SIR_ARATH
ID SIR_ARATH Reviewed; 642 AA.
AC Q9LZ66; O23650; Q0WMF4; Q42590; Q94AB9;
DT 18-APR-2012, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 134.
DE RecName: Full=Assimilatory sulfite reductase (ferredoxin), chloroplastic;
DE Short=AtSiR;
DE EC=1.8.7.1 {ECO:0000269|PubMed:9661674};
DE AltName: Full=Sulfite reductase (ferredoxin);
DE Flags: Precursor;
GN Name=SIR; OrderedLocusNames=At5g04590; ORFNames=T32M21.190;
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 [MRNA].
RC STRAIN=cv. Landsberg erecta; TISSUE=Leaf;
RX PubMed=8695637; DOI=10.1016/0167-4838(96)00066-0;
RA Bruehl A., Haverkamp T., Gisselmann G., Schwenn J.D.;
RT "A cDNA clone from Arabidopsis thaliana encoding plastidic
RT ferredoxin:sulfite reductase.";
RL Biochim. Biophys. Acta 1295:119-124(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], CATALYTIC ACTIVITY, AND TISSUE
RP SPECIFICITY.
RC STRAIN=cv. Columbia;
RX PubMed=9661674; DOI=10.1016/s0378-1119(98)00155-3;
RA Bork C., Schwenn J.D., Hell R.;
RT "Isolation and characterization of a gene for assimilatory sulfite
RT reductase from Arabidopsis thaliana.";
RL Gene 212:147-153(1998).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130714; DOI=10.1038/35048507;
RA Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E.,
RA Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M.,
RA Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.,
RA Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M.,
RA Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L.,
RA O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D.,
RA Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M.,
RA Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L.,
RA Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B.,
RA Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P.,
RA Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M.,
RA Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D.,
RA Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A.,
RA Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I.,
RA Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T.,
RA Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A.,
RA McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U.,
RA Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W.,
RA Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M.,
RA Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S.,
RA Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G.,
RA Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W.,
RA Bevan M., Fransz P.F.;
RT "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.";
RL Nature 408:823-826(2000).
RN [4]
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 [5]
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 [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 295-642.
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 [7]
RP INDUCTION BY SULFUR DIOXIDE.
RX PubMed=17425719; DOI=10.1111/j.1365-313x.2007.03080.x;
RA Brychkova G., Xia Z., Yang G., Yesbergenova Z., Zhang Z., Davydov O.,
RA Fluhr R., Sagi M.;
RT "Sulfite oxidase protects plants against sulfur dioxide toxicity.";
RL Plant J. 50:696-709(2007).
RN [8]
RP IDENTIFICATION BY MASS SPECTROMETRY, AND SUBCELLULAR LOCATION [LARGE SCALE
RP ANALYSIS].
RX PubMed=18431481; DOI=10.1371/journal.pone.0001994;
RA Zybailov B., Rutschow H., Friso G., Rudella A., Emanuelsson O., Sun Q.,
RA van Wijk K.J.;
RT "Sorting signals, N-terminal modifications and abundance of the chloroplast
RT proteome.";
RL PLoS ONE 3:E1994-E1994(2008).
RN [9]
RP FUNCTION.
RC STRAIN=cv. Columbia;
RX PubMed=20424176; DOI=10.1105/tpc.110.074088;
RA Khan M.S., Haas F.H., Samami A.A., Gholami A.M., Bauer A., Fellenberg K.,
RA Reichelt M., Haensch R., Mendel R.R., Meyer A.J., Wirtz M., Hell R.;
RT "Sulfite reductase defines a newly discovered bottleneck for assimilatory
RT sulfate reduction and is essential for growth and development in
RT Arabidopsis thaliana.";
RL Plant Cell 22:1216-1231(2010).
CC -!- FUNCTION: Essential protein with sulfite reductase activity required in
CC assimilatory sulfate reduction pathway during both primary and
CC secondary metabolism and thus involved in development and growth.
CC {ECO:0000269|PubMed:20424176}.
CC -!- FUNCTION: DNA-binding protein that binds to both double-stranded and
CC single-stranded DNA without significant sequence specificity to
CC reversibly repress the transcriptional activity of chloroplast
CC nucleoids by promoting DNA compaction and possibly regulate DNA
CC replication. {ECO:0000250|UniProtKB:Q75NZ0}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=3 H2O + hydrogen sulfide + 6 oxidized [2Fe-2S]-[ferredoxin] =
CC 7 H(+) + 6 reduced [2Fe-2S]-[ferredoxin] + sulfite;
CC Xref=Rhea:RHEA:23132, Rhea:RHEA-COMP:10000, Rhea:RHEA-COMP:10001,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:17359,
CC ChEBI:CHEBI:29919, ChEBI:CHEBI:33737, ChEBI:CHEBI:33738; EC=1.8.7.1;
CC Evidence={ECO:0000269|PubMed:9661674};
CC -!- COFACTOR:
CC Name=siroheme; Xref=ChEBI:CHEBI:60052; Evidence={ECO:0000250};
CC Note=Binds 1 siroheme per subunit. {ECO:0000250};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883; Evidence={ECO:0000250};
CC Note=Binds 1 [4Fe-4S] cluster per subunit. {ECO:0000250};
CC -!- SUBUNIT: Monomer. Interacts with ferredoxin (By similarity).
CC {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast stroma, chloroplast nucleoid
CC {ECO:0000250}. Plastid stroma. Plastid, chloroplast stroma
CC {ECO:0000269|PubMed:18431481}.
CC -!- TISSUE SPECIFICITY: Present in leaves and roots.
CC {ECO:0000269|PubMed:9661674}.
CC -!- INDUCTION: Rapidly induced by sulfur dioxide SO(2) in a sulfite oxidase
CC (SO)-dependent manner. {ECO:0000269|PubMed:17425719}.
CC -!- PTM: Phosphorylated; this phosphorylation reduces DNA-binding.
CC {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the nitrite and sulfite reductase 4Fe-4S domain
CC family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAK82552.1; Type=Erroneous termination; Note=Truncated C-terminus.; Evidence={ECO:0000305};
CC Sequence=AAN18162.1; Type=Erroneous termination; Note=Truncated C-terminus.; Evidence={ECO:0000305};
CC Sequence=CAA71239.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; Z49217; CAA89154.1; -; mRNA.
DR EMBL; Y10157; CAA71239.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL162875; CAB85565.1; -; Genomic_DNA.
DR EMBL; CP002688; AED90762.1; -; Genomic_DNA.
DR EMBL; AF325027; AAG40379.1; -; mRNA.
DR EMBL; AY048290; AAK82552.1; ALT_SEQ; mRNA.
DR EMBL; BT000593; AAN18162.1; ALT_SEQ; mRNA.
DR EMBL; AK229873; BAF01702.1; -; mRNA.
DR PIR; S71437; S71437.
DR PIR; T48455; T48455.
DR RefSeq; NP_196079.1; NM_120541.4.
DR AlphaFoldDB; Q9LZ66; -.
DR SMR; Q9LZ66; -.
DR BioGRID; 15615; 1.
DR IntAct; Q9LZ66; 1.
DR STRING; 3702.AT5G04590.1; -.
DR MetOSite; Q9LZ66; -.
DR SwissPalm; Q9LZ66; -.
DR PaxDb; Q9LZ66; -.
DR PRIDE; Q9LZ66; -.
DR ProteomicsDB; 232619; -.
DR EnsemblPlants; AT5G04590.1; AT5G04590.1; AT5G04590.
DR GeneID; 830336; -.
DR Gramene; AT5G04590.1; AT5G04590.1; AT5G04590.
DR KEGG; ath:AT5G04590; -.
DR Araport; AT5G04590; -.
DR TAIR; locus:2184457; AT5G04590.
DR eggNOG; KOG0560; Eukaryota.
DR HOGENOM; CLU_001975_3_0_1; -.
DR InParanoid; Q9LZ66; -.
DR OMA; WQMMLRL; -.
DR OrthoDB; 463531at2759; -.
DR PhylomeDB; Q9LZ66; -.
DR BioCyc; MetaCyc:AT5G04590-MON; -.
DR PRO; PR:Q9LZ66; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9LZ66; baseline and differential.
DR Genevisible; Q9LZ66; AT.
DR GO; GO:0048046; C:apoplast; HDA:TAIR.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0009941; C:chloroplast envelope; HDA:TAIR.
DR GO; GO:0042644; C:chloroplast nucleoid; ISS:UniProtKB.
DR GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR GO; GO:0005886; C:plasma membrane; HDA:TAIR.
DR GO; GO:0009536; C:plastid; TAS:TAIR.
DR GO; GO:0010319; C:stromule; IDA:TAIR.
DR GO; GO:0009337; C:sulfite reductase complex (NADPH); IBA:GO_Central.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0005507; F:copper ion binding; HDA:TAIR.
DR GO; GO:0003677; F:DNA binding; ISS:UniProtKB.
DR GO; GO:0020037; F:heme binding; IEA:InterPro.
DR GO; GO:0050311; F:sulfite reductase (ferredoxin) activity; IMP:UniProtKB.
DR GO; GO:0016002; F:sulfite reductase activity; IDA:TAIR.
DR GO; GO:0045892; P:negative regulation of transcription, DNA-templated; ISS:UniProtKB.
DR GO; GO:0009409; P:response to cold; IEP:TAIR.
DR GO; GO:0000103; P:sulfate assimilation; IBA:GO_Central.
DR GO; GO:0019424; P:sulfide oxidation, using siroheme sulfite reductase; ISS:UniProtKB.
DR GO; GO:0006790; P:sulfur compound metabolic process; IMP:TAIR.
DR Gene3D; 3.30.413.10; -; 2.
DR InterPro; IPR005117; NiRdtase/SiRdtase_haem-b_fer.
DR InterPro; IPR036136; Nit/Sulf_reduc_fer-like_dom_sf.
DR InterPro; IPR006067; NO2/SO3_Rdtase_4Fe4S_dom.
DR InterPro; IPR045169; NO2/SO3_Rdtase_4Fe4S_prot.
DR InterPro; IPR045854; NO2/SO3_Rdtase_4Fe4S_sf.
DR InterPro; IPR006066; NO2/SO3_Rdtase_FeS/sirohaem_BS.
DR InterPro; IPR011787; SiR_ferredoxin-dep.
DR PANTHER; PTHR11493; PTHR11493; 1.
DR Pfam; PF01077; NIR_SIR; 2.
DR Pfam; PF03460; NIR_SIR_ferr; 2.
DR PRINTS; PR00397; SIROHAEM.
DR SUPFAM; SSF55124; SSF55124; 2.
DR SUPFAM; SSF56014; SSF56014; 2.
DR TIGRFAMs; TIGR02042; sir; 1.
DR PROSITE; PS00365; NIR_SIR; 1.
PE 1: Evidence at protein level;
KW 4Fe-4S; Chloroplast; DNA-binding; Heme; Iron; Iron-sulfur; Metal-binding;
KW Oxidoreductase; Plastid; Reference proteome; Thioether bond;
KW Transit peptide.
FT TRANSIT 1..61
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 62..642
FT /note="Assimilatory sulfite reductase (ferredoxin),
FT chloroplastic"
FT /id="PRO_0000416844"
FT REGION 46..74
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 48..70
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 503
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250"
FT BINDING 509
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250"
FT BINDING 549
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250"
FT BINDING 553
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250"
FT BINDING 553
FT /ligand="siroheme"
FT /ligand_id="ChEBI:CHEBI:60052"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT /evidence="ECO:0000250"
FT CONFLICT 203
FT /note="R -> K (in Ref. 5; AAK82552/AAN18162)"
FT /evidence="ECO:0000305"
FT CONFLICT 426
FT /note="A -> T (in Ref. 1; CAA89154)"
FT /evidence="ECO:0000305"
FT CONFLICT 554
FT /note="A -> R (in Ref. 2; CAA71239)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 642 AA; 71950 MW; A00E4F12C278CFA3 CRC64;
MSSTFRAPAG AATVFTADQK IRLGRLDALR SSHSVFLGRY GRGGVPVPPS ASSSSSSPIQ
AVSTPAKPET ATKRSKVEII KEKSNFIRYP LNEELLTEAP NVNESAVQLI KFHGSYQQYN
REERGGRSYS FMLRTKNPSG KVPNQLYLTM DDLADEFGIG TLRLTTRQTF QLHGVLKQNL
KTVMSSIIKN MGSTLGACGD LNRNVLAPAA PYVKKDYLFA QETADNIAAL LSPQSGFYYD
MWVDGEQFMT AEPPEVVKAR NDNSHGTNFV DSPEPIYGTQ FLPRKFKVAV TVPTDNSVDL
LTNDIGVVVV SDENGEPQGF NIYVGGGMGR THRMESTFAR LAEPIGYVPK EDILYAVKAI
VVTQREHGRR DDRKYSRMKY LISSWGIEKF RDVVEQYYGK KFEPSRELPE WEFKSYLGWH
EQGDGAWFCG LHVDSGRVGG IMKKTLREVI EKYKIDVRIT PNQNIVLCDI KTEWKRPITT
VLAQAGLLQP EFVDPLNQTA MACPAFPLCP LAITEAERGI PSILKRVRAM FEKVGLDYDE
SVVIRVTGCP NGCARPYMAE LGLVGDGPNS YQVWLGGTPN LTQIARSFMD KVKVHDLEKV
CEPLFYHWKL ERQTKESFGE YTTRMGFEKL KELIDTYKGV SQ
