NB1_MYCTU
ID NB1_MYCTU Reviewed; 164 AA.
AC P9WFG7; L0TAF4; O07216; Q7D6Q1;
DT 16-APR-2014, integrated into UniProtKB/Swiss-Prot.
DT 16-APR-2014, sequence version 1.
DT 03-AUG-2022, entry version 42.
DE RecName: Full=Peroxynitrite isomerase 1 {ECO:0000305|PubMed:32295384};
DE EC=5.99.-.- {ECO:0000269|PubMed:32295384};
DE AltName: Full=Ferric Mycobacterium tuberculosis nitrobindin {ECO:0000303|PubMed:32295384};
DE Short=Mt-Nb(III) {ECO:0000303|PubMed:32295384};
GN OrderedLocusNames=Rv2717c;
OS Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
OC Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC Mycobacterium; Mycobacterium tuberculosis complex.
OX NCBI_TaxID=83332;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=9634230; DOI=10.1038/31159;
RA Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M., Harris D.E.,
RA Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III, Tekaia F., Badcock K.,
RA Basham D., Brown D., Chillingworth T., Connor R., Davies R.M., Devlin K.,
RA Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K.,
RA Krogh A., McLean J., Moule S., Murphy L.D., Oliver S., Osborne J.,
RA Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton S.,
RA Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S.,
RA Barrell B.G.;
RT "Deciphering the biology of Mycobacterium tuberculosis from the complete
RT genome sequence.";
RL Nature 393:537-544(1998).
RN [2]
RP IDENTIFICATION.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=12368430; DOI=10.1099/00221287-148-10-2967;
RA Camus J.-C., Pryor M.J., Medigue C., Cole S.T.;
RT "Re-annotation of the genome sequence of Mycobacterium tuberculosis
RT H37Rv.";
RL Microbiology 148:2967-2973(2002).
RN [3]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=21969609; DOI=10.1074/mcp.m111.011627;
RA Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B., Yadav A.K.,
RA Shrivastava P., Marimuthu A., Anand S., Sundaram H., Kingsbury R.,
RA Harsha H.C., Nair B., Prasad T.S., Chauhan D.S., Katoch K., Katoch V.M.,
RA Kumar P., Chaerkady R., Ramachandran S., Dash D., Pandey A.;
RT "Proteogenomic analysis of Mycobacterium tuberculosis by high resolution
RT mass spectrometry.";
RL Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS), DOMAIN, AND SUBUNIT.
RG Mycobacterium tuberculosis structural genomics consortium (TB);
RT "Crystal structure of Rv2717c from Mycobacterium tuberculosis.";
RL Submitted (JAN-2006) to the PDB data bank.
RN [5] {ECO:0007744|PDB:6R3W, ECO:0007744|PDB:6R3Y}
RP X-RAY CRYSTALLOGRAPHY (1.20 ANGSTROMS) IN COMPLEX WITH HEME, FUNCTION,
RP CATALYTIC ACTIVITY, COFACTOR, 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).
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). In M.tuberculosis, could be part
CC of the pool of proteins required to scavenge RNS and ROS produced by
CC the host during the immunity response. Is able to bind nitric oxide
CC (NO) in vitro, but may act as a sensor of peroxynitrite levels in vivo.
CC {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:32295384};
CC Note=Binds 1 heme b group per subunit, that coordinates a highly
CC solvent-exposed Fe(III) atom. {ECO:0000269|PubMed:32295384};
CC -!- PATHWAY: Nitrogen metabolism. {ECO:0000305|PubMed:32295384}.
CC -!- SUBUNIT: Homodimer. {ECO:0000305|Ref.4}.
CC -!- DOMAIN: Forms a 10-stranded antiparallel beta-barrel structure able to
CC accommodate a hydrophobic ligand in its interior (Ref.4). In fact, this
CC fold hosts the heme group, which is located in a wide surface cleft
CC (PubMed:32295384). {ECO:0000269|PubMed:32295384, ECO:0000269|Ref.4}.
CC -!- SIMILARITY: Belongs to the nitrobindin family. {ECO:0000305}.
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DR EMBL; AL123456; CCP45515.1; -; Genomic_DNA.
DR PIR; H70532; H70532.
DR RefSeq; NP_217233.1; NC_000962.3.
DR RefSeq; WP_003900559.1; NZ_NVQJ01000017.1.
DR PDB; 2FR2; X-ray; 1.50 A; A=1-164.
DR PDB; 6R3W; X-ray; 1.20 A; A=1-164.
DR PDB; 6R3Y; X-ray; 1.60 A; A=1-164.
DR PDBsum; 2FR2; -.
DR PDBsum; 6R3W; -.
DR PDBsum; 6R3Y; -.
DR AlphaFoldDB; P9WFG7; -.
DR SMR; P9WFG7; -.
DR STRING; 83332.Rv2717c; -.
DR PaxDb; P9WFG7; -.
DR DNASU; 887284; -.
DR GeneID; 45426704; -.
DR GeneID; 887284; -.
DR KEGG; mtu:Rv2717c; -.
DR TubercuList; Rv2717c; -.
DR eggNOG; COG4044; Bacteria.
DR OMA; YSQKTWK; -.
DR PhylomeDB; P9WFG7; -.
DR Proteomes; UP000001584; Chromosome.
DR GO; GO:0020037; F:heme binding; IEA:UniProtKB-UniRule.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0062213; F:peroxynitrite isomerase activity; IEA:UniProtKB-UniRule.
DR CDD; cd07828; lipocalin_heme-bd-THAP4-like; 1.
DR Gene3D; 2.40.128.20; -; 1.
DR HAMAP; MF_01297; nitrobindin; 1.
DR InterPro; IPR012674; Calycin.
DR InterPro; IPR022939; Nb(III)_bact/plant.
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; Heme; Iron; Isomerase; Metal-binding; Reference proteome.
FT CHAIN 1..164
FT /note="Peroxynitrite isomerase 1"
FT /id="PRO_0000356934"
FT MOTIF 17..23
FT /note="GXWXGXG"
FT BINDING 29
FT /ligand="heme b"
FT /ligand_id="ChEBI:CHEBI:60344"
FT /evidence="ECO:0000269|PubMed:32295384,
FT ECO:0007744|PDB:6R3W"
FT BINDING 123
FT /ligand="heme b"
FT /ligand_id="ChEBI:CHEBI:60344"
FT /evidence="ECO:0000269|PubMed:32295384,
FT ECO:0007744|PDB:6R3W"
FT BINDING 155
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:32295384,
FT ECO:0007744|PDB:6R3W"
FT HELIX 7..15
FT /evidence="ECO:0007829|PDB:6R3W"
FT STRAND 17..25
FT /evidence="ECO:0007829|PDB:6R3W"
FT STRAND 33..42
FT /evidence="ECO:0007829|PDB:6R3W"
FT STRAND 44..57
FT /evidence="ECO:0007829|PDB:6R3W"
FT TURN 58..60
FT /evidence="ECO:0007829|PDB:6R3W"
FT STRAND 63..75
FT /evidence="ECO:0007829|PDB:6R3W"
FT STRAND 78..85
FT /evidence="ECO:0007829|PDB:6R3W"
FT TURN 86..88
FT /evidence="ECO:0007829|PDB:6R3W"
FT STRAND 89..100
FT /evidence="ECO:0007829|PDB:6R3W"
FT STRAND 103..109
FT /evidence="ECO:0007829|PDB:6R3W"
FT TURN 110..113
FT /evidence="ECO:0007829|PDB:6R3W"
FT STRAND 115..118
FT /evidence="ECO:0007829|PDB:6R3W"
FT STRAND 125..135
FT /evidence="ECO:0007829|PDB:6R3W"
FT STRAND 138..147
FT /evidence="ECO:0007829|PDB:6R3W"
FT STRAND 150..162
FT /evidence="ECO:0007829|PDB:6R3W"
SQ SEQUENCE 164 AA; 17846 MW; F3194F002502BB28 CRC64;
MTRDLAPALQ ALSPLLGSWA GRGAGKYPTI RPFEYLEEVV FAHVGKPFLT YTQQTRAVAD
GKPLHSETGY LRVCRPGCVE LVLAHPSGIT EIEVGTYSVT GDVIELELST RADGSIGLAP
TAKEVTALDR SYRIDGDELS YSLQMRAVGQ PLQDHLAAVL HRQR
