NB_ARATH
ID NB_ARATH Reviewed; 166 AA.
AC O64527;
DT 03-OCT-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1998, sequence version 1.
DT 03-AUG-2022, entry version 111.
DE RecName: Full=Peroxynitrite isomerase Rv2717c {ECO:0000305|PubMed:32295384};
DE EC=5.99.-.- {ECO:0000269|PubMed:32295384};
DE AltName: Full=Ferric Arabidopsis thaliana nitrobindin {ECO:0000303|PubMed:32295384};
DE Short=At-Nb(III) {ECO:0000303|PubMed:32295384};
GN OrderedLocusNames=At1g79260; ORFNames=YUP8H12R.14;
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=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(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 FUNCTION, CATALYTIC ACTIVITY, AND NO-BINDING.
RX PubMed=32295384; DOI=10.1089/ars.2019.7874;
RA De Simone G., di Masi A., Vita G.M., Polticelli F., Pesce A., Nardini M.,
RA Bolognesi M., Ciaccio C., Coletta M., Turilli E.S., Fasano M.,
RA Tognaccini L., Smulevich G., Abbruzzetti S., Viappiani C., Bruno S.,
RA Ascenzi P.;
RT "Mycobacterial and Human Nitrobindins: Structure and Function.";
RL Antioxid. Redox Signal. 33:229-246(2020).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (1.32 ANGSTROMS) OF 2-166.
RG Center for eukaryotic structural genomics (CESG);
RT "X-ray structure of protein from Arabidopsis thaliana At1g79260.";
RL Submitted (FEB-2005) to the PDB data bank.
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.32 ANGSTROMS) OF 2-166.
RX PubMed=17850744; DOI=10.1016/j.str.2007.06.019;
RA Levin E.J., Kondrashov D.A., Wesenberg G.E., Phillips G.N. Jr.;
RT "Ensemble refinement of protein crystal structures: validation and
RT application.";
RL Structure 15:1040-1052(2007).
RN [7] {ECO:0007744|PDB:2A13, ECO:0007744|PDB:3EMM}
RP X-RAY CRYSTALLOGRAPHY (1.32 ANGSTROMS) OF 2-166 IN COMPLEX WITH HEME,
RP COFACTOR, NO-BINDING, AND SUBUNIT.
RX PubMed=19938152; DOI=10.1002/prot.22617;
RA Bianchetti C.M., Blouin G.C., Bitto E., Olson J.S., Phillips G.N. Jr.;
RT "The structure and NO binding properties of the nitrophorin-like heme-
RT binding protein from Arabidopsis thaliana gene locus At1g79260.1.";
RL Proteins 78:917-931(2010).
CC -!- FUNCTION: Heme-binding protein able to scavenge peroxynitrite and to
CC protect free L-tyrosine against peroxynitrite-mediated nitration, by
CC acting as a peroxynitrite isomerase that converts peroxynitrite to
CC nitrate. Therefore, this protein likely plays a role in peroxynitrite
CC sensing and in the detoxification of reactive nitrogen and oxygen
CC species (RNS and ROS, respectively) (PubMed:32295384). Is able to bind
CC nitric oxide (NO) in vitro, but may act as a sensor of peroxynitrite
CC levels in vivo (PubMed:32295384, PubMed:19938152).
CC {ECO:0000269|PubMed:19938152, ECO:0000269|PubMed:32295384}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=peroxynitrite = nitrate; Xref=Rhea:RHEA:63116,
CC ChEBI:CHEBI:17632, ChEBI:CHEBI:25941;
CC Evidence={ECO:0000269|PubMed:32295384};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:63117;
CC Evidence={ECO:0000305|PubMed:32295384};
CC -!- COFACTOR:
CC Name=heme b; Xref=ChEBI:CHEBI:60344;
CC Evidence={ECO:0000269|PubMed:19938152};
CC Note=Binds 1 heme b group per subunit, that coordinates a highly
CC solvent-exposed Fe(III) atom. {ECO:0000269|PubMed:19938152};
CC -!- PATHWAY: Nitrogen metabolism. {ECO:0000305|PubMed:32295384}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:19938152}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- DOMAIN: Forms a 10-stranded antiparallel beta-barrel structure able to
CC accommodate a hydrophobic ligand in its interior. In fact, this fold
CC hosts the heme group, which is located in a wide surface cleft.
CC {ECO:0000269|PubMed:19938152}.
CC -!- SIMILARITY: Belongs to the nitrobindin family. {ECO:0000305}.
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DR EMBL; AC002986; AAC17039.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE36224.1; -; Genomic_DNA.
DR EMBL; BT002660; AAO11576.1; -; mRNA.
DR EMBL; AY048206; AAK82469.1; -; mRNA.
DR PIR; T01031; T01031.
DR RefSeq; NP_565204.1; NM_106576.4.
DR PDB; 2A13; X-ray; 1.32 A; A=2-166.
DR PDB; 2Q4N; X-ray; 1.32 A; A=2-166.
DR PDB; 3EMM; X-ray; 1.36 A; A=1-166.
DR PDB; 3WJB; X-ray; 2.20 A; A/B=2-166.
DR PDB; 3WJC; X-ray; 2.00 A; A/B=2-166.
DR PDB; 3WJD; X-ray; 1.10 A; A=2-166.
DR PDB; 3WJE; X-ray; 1.70 A; A/B=2-166.
DR PDB; 3WJF; X-ray; 2.20 A; A/B=2-166.
DR PDB; 3WJG; X-ray; 1.10 A; A=2-166.
DR PDB; 4YMY; X-ray; 1.00 A; A=2-166.
DR PDB; 7BBM; X-ray; 1.14 A; A=1-166.
DR PDBsum; 2A13; -.
DR PDBsum; 2Q4N; -.
DR PDBsum; 3EMM; -.
DR PDBsum; 3WJB; -.
DR PDBsum; 3WJC; -.
DR PDBsum; 3WJD; -.
DR PDBsum; 3WJE; -.
DR PDBsum; 3WJF; -.
DR PDBsum; 3WJG; -.
DR PDBsum; 4YMY; -.
DR PDBsum; 7BBM; -.
DR AlphaFoldDB; O64527; -.
DR SMR; O64527; -.
DR STRING; 3702.AT1G79260.1; -.
DR PaxDb; O64527; -.
DR PRIDE; O64527; -.
DR ProteomicsDB; 232389; -.
DR DNASU; 844266; -.
DR EnsemblPlants; AT1G79260.1; AT1G79260.1; AT1G79260.
DR GeneID; 844266; -.
DR Gramene; AT1G79260.1; AT1G79260.1; AT1G79260.
DR KEGG; ath:AT1G79260; -.
DR Araport; AT1G79260; -.
DR TAIR; locus:2207465; AT1G79260.
DR eggNOG; KOG3371; Eukaryota.
DR HOGENOM; CLU_085483_1_1_1; -.
DR InParanoid; O64527; -.
DR PhylomeDB; O64527; -.
DR EvolutionaryTrace; O64527; -.
DR PRO; PR:O64527; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; O64527; baseline and differential.
DR Genevisible; O64527; AT.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0016853; F:isomerase activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR CDD; cd07828; lipocalin_heme-bd-THAP4-like; 1.
DR Gene3D; 2.40.128.20; -; 1.
DR InterPro; IPR012674; Calycin.
DR InterPro; IPR045165; Nitrobindin.
DR InterPro; IPR014878; THAP4-like_heme-bd.
DR PANTHER; PTHR15854; PTHR15854; 1.
DR Pfam; PF08768; THAP4_heme-bd; 1.
DR SUPFAM; SSF50814; SSF50814; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Heme; Iron; Isomerase; Metal-binding;
KW Reference proteome.
FT CHAIN 1..166
FT /note="Peroxynitrite isomerase Rv2717c"
FT /id="PRO_0000250540"
FT MOTIF 28..34
FT /note="GXWXGXG"
FT BINDING 40
FT /ligand="heme b"
FT /ligand_id="ChEBI:CHEBI:60344"
FT /evidence="ECO:0000269|PubMed:19938152,
FT ECO:0007744|PDB:3EMM"
FT BINDING 158
FT /ligand="heme b"
FT /ligand_id="ChEBI:CHEBI:60344"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT /evidence="ECO:0000269|PubMed:19938152,
FT ECO:0007744|PDB:3EMM"
FT TURN 18..20
FT /evidence="ECO:0007829|PDB:4YMY"
FT HELIX 21..26
FT /evidence="ECO:0007829|PDB:4YMY"
FT STRAND 28..38
FT /evidence="ECO:0007829|PDB:4YMY"
FT STRAND 41..53
FT /evidence="ECO:0007829|PDB:4YMY"
FT STRAND 56..58
FT /evidence="ECO:0007829|PDB:4YMY"
FT STRAND 60..67
FT /evidence="ECO:0007829|PDB:4YMY"
FT TURN 69..71
FT /evidence="ECO:0007829|PDB:4YMY"
FT STRAND 74..84
FT /evidence="ECO:0007829|PDB:4YMY"
FT STRAND 88..96
FT /evidence="ECO:0007829|PDB:4YMY"
FT TURN 97..99
FT /evidence="ECO:0007829|PDB:3WJC"
FT STRAND 101..109
FT /evidence="ECO:0007829|PDB:4YMY"
FT TURN 110..113
FT /evidence="ECO:0007829|PDB:4YMY"
FT STRAND 114..124
FT /evidence="ECO:0007829|PDB:4YMY"
FT STRAND 126..138
FT /evidence="ECO:0007829|PDB:4YMY"
FT STRAND 141..153
FT /evidence="ECO:0007829|PDB:4YMY"
FT STRAND 155..165
FT /evidence="ECO:0007829|PDB:4YMY"
SQ SEQUENCE 166 AA; 18486 MW; 009BFDD20CCC291F CRC64;
MNQLQQLQNP GESPPVHPFV APLSYLLGTW RGQGEGEYPT IPSFRYGEEI RFSHSGKPVI
AYTQKTWKLE SGAPMHAESG YFRPRPDGSI EVVIAQSTGL VEVQKGTYNV DEQSIKLKSD
LVGNASKVKE ISREFELVDG KLSYVVRMST TTNPLQPHLK AILDKL
