsemblPlants; AT3G14930.2; AT3G14930.2; AT3G14930. [Q93ZB6-1]
DR EnsemblPlants; AT3G14930.3; AT3G14930.3; AT3G14930. [Q93ZB6-2]
DR GeneID; 820722; -.
DR Gramene; AT3G14930.1; AT3G14930.1; AT3G14930. [Q93ZB6-1]
DR Gramene; AT3G14930.2; AT3G14930.2; AT3G14930. [Q93ZB6-1]
DR Gramene; AT3G14930.3; AT3G14930.3; AT3G14930. [Q93ZB6-2]
DR KEGG; ath:AT3G14930; -.
DR Araport; AT3G14930; -.
DR TAIR; locus:2086300; AT3G14930.
DR eggNOG; KOG2872; Eukaryota.
DR HOGENOM; CLU_040933_0_2_1; -.
DR InParanoid; Q93ZB6; -.
DR OMA; TIDMEDG; -.
DR OrthoDB; 1114675at2759; -.
DR PhylomeDB; Q93ZB6; -.
DR BioCyc; ARA:AT3G14930-MON; -.
DR UniPathway; UPA00251; UER00321.
DR UniPathway; UPA00668; -.
DR PRO; PR:Q93ZB6; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q93ZB6; baseline and differential.
DR Genevisible; Q93ZB6; AT.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR GO; GO:0004853; F:uroporphyrinogen decarboxylase activity; IEA:UniProtKB-EC.
DR GO; GO:0015995; P:chlorophyll biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0006782; P:protoporphyrinogen IX biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0046686; P:response to cadmium ion; IEP:TAIR.
DR CDD; cd00717; URO-D; 1.
DR Gene3D; 3.20.20.210; -; 1.
DR HAMAP; MF_00218; URO_D; 1.
DR InterPro; IPR038071; UROD/MetE-like_sf.
DR InterPro; IPR006361; Uroporphyrinogen_deCO2ase_HemE.
DR InterPro; IPR000257; Uroporphyrinogen_deCOase.
DR Pfam; PF01208; URO-D; 1.
DR SUPFAM; SSF51726; SSF51726; 1.
DR TIGRFAMs; TIGR01464; hemE; 1.
DR PROSITE; PS00906; UROD_1; 1.
DR PROSITE; PS00907; UROD_2; 1.
PE 2: Evidence at transcript level;
KW Alternative splicing; Chlorophyll biosynthesis; Chloroplast; Decarboxylase;
KW Lyase; Plastid; Porphyrin biosynthesis; Reference proteome;
KW Transit peptide.
FT TRANSIT 1..53
FT /note="Chloroplast"
FT /evidence="ECO:0000305"
FT CHAIN 54..418
FT /note="Uroporphyrinogen decarboxylase 1, chloroplastic"
FT /id="PRO_0000376071"
FT BINDING 80..84
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 99
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 129
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 130
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 206
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 261
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 376
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT SITE 130
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000250"
FT VAR_SEQ 1..77
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14993207"
FT /id="VSP_037402"
FT CONFLICT 36
FT /note="V -> G (in Ref. 3; AAL15294)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 418 AA; 46254 MW; F8A78980A6B08CB2 CRC64;
MSLSSPTSAC SSSRCYSSGL SFPIGFGSNP INVGLVCYPK RYSIAARKFV VACSSSSSDP
LLVKAAKGQA ISRPPAWMMR QAGRYMAVYQ KLAKKHPSFR ERSENTDLIV EISLQPWQAF
RPDGVIIFSD ILTPLPAFGV PFDIEEVKGP VIQSPIRTEE DMKRLHPIDF EKLQFVGDSL
KILRREVGEH AAVLGFVGAP WTIATYIVEG GTTRTYTVIK NMCHTAPDVL RALLSHLTKA
ITEYVVYQVE HGAHCIQIFD SWGGQLTPEM WERWSKPYIE EIIHAVKKRC PDTPIVFYIN
GNGGLLERMK GTGADVIGLD WTVDMADGRR RLGSEVSVQG NVDPAYLFSP LPALTEEIER
VVKCAGPKGH ILNLGHGVLV GTPEEAVAHF FETARNLDYQ TLFQNHVPAE KAEPELVV
