DYP_MYCTU
ID DYP_MYCTU Reviewed; 335 AA.
AC I6Y4U9;
DT 25-MAY-2022, integrated into UniProtKB/Swiss-Prot.
DT 03-OCT-2012, sequence version 1.
DT 03-AUG-2022, entry version 57.
DE RecName: Full=Dye-decolorizing peroxidase;
DE Short=DyP {ECO:0000303|PubMed:24855650};
DE EC=1.11.1.7 {ECO:0000269|PubMed:24855650, ECO:0000269|PubMed:34751132};
GN Name=dyp {ECO:0000303|PubMed:24855650}; OrderedLocusNames=Rv0799c;
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] {ECO:0007744|PubMed:21969609}
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 [3]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, HEME-BINDING, SUBUNIT,
RP SUBCELLULAR LOCATION, DOMAIN, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF
RP 312-LEU--ARG-335.
RC STRAIN=H37Rv;
RX PubMed=24855650; DOI=10.1074/jbc.m114.570119;
RA Contreras H., Joens M.S., McMath L.M., Le V.P., Tullius M.V., Kimmey J.M.,
RA Bionghi N., Horwitz M.A., Fitzpatrick J.A., Goulding C.W.;
RT "Characterization of a Mycobacterium tuberculosis nanocompartment and its
RT potential cargo proteins.";
RL J. Biol. Chem. 289:18279-18289(2014).
RN [4]
RP IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION, CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, SUBCELLULAR LOCATION, AND
RP DISRUPTION PHENOTYPE.
RC STRAIN=H37Rv;
RX PubMed=34751132; DOI=10.7554/elife.74358;
RA Lien K.A., Dinshaw K., Nichols R.J., Cassidy-Amstutz C., Knight M.,
RA Singh R., Eltis L.D., Savage D.F., Stanley S.A.;
RT "A nanocompartment system contributes to defense against oxidative stress
RT in Mycobacterium tuberculosis.";
RL Elife 10:0-0(2021).
CC -!- FUNCTION: Cargo of a type 1 encapsulin nanocompartment in situ; this
CC cargo protects against oxidative stress at low pH. When expressed in
CC the cytoplasm (absence of the encapsulin shell gene) it is almost as
CC protective as the intact nanocompartment; its encapsulation has a
CC modest yet significant effect on protection against oxidative stress at
CC low pH (PubMed:34751132). A heme-dependent peroxidase, it probably does
CC not have deferrochelatase activity. Converts guaiacol and H2O2 to
CC tetraguaiacol, also acts on 2,2'-azino-bis(3-ethylbenzothiazoline-6-
CC sulfonic acid) (ABTS). Retains peroxidase activity when encapsulated
CC but has a reduced set of substrates; acts on ABTS but not guaiacol
CC (PubMed:24855650, PubMed:34751132). {ECO:0000269|PubMed:24855650,
CC ECO:0000269|PubMed:34751132}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2 a phenolic donor + H2O2 = 2 a phenolic radical donor + 2
CC H2O; Xref=Rhea:RHEA:56136, ChEBI:CHEBI:15377, ChEBI:CHEBI:16240,
CC ChEBI:CHEBI:139520, ChEBI:CHEBI:139521; EC=1.11.1.7;
CC Evidence={ECO:0000269|PubMed:24855650, ECO:0000269|PubMed:34751132};
CC -!- COFACTOR:
CC Name=heme b; Xref=ChEBI:CHEBI:60344;
CC Evidence={ECO:0000269|PubMed:24855650};
CC Note=Tetramer binds heme in a 1:1 ratio (PubMed:24855650). Addition of
CC hemin to purified protein yields a tetrameric protein (Probable).
CC {ECO:0000269|PubMed:24855650, ECO:0000305|PubMed:9634230};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 4.0 or less. {ECO:0000269|PubMed:34751132};
CC -!- SUBUNIT: Homotetramer, presumably also in the encapsulin
CC nanocompartment. {ECO:0000269|PubMed:24855650}.
CC -!- SUBCELLULAR LOCATION: Encapsulin nanocompartment
CC {ECO:0000269|PubMed:24855650}. Note=Consistently identified in
CC encapsulin nanocompartments isolated in situ (PubMed:34751132). Located
CC inside the nanocompartment in E.coli (Probable).
CC {ECO:0000269|PubMed:34751132, ECO:0000305|PubMed:24855650}.
CC -!- DOMAIN: The C-terminus (residues 312-335) targets the protein to the
CC encapsulin nanocompartment. {ECO:0000269|PubMed:24855650}.
CC -!- DISRUPTION PHENOTYPE: No change in ability to grow on an exogenous
CC siderophore (mycobactin), suggesting it does not have an iron-chelating
CC function (PubMed:24855650). A double dyp-enc deletion mutant cannot
CC produce encapsulin nanocompartments, cells are highly sensitive to H2O2
CC at pH 4.5 (mimics growth in the phagolysosome), mutants exhibit
CC significant dysregulation of redox homeostasis, survive less well in
CC C57BL/6 mouse-derived bone marrow cells and are more sensitive to
CC pyrazinamide treatment in infected BALB/C mice (PubMed:34751132).
CC {ECO:0000269|PubMed:24855650, ECO:0000269|PubMed:34751132}.
CC -!- SIMILARITY: Belongs to the DyP-type peroxidase family. {ECO:0000305}.
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DR EMBL; AL123456; CCP43547.1; -; Genomic_DNA.
DR RefSeq; NP_215314.1; NC_000962.3.
DR RefSeq; WP_003404098.1; NZ_NVQJ01000064.1.
DR AlphaFoldDB; I6Y4U9; -.
DR SMR; I6Y4U9; -.
DR STRING; 83332.Rv0799c; -.
DR PaxDb; I6Y4U9; -.
DR PRIDE; I6Y4U9; -.
DR DNASU; 885388; -.
DR GeneID; 885388; -.
DR KEGG; mtu:Rv0799c; -.
DR PATRIC; fig|83332.111.peg.886; -.
DR TubercuList; Rv0799c; -.
DR eggNOG; COG2837; Bacteria.
DR OMA; CAEPNLH; -.
DR PhylomeDB; I6Y4U9; -.
DR Proteomes; UP000001584; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0140737; C:encapsulin nanocompartment; IDA:UniProtKB.
DR GO; GO:0020037; F:heme binding; IDA:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004601; F:peroxidase activity; IDA:UniProtKB.
DR InterPro; IPR011008; Dimeric_a/b-barrel.
DR InterPro; IPR006314; Dyp_peroxidase.
DR Pfam; PF04261; Dyp_perox; 1.
DR SUPFAM; SSF54909; SSF54909; 1.
DR TIGRFAMs; TIGR01413; Dyp_perox_fam; 1.
DR PROSITE; PS51404; DYP_PEROXIDASE; 1.
PE 1: Evidence at protein level;
KW Encapsulin nanocompartment; Heme; Iron; Metal-binding; Oxidoreductase;
KW Peroxidase; Reference proteome; Virulence.
FT CHAIN 1..335
FT /note="Dye-decolorizing peroxidase"
FT /id="PRO_0000455327"
FT REGION 312..335
FT /note="Targeting peptide"
FT /evidence="ECO:0000269|PubMed:24855650"
FT ACT_SITE 149
FT /note="Proton acceptor"
FT /evidence="ECO:0000250|UniProtKB:Q47KB1"
FT BINDING 222
FT /ligand="heme"
FT /ligand_id="ChEBI:CHEBI:30413"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="proximal binding residue"
FT /evidence="ECO:0000250|UniProtKB:Q47KB1"
FT MUTAGEN 312..335
FT /note="Missing: Protein no longer targeted to encapsulin
FT nanocompartments, retains enzyme activity."
FT /evidence="ECO:0000269|PubMed:24855650"
SQ SEQUENCE 335 AA; 36048 MW; 2248C5CDE8606C30 CRC64;
MAVPAVSPQP ILAPLTPAAI FLVATIGADG EATVHDALSK ISGLVRAIGF RDPTKHLSVV
VSIGSDAWDR LFAGPRPTEL HPFVELTGPR HTAPATPGDL LFHIRAETMD VCFELAGRIL
KSMGDAVTVV DEVHGFRFFD NRDLLGFVDG TENPSGPIAI KATTIGDEDR NFAGSCYVHV
QKYVHDMASW ESLSVTEQER VIGRTKLDDI ELDDNAKPAN SHVALNVITD DDGTERKIVR
HNMPFGEVGK GEYGTYFIGY SRTPTVTEQM LRNMFLGDPA GNTDRVLDFS TAVTGGLFFS
PTIDFLDHPP PLPQAATPTL AAGSLSIGSL KGSPR
