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Protein

Sulfite reductase [ferredoxin], chloroplastic

Gene

SIR

Organism
Zea mays (Maize)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Essential protein with sulfite reductase activity required in assimilatory sulfate reduction pathway during both primary and secondary metabolism and thus involved in development and growth.4 Publications
DNA-binding protein that binds to both double-stranded and single-stranded DNA without significant sequence specificity to reversibly repress the transcriptional activity of chloroplast nucleoids by promoting DNA compaction and possibly regulate DNA replication.1 Publication

Catalytic activityi

Hydrogen sulfide + 6 oxidized ferredoxin [iron-sulfur] cluster + 3 H2O = sulfite + 6 reduced ferredoxin [iron-sulfur] cluster + 6 H+.2 Publications

Cofactori

Protein has several cofactor binding sites:
  • sirohemeBy similarityNote: Binds 1 siroheme per subunit.By similarity
  • [4Fe-4S] clusterNote: Binds 1 [4Fe-4S] cluster per subunit.

Enzyme regulationi

Inhibited by the tryptophan-modifying reagent, N-bromosuccinimide (NBS), by the lysine-modifying reagent, N-acetylsuccinimide and by the arginine-modifying reagent, phenylglyoxal. Complex formation with ferredoxin prevents these inhibitions.

Redox potential

E is -285 +/- 5 mV for siroheme and -400 +/- 5 mV for 2Fe-2S at pH 7.5.4 Publications

Manual assertion based on experiment ini

Kineticsi

  1. KM=1.7 µM for ferredoxin4 Publications
  2. KM=1 mM for nitrite4 Publications

    pH dependencei

    Optimum pH is 7.5.4 Publications

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Metal bindingi494Iron-sulfur (4Fe-4S)By similarity1
    Metal bindingi500Iron-sulfur (4Fe-4S)By similarity1
    Metal bindingi540Iron-sulfur (4Fe-4S)By similarity1
    Metal bindingi544Iron (siroheme axial ligand)By similarity1
    Metal bindingi544Iron-sulfur (4Fe-4S)By similarity1

    GO - Molecular functioni

    • 4 iron, 4 sulfur cluster binding Source: UniProtKB-KW
    • DNA binding Source: UniProtKB
    • heme binding Source: InterPro
    • metal ion binding Source: UniProtKB-KW
    • sulfite reductase (ferredoxin) activity Source: UniProtKB

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Ligandi

    4Fe-4S, DNA-binding, Heme, Iron, Iron-sulfur, Metal-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Sulfite reductase [ferredoxin], chloroplastic (EC:1.8.7.12 Publications)
    Short name:
    ZmSiR
    Gene namesi
    Name:SIR
    OrganismiZea mays (Maize)
    Taxonomic identifieri4577 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaLiliopsidaPoalesPoaceaePACMAD cladePanicoideaeAndropogonodaeAndropogoneaeTripsacinaeZea
    Proteomesi
    • UP000007305 Componenti: Unplaced

    Organism-specific databases

    MaizeGDBi275273.

    Subcellular locationi

    GO - Cellular componenti

    • chloroplast nucleoid Source: UniProtKB
    • chloroplast stroma Source: UniProtKB
    Complete GO annotation...

    Keywords - Cellular componenti

    Chloroplast, Plastid

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi193R → A: Loss of sulfite reductase activity, low nitrite reductase activity and reduced siroheme redox potential. 2 Publications1
    Mutagenesisi193R → E: Loss of sulfite reductase activity, increased nitrite reductase activity and reduced siroheme redox potential. 2 Publications1
    Mutagenesisi276K → Q: Loss of sulfite reductase activity, no nitrite reductase activity. 1 Publication1
    Mutagenesisi278K → N: Loss of sulfite reductase activity, basal nitrite reductase activity. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Transit peptidei1 – 50ChloroplastBy similarityAdd BLAST50
    ChainiPRO_500013999251 – 635Sulfite reductase [ferredoxin], chloroplasticAdd BLAST585

    Post-translational modificationi

    Phosphorylated; this phosphorylation reduces DNA-binding.By similarity

    Keywords - PTMi

    Thioether bond

    Proteomic databases

    PaxDbiO23813.
    PRIDEiO23813.

    Expressioni

    Tissue specificityi

    Present in roots and leaves (at protein level). In leaves, sulfite reductase activity is detected in both bundle sheath and mesophyll cell types.2 Publications

    Interactioni

    Subunit structurei

    Monomer (By similarity). Interacts with ferredoxin.By similarity2 Publications

    Protein-protein interaction databases

    STRINGi4577.GRMZM2G090338_P01.

    Structurei

    Secondary structure

    1635
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi66 – 72Combined sources7
    Turni75 – 80Combined sources6
    Helixi81 – 84Combined sources4
    Beta strandi87 – 91Combined sources5
    Helixi94 – 100Combined sources7
    Helixi101 – 103Combined sources3
    Beta strandi105 – 109Combined sources5
    Beta strandi111 – 113Combined sources3
    Beta strandi119 – 124Combined sources6
    Helixi128 – 130Combined sources3
    Helixi134 – 147Combined sources14
    Beta strandi148 – 150Combined sources3
    Beta strandi152 – 154Combined sources3
    Beta strandi160 – 165Combined sources6
    Helixi167 – 169Combined sources3
    Helixi170 – 178Combined sources9
    Turni179 – 181Combined sources3
    Beta strandi187 – 192Combined sources6
    Helixi205 – 220Combined sources16
    Helixi227 – 232Combined sources6
    Helixi245 – 252Combined sources8
    Beta strandi263 – 265Combined sources3
    Turni266 – 268Combined sources3
    Beta strandi279 – 283Combined sources5
    Helixi291 – 293Combined sources3
    Beta strandi294 – 302Combined sources9
    Beta strandi308 – 315Combined sources8
    Beta strandi334 – 340Combined sources7
    Helixi341 – 343Combined sources3
    Helixi344 – 358Combined sources15
    Helixi364 – 366Combined sources3
    Helixi369 – 376Combined sources8
    Helixi378 – 389Combined sources12
    Beta strandi409 – 412Combined sources4
    Beta strandi414 – 416Combined sources3
    Beta strandi418 – 422Combined sources5
    Helixi425 – 427Combined sources3
    Helixi431 – 443Combined sources13
    Beta strandi448 – 450Combined sources3
    Beta strandi456 – 461Combined sources6
    Helixi463 – 465Combined sources3
    Helixi466 – 475Combined sources10
    Helixi481 – 483Combined sources3
    Helixi486 – 490Combined sources5
    Turni497 – 499Combined sources3
    Helixi508 – 525Combined sources18
    Beta strandi535 – 540Combined sources6
    Helixi547 – 549Combined sources3
    Beta strandi550 – 558Combined sources9
    Beta strandi561 – 566Combined sources6
    Beta strandi577 – 584Combined sources8
    Helixi585 – 587Combined sources3
    Helixi588 – 602Combined sources15
    Helixi609 – 616Combined sources8
    Helixi618 – 628Combined sources11

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    5H8VX-ray2.20A/B53-635[»]
    5H8YX-ray2.20A/B/C/D53-635[»]
    5H92X-ray2.08A/B53-635[»]
    ProteinModelPortaliO23813.
    SMRiO23813.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Keywords - Domaini

    Transit peptide

    Phylogenomic databases

    eggNOGiKOG0560. Eukaryota.
    COG0155. LUCA.
    HOGENOMiHOG000218417.
    KOiK00392.

    Family and domain databases

    Gene3Di3.90.480.10. 2 hits.
    InterProiIPR005117. NiRdtase/SiRdtase_haem-b_fer.
    IPR006067. NO2/SO3_Rdtase_4Fe4S_dom.
    IPR006066. NO2/SO3_Rdtase_FeS/sirohaem_BS.
    IPR011787. SiR_ferredoxin-dep.
    [Graphical view]
    PfamiPF01077. NIR_SIR. 2 hits.
    PF03460. NIR_SIR_ferr. 2 hits.
    [Graphical view]
    PRINTSiPR00397. SIROHAEM.
    SUPFAMiSSF55124. SSF55124. 2 hits.
    TIGRFAMsiTIGR02042. sir. 1 hit.
    PROSITEiPS00365. NIR_SIR. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    O23813-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSGAIGGAEV HGFRGAAAQL PRSRVLGRPI RVAPPAAARP GGASAGSIRA
    60 70 80 90 100
    VSAPAKKDAS EVKRSKVEII KEKSNFLRYP LNEELVSEAP NINESAVQLI
    110 120 130 140 150
    KFHGSYQQTD RDVRGQKNYS FMLRTKNPCG KVPNQLYLAM DTLADEFGIG
    160 170 180 190 200
    TLRLTTRQTF QLHGVLKKNL KTVLSTVIKN MGSTLGACGD LNRNVLAPAA
    210 220 230 240 250
    PYVKKDILFA QQTAENIAAL LTPQSGAYYD LWVDGEKIMS AEEPPEVTKA
    260 270 280 290 300
    RNDNSHGTNF PDSPEPIYGT QYLPRKFKVA VTAAGDNSVD ILTNDIGVVV
    310 320 330 340 350
    VSDDAGEPIG FNIYVGGGMG RTHRVETTFP RLADPLGYVP KEDILYAIKA
    360 370 380 390 400
    IVVTQRENGR RDDRKYSRMK YMIDRWGIDR FRAEVEKYYG KKFESFRPLP
    410 420 430 440 450
    EWQFNSYLGW QEQGDGKLFY GVHVDNGRVG GQAKKTLREI IEKYNLDVSI
    460 470 480 490 500
    TPNQNLILCG IDQAWREPIT TALAQAGLLE PKDVDPLNLT AMACPALPLC
    510 520 530 540 550
    PLAQTEAERG ILPILKRIRA VFNKVGIKDS ESVVVRITGC PNGCARPYMA
    560 570 580 590 600
    ELGFVGDGPK SYQIWLGGTP NQSTLAESFM DKVKLDDIEK VLEPLFTYWN
    610 620 630
    GTRQEGESFG SFTNRTGFDK LKEVVNKWAE SPSAA
    Length:635
    Mass (Da):70,015
    Last modified:January 1, 1998 - v1
    Checksum:i759B0564472E163B
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    D50679 mRNA. Translation: BAA23641.1.
    PIRiT01695.
    RefSeqiNP_001105302.1. NM_001111832.1.
    UniGeneiZm.94307.

    Genome annotation databases

    GeneIDi542221.
    KEGGizma:542221.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    D50679 mRNA. Translation: BAA23641.1.
    PIRiT01695.
    RefSeqiNP_001105302.1. NM_001111832.1.
    UniGeneiZm.94307.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    5H8VX-ray2.20A/B53-635[»]
    5H8YX-ray2.20A/B/C/D53-635[»]
    5H92X-ray2.08A/B53-635[»]
    ProteinModelPortaliO23813.
    SMRiO23813.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi4577.GRMZM2G090338_P01.

    Proteomic databases

    PaxDbiO23813.
    PRIDEiO23813.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    GeneIDi542221.
    KEGGizma:542221.

    Organism-specific databases

    MaizeGDBi275273.

    Phylogenomic databases

    eggNOGiKOG0560. Eukaryota.
    COG0155. LUCA.
    HOGENOMiHOG000218417.
    KOiK00392.

    Family and domain databases

    Gene3Di3.90.480.10. 2 hits.
    InterProiIPR005117. NiRdtase/SiRdtase_haem-b_fer.
    IPR006067. NO2/SO3_Rdtase_4Fe4S_dom.
    IPR006066. NO2/SO3_Rdtase_FeS/sirohaem_BS.
    IPR011787. SiR_ferredoxin-dep.
    [Graphical view]
    PfamiPF01077. NIR_SIR. 2 hits.
    PF03460. NIR_SIR_ferr. 2 hits.
    [Graphical view]
    PRINTSiPR00397. SIROHAEM.
    SUPFAMiSSF55124. SSF55124. 2 hits.
    TIGRFAMsiTIGR02042. sir. 1 hit.
    PROSITEiPS00365. NIR_SIR. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiSIR_MAIZE
    AccessioniPrimary (citable) accession number: O23813
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 18, 2012
    Last sequence update: January 1, 1998
    Last modified: November 2, 2016
    This is version 89 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.