UPM1_ARATH
ID UPM1_ARATH Reviewed; 369 AA.
AC Q42606; Q96532;
DT 07-OCT-2020, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 162.
DE RecName: Full=S-adenosyl-L-methionine-dependent uroporphyrinogen III methyltransferase, chloroplastic {ECO:0000303|PubMed:29472934, ECO:0000303|PubMed:9006913};
DE Short=Urophorphyrin III methylase {ECO:0000303|PubMed:29472934, ECO:0000303|PubMed:9006913};
DE EC=2.1.1.107 {ECO:0000269|PubMed:9006913};
DE AltName: Full=Urophorphyrin methylase 1 {ECO:0000303|PubMed:29472934, ECO:0000303|PubMed:9006913};
DE Short=AtUPM1 {ECO:0000303|PubMed:29472934, ECO:0000303|PubMed:9006913};
DE Flags: Precursor;
GN Name=UPM1 {ECO:0000303|PubMed:29472934, ECO:0000303|PubMed:9006913};
GN OrderedLocusNames=At5g40850 {ECO:0000312|Araport:AT5G40850};
GN ORFNames=MHK7.8 {ECO:0000312|EMBL:BAB11347.1};
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 [GENOMIC DNA / MRNA], FUNCTION, CATALYTIC ACTIVITY,
RP SUBCELLULAR LOCATION, AND PATHWAY.
RC STRAIN=cv. Columbia;
RX PubMed=9006913; DOI=10.1074/jbc.272.5.2744;
RA Leustek T., Smith M., Murillo M., Singh D.P., Smith A.G., Woodcock S.C.,
RA Awan S.J., Warren M.J.;
RT "Siroheme biosynthesis in higher plants. Analysis of an S-adenosyl-L-
RT methionine-dependent uroporphyrinogen III methyltransferase from
RT Arabidopsis thaliana.";
RL J. Biol. Chem. 272:2744-2752(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=9679202; DOI=10.1093/dnares/5.2.131;
RA Kaneko T., Kotani H., Nakamura Y., Sato S., Asamizu E., Miyajima N.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. V. Sequence
RT features of the regions of 1,381,565 bp covered by twenty one physically
RT assigned P1 and TAC clones.";
RL DNA Res. 5:131-145(1998).
RN [3]
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 [4]
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 [5]
RP INDUCTION BY LIGHT.
RC STRAIN=cv. Columbia;
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).
RN [6]
RP FUNCTION, DISRUPTION PHENOTYPE, AND REVIEW ON SIROHEME.
RX PubMed=20592802; DOI=10.4161/psb.5.1.10173;
RA Tripathy B.C., Sherameti I., Oelmueller R.;
RT "Siroheme: an essential component for life on earth.";
RL Plant Signal. Behav. 5:14-20(2010).
RN [7]
RP TISSUE SPECIFICITY, AND INDUCTION BY LIGHT.
RC STRAIN=cv. Columbia;
RX PubMed=27729721; DOI=10.1007/s12298-016-0363-1;
RA Garai S., Joshi N.C., Tripathy B.C.;
RT "Phylogenetic analysis and photoregulation of siroheme biosynthesis genes:
RT uroporphyrinogen III methyltransferase and sirohydrochlorin ferrochelatase
RT of Arabidopsis thaliana.";
RL Physiol. Mol. Biol. Plants 22:351-359(2016).
RN [8]
RP FUNCTION.
RC STRAIN=cv. Columbia;
RX PubMed=29472934; DOI=10.3389/fpls.2017.02265;
RA Garai S., Tripathy B.C.;
RT "Alleviation of nitrogen and sulfur deficiency and enhancement of
RT photosynthesis in Arabidopsis thaliana by overexpression of
RT uroporphyrinogen III methyltransferase (UPM1).";
RL Front. Plant Sci. 8:2265-2265(2017).
CC -!- FUNCTION: Essential protein required for siroheme biosynthesis
CC (PubMed:20592802). Catalyzes the two successive C-2 and C-7 methylation
CC reactions involved in the conversion of uroporphyrinogen III to
CC precorrin-2 via the intermediate formation of precorrin-1
CC (PubMed:9006913). It is a step in the biosynthesis of siroheme
CC (PubMed:9006913). Promotes nitrogen and sulfur assimilation as well as
CC photosynthesis efficiency by triggering chlorophyll, nitrite reductase
CC (NiR) and sulfite reductase (SiR) biosynthesis (PubMed:29472934).
CC {ECO:0000269|PubMed:20592802, ECO:0000269|PubMed:29472934,
CC ECO:0000269|PubMed:9006913}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2 S-adenosyl-L-methionine + uroporphyrinogen III = H(+) +
CC precorrin-2 + 2 S-adenosyl-L-homocysteine; Xref=Rhea:RHEA:32459,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57308, ChEBI:CHEBI:57856,
CC ChEBI:CHEBI:58827, ChEBI:CHEBI:59789; EC=2.1.1.107;
CC Evidence={ECO:0000269|PubMed:9006913};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:32460;
CC Evidence={ECO:0000269|PubMed:9006913};
CC -!- PATHWAY: Porphyrin-containing compound metabolism; siroheme
CC biosynthesis; precorrin-2 from uroporphyrinogen III: step 1/1.
CC {ECO:0000269|PubMed:9006913}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000269|PubMed:9006913}.
CC -!- TISSUE SPECIFICITY: Mostly expressed in leaves, and, to a lower extent,
CC in stems, flowers and siliques. {ECO:0000269|PubMed:27729721}.
CC -!- INDUCTION: By light (PubMed:15326282, PubMed:27729721). Accumulates
CC within two hours in etiolated seedlings exposed to light
CC (PubMed:27729721). {ECO:0000269|PubMed:15326282,
CC ECO:0000269|PubMed:27729721}.
CC -!- DISRUPTION PHENOTYPE: Embryo lethal. {ECO:0000269|PubMed:20592802}.
CC -!- SIMILARITY: Belongs to the precorrin methyltransferase family.
CC {ECO:0000305}.
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DR EMBL; L47479; AAB92676.1; -; mRNA.
DR EMBL; U63734; AAB92677.1; -; Genomic_DNA.
DR EMBL; AB011477; BAB11347.1; -; Genomic_DNA.
DR EMBL; CP002688; AED94606.1; -; Genomic_DNA.
DR EMBL; AF462833; AAL58921.1; -; mRNA.
DR EMBL; AY058093; AAL24201.1; -; mRNA.
DR EMBL; AY079029; AAL84983.1; -; mRNA.
DR EMBL; AY142030; AAM98294.1; -; mRNA.
DR RefSeq; NP_198901.1; NM_123450.5.
DR AlphaFoldDB; Q42606; -.
DR SMR; Q42606; -.
DR STRING; 3702.AT5G40850.1; -.
DR PaxDb; Q42606; -.
DR PRIDE; Q42606; -.
DR ProteomicsDB; 178814; -.
DR EnsemblPlants; AT5G40850.1; AT5G40850.1; AT5G40850.
DR GeneID; 834085; -.
DR Gramene; AT5G40850.1; AT5G40850.1; AT5G40850.
DR KEGG; ath:AT5G40850; -.
DR Araport; AT5G40850; -.
DR TAIR; locus:2164506; AT5G40850.
DR eggNOG; KOG1527; Eukaryota.
DR HOGENOM; CLU_011276_7_4_1; -.
DR InParanoid; Q42606; -.
DR OMA; TRPEQEE; -.
DR OrthoDB; 1510236at2759; -.
DR PhylomeDB; Q42606; -.
DR BioCyc; ARA:AT5G40850-MON; -.
DR BRENDA; 2.1.1.107; 399.
DR UniPathway; UPA00262; UER00211.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q42606; baseline and differential.
DR GO; GO:0009507; C:chloroplast; IDA:TAIR.
DR GO; GO:0004851; F:uroporphyrin-III C-methyltransferase activity; IDA:TAIR.
DR GO; GO:0032259; P:methylation; IEA:UniProtKB-KW.
DR GO; GO:1902326; P:positive regulation of chlorophyll biosynthetic process; IMP:UniProtKB.
DR GO; GO:0090352; P:regulation of nitrate assimilation; IMP:UniProtKB.
DR GO; GO:1900058; P:regulation of sulfate assimilation; IMP:UniProtKB.
DR GO; GO:0009416; P:response to light stimulus; IEP:UniProtKB.
DR GO; GO:0019354; P:siroheme biosynthetic process; IDA:TAIR.
DR CDD; cd11642; SUMT; 1.
DR Gene3D; 3.30.950.10; -; 1.
DR Gene3D; 3.40.1010.10; -; 1.
DR InterPro; IPR000878; 4pyrrol_Mease.
DR InterPro; IPR035996; 4pyrrol_Methylase_sf.
DR InterPro; IPR014777; 4pyrrole_Mease_sub1.
DR InterPro; IPR014776; 4pyrrole_Mease_sub2.
DR InterPro; IPR006366; CobA/CysG_C.
DR InterPro; IPR003043; Uropor_MeTrfase_CS.
DR InterPro; IPR012383; Uropor_MeTrfase_pln.
DR Pfam; PF00590; TP_methylase; 1.
DR PIRSF; PIRSF036478; Uropor_mtas_plnt; 1.
DR SUPFAM; SSF53790; SSF53790; 1.
DR TIGRFAMs; TIGR01469; cobA_cysG_Cterm; 1.
DR PROSITE; PS00839; SUMT_1; 1.
DR PROSITE; PS00840; SUMT_2; 1.
PE 1: Evidence at protein level;
KW Chloroplast; Methyltransferase; Plastid; Porphyrin biosynthesis;
KW Reference proteome; S-adenosyl-L-methionine; Transferase; Transit peptide.
FT TRANSIT 1..28
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 29..369
FT /note="S-adenosyl-L-methionine-dependent uroporphyrinogen
FT III methyltransferase, chloroplastic"
FT /id="PRO_0000450860"
FT BINDING 124
FT /ligand="S-adenosyl-L-homocysteine"
FT /ligand_id="ChEBI:CHEBI:57856"
FT /evidence="ECO:0000250|UniProtKB:P21631"
FT BINDING 200..202
FT /ligand="S-adenosyl-L-homocysteine"
FT /ligand_id="ChEBI:CHEBI:57856"
FT /evidence="ECO:0000250|UniProtKB:P21631"
FT BINDING 230..231
FT /ligand="S-adenosyl-L-homocysteine"
FT /ligand_id="ChEBI:CHEBI:57856"
FT /evidence="ECO:0000250|UniProtKB:P21631"
FT BINDING 284
FT /ligand="S-adenosyl-L-homocysteine"
FT /ligand_id="ChEBI:CHEBI:57856"
FT /evidence="ECO:0000250|UniProtKB:P21631"
FT BINDING 341
FT /ligand="S-adenosyl-L-homocysteine"
FT /ligand_id="ChEBI:CHEBI:57856"
FT /evidence="ECO:0000250|UniProtKB:P21631"
FT CONFLICT 163
FT /note="R -> K (in Ref. 1; AAB92677)"
FT /evidence="ECO:0000305"
FT CONFLICT 175..176
FT /note="SR -> TK (in Ref. 1; AAB92677)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 369 AA; 39930 MW; D4E73A2C4AD937F3 CRC64;
MALVQRIPIS SSSIRNWQQA RTNLTPICCL HYNTASSSSS PFTEKHSVER YQRDQWLYKA
VEPTPPSTPS PSPFEDEVFV RENDIASQLP ELKKLLAVLK EKRVKGCKGG DCGPGDVYLV
GTGPGDPELL TLKAVRVIQS ADLLLYDRLV SNDVLELVAP DARLLYVGKT AGYHSRTQEE
IHELLLNFAE AGATVVRLKG GDPLVFGRGG EEMDFLQQQG IRVQVIPGIT AASGIAAELG
IPLTHRGVAT SVRFLTGHSR KGGTDPLFVA ENAADPDTTL VVYMGLGTLP SLAQKLMDHG
LPSDTPAVAV ERGTTPLQRT VFAELKDFAT EIQSAGLVSP TLIIIGKVVE LSPLWPHCTK
ESSCLVETR
