NB2_MYCTU
ID NB2_MYCTU Reviewed; 226 AA.
AC P9WFG9; L0T4Z5; O53827; Q7D987;
DT 16-APR-2014, integrated into UniProtKB/Swiss-Prot.
DT 16-APR-2014, sequence version 1.
DT 03-AUG-2022, entry version 41.
DE RecName: Full=Peroxynitrite isomerase 2;
DE EC=5.99.-.- {ECO:0000255|HAMAP-Rule:MF_01297};
DE AltName: Full=Ferric nitrobindin;
DE Short=Nb(III);
GN OrderedLocusNames=Rv0813c;
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 AS A DRUG TARGET [LARGE SCALE ANALYSIS].
RX PubMed=19099550; DOI=10.1186/1752-0509-2-109;
RA Raman K., Yeturu K., Chandra N.;
RT "targetTB: a target identification pipeline for Mycobacterium tuberculosis
RT through an interactome, reactome and genome-scale structural analysis.";
RL BMC Syst. Biol. 2:109-109(2008).
RN [4]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, CLEAVAGE OF INITIATOR
RP METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS SPECTROMETRY
RP [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 [5]
RP X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS), AND SUBUNIT.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=17172346; DOI=10.1128/jb.01435-06;
RA Shepard W., Haouz A., Grana M., Buschiazzo A., Betton J.-M., Cole S.T.,
RA Alzari P.M.;
RT "The crystal structure of Rv0813c from Mycobacterium tuberculosis reveals a
RT new family of fatty acid-binding protein-like proteins in bacteria.";
RL J. Bacteriol. 189:1899-1904(2007).
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). Is able to bind nitric oxide (NO)
CC in vitro, but may act as a sensor of peroxynitrite levels in vivo.
CC {ECO:0000255|HAMAP-Rule:MF_01297}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=peroxynitrite = nitrate; Xref=Rhea:RHEA:63116,
CC ChEBI:CHEBI:17632, ChEBI:CHEBI:25941; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_01297};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:63117;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01297};
CC -!- COFACTOR:
CC Name=heme b; Xref=ChEBI:CHEBI:60344;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01297};
CC Note=Binds 1 heme b group per subunit, that coordinates a highly
CC solvent-exposed Fe(III) atom. {ECO:0000255|HAMAP-Rule:MF_01297};
CC -!- PATHWAY: Nitrogen metabolism. {ECO:0000255|HAMAP-Rule:MF_01297}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:17172346}.
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:0000255|HAMAP-Rule:MF_01297}.
CC -!- MISCELLANEOUS: Was identified as a high-confidence drug target.
CC -!- SIMILARITY: Belongs to the nitrobindin family. {ECO:0000255|HAMAP-
CC Rule:MF_01297}.
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DR EMBL; AL123456; CCP43561.1; -; Genomic_DNA.
DR PIR; E70809; E70809.
DR RefSeq; NP_215328.1; NC_000962.3.
DR RefSeq; WP_003898596.1; NZ_NVQJ01000064.1.
DR PDB; 2FWV; X-ray; 1.70 A; A=1-226.
DR PDBsum; 2FWV; -.
DR AlphaFoldDB; P9WFG9; -.
DR SMR; P9WFG9; -.
DR STRING; 83332.Rv0813c; -.
DR iPTMnet; P9WFG9; -.
DR PaxDb; P9WFG9; -.
DR PRIDE; P9WFG9; -.
DR DNASU; 885395; -.
DR GeneID; 45424776; -.
DR GeneID; 885395; -.
DR KEGG; mtu:Rv0813c; -.
DR TubercuList; Rv0813c; -.
DR eggNOG; COG4044; Bacteria.
DR OMA; EKCNFGQ; -.
DR PhylomeDB; P9WFG9; -.
DR Proteomes; UP000001584; Chromosome.
DR GO; GO:0005886; C:plasma membrane; HDA:MTBBASE.
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; Acetylation; Heme; Iron; Isomerase; Metal-binding;
KW Reference proteome.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0007744|PubMed:21969609"
FT CHAIN 2..226
FT /note="Peroxynitrite isomerase 2"
FT /id="PRO_0000356933"
FT MOTIF 73..79
FT /note="GXWXGXG"
FT BINDING 189
FT /ligand="heme b"
FT /ligand_id="ChEBI:CHEBI:60344"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01297"
FT BINDING 216
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:0000255|HAMAP-Rule:MF_01297"
FT MOD_RES 2
FT /note="N-acetylserine"
FT /evidence="ECO:0007744|PubMed:21969609"
FT HELIX 28..36
FT /evidence="ECO:0007829|PDB:2FWV"
FT STRAND 46..48
FT /evidence="ECO:0007829|PDB:2FWV"
FT STRAND 57..59
FT /evidence="ECO:0007829|PDB:2FWV"
FT HELIX 63..71
FT /evidence="ECO:0007829|PDB:2FWV"
FT STRAND 73..83
FT /evidence="ECO:0007829|PDB:2FWV"
FT STRAND 86..98
FT /evidence="ECO:0007829|PDB:2FWV"
FT STRAND 100..113
FT /evidence="ECO:0007829|PDB:2FWV"
FT STRAND 119..132
FT /evidence="ECO:0007829|PDB:2FWV"
FT STRAND 145..151
FT /evidence="ECO:0007829|PDB:2FWV"
FT TURN 152..154
FT /evidence="ECO:0007829|PDB:2FWV"
FT STRAND 155..165
FT /evidence="ECO:0007829|PDB:2FWV"
FT STRAND 168..178
FT /evidence="ECO:0007829|PDB:2FWV"
FT STRAND 188..194
FT /evidence="ECO:0007829|PDB:2FWV"
FT STRAND 200..207
FT /evidence="ECO:0007829|PDB:2FWV"
FT STRAND 213..225
FT /evidence="ECO:0007829|PDB:2FWV"
SQ SEQUENCE 226 AA; 23900 MW; 9EC0562C72F22495 CRC64;
MSSGAGSDAT GAGGVHAAGS GDRAVAAAVE RAKATAARNI PAFDDLPVPA DTANLREGAD
LNNALLALLP LVGVWRGEGE GRGPDGDYRF GQQIVVSHDG GDYLNWESRS WRLTATGDYQ
EPGLREAGFW RFVADPYDPS ESQAIELLLA HSAGYVELFY GRPRTQSSWE LVTDALARSR
SGVLVGGAKR LYGIVEGGDL AYVEERVDAD GGLVPHLSAR LSRFVG
