DDN_MYCTU
ID DDN_MYCTU Reviewed; 151 AA.
AC P9WP15; L0TD35; P71854; Q7D5B2;
DT 16-APR-2014, integrated into UniProtKB/Swiss-Prot.
DT 16-APR-2014, sequence version 1.
DT 03-AUG-2022, entry version 43.
DE RecName: Full=Deazaflavin-dependent nitroreductase {ECO:0000303|PubMed:23240649};
DE EC=1.-.-.- {ECO:0000269|PubMed:19039139, ECO:0000269|PubMed:22023140};
DE AltName: Full=F420H(2)-dependent quinone reductase Ddn {ECO:0000303|PubMed:23240649};
DE Short=Fqr {ECO:0000303|PubMed:23240649};
DE EC=1.1.98.- {ECO:0000269|PubMed:23240649};
GN Name=ddn {ECO:0000303|PubMed:23240649}; OrderedLocusNames=Rv3547;
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 BY MASS SPECTROMETRY, AND SUBCELLULAR LOCATION.
RC STRAIN=H37Rv;
RX PubMed=16000731; DOI=10.1099/mic.0.27799-0;
RA Sinha S., Kosalai K., Arora S., Namane A., Sharma P., Gaikwad A.N.,
RA Brodin P., Cole S.T.;
RT "Immunogenic membrane-associated proteins of Mycobacterium tuberculosis
RT revealed by proteomics.";
RL Microbiology 151:2411-2419(2005).
RN [3]
RP FUNCTION IN THE ACTIVATION OF PA-824.
RX PubMed=16387854; DOI=10.1073/pnas.0508392103;
RA Manjunatha U.H., Boshoff H., Dowd C.S., Zhang L., Albert T.J., Norton J.E.,
RA Daniels L., Dick T., Pang S.S., Barry C.E. III;
RT "Identification of a nitroimidazo-oxazine-specific protein involved in PA-
RT 824 resistance in Mycobacterium tuberculosis.";
RL Proc. Natl. Acad. Sci. U.S.A. 103:431-436(2006).
RN [4]
RP FUNCTION AS A F420-DEPENDENT NITROREDUCTASE, AND CATALYTIC ACTIVITY.
RX PubMed=19039139; DOI=10.1126/science.1164571;
RA Singh R., Manjunatha U., Boshoff H.I., Ha Y.H., Niyomrattanakit P.,
RA Ledwidge R., Dowd C.S., Lee I.Y., Kim P., Zhang L., Kang S., Keller T.H.,
RA Jiricek J., Barry C.E. III;
RT "PA-824 kills nonreplicating Mycobacterium tuberculosis by intracellular NO
RT release.";
RL Science 322:1392-1395(2008).
RN [5]
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 [6]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, AND BIOPHYSICOCHEMICAL
RP PROPERTIES.
RX PubMed=22023140; DOI=10.1111/j.1742-4658.2011.08404.x;
RA Gurumurthy M., Mukherjee T., Dowd C.S., Singh R., Niyomrattanakit P.,
RA Tay J.A., Nayyar A., Lee Y.S., Cherian J., Boshoff H.I., Dick T.,
RA Barry C.E. III, Manjunatha U.H.;
RT "Substrate specificity of the deazaflavin-dependent nitroreductase from
RT Mycobacterium tuberculosis responsible for the bioreductive activation of
RT bicyclic nitroimidazoles.";
RL FEBS J. 279:113-125(2012).
RN [7]
RP FUNCTION AS A F420-DEPENDENT QUINONE REDUCTASE, CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE SPECIFICITY, AND MUTAGENESIS OF
RP TYR-65.
RC STRAIN=ATCC 27294 / TMC 102 / H37Rv;
RX PubMed=23240649; DOI=10.1111/mmi.12127;
RA Gurumurthy M., Rao M., Mukherjee T., Rao S.P., Boshoff H.I., Dick T.,
RA Barry C.E. III, Manjunatha U.H.;
RT "A novel F(420)-dependent anti-oxidant mechanism protects Mycobacterium
RT tuberculosis against oxidative stress and bactericidal agents.";
RL Mol. Microbiol. 87:744-755(2013).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (1.55 ANGSTROMS) OF 31-151 OF APOENZYME AND IN
RP COMPLEX WITH COENZYME F420, 3D-STRUCTURE MODELING, FUNCTION, AND
RP MUTAGENESIS OF TYR-65; ALA-76; SER-78; LYS-79; TYR-130; TYR-133; TYR-136;
RP ARG-142 AND ILE-144.
RX PubMed=22244759; DOI=10.1016/j.str.2011.11.001;
RA Cellitti S.E., Shaffer J., Jones D.H., Mukherjee T., Gurumurthy M.,
RA Bursulaya B., Boshoff H.I., Choi I., Nayyar A., Lee Y.S., Cherian J.,
RA Niyomrattanakit P., Dick T., Manjunatha U.H., Barry C.E. III, Spraggon G.,
RA Geierstanger B.H.;
RT "Structure of Ddn, the deazaflavin-dependent nitroreductase from
RT Mycobacterium tuberculosis involved in bioreductive activation of PA-824.";
RL Structure 20:101-112(2012).
CC -!- FUNCTION: Involved in a F420-dependent anti-oxidant mechanism that
CC protects M.tuberculosis against oxidative stress and bactericidal
CC agents. Catalyzes the F420H(2)-dependent two-electron reduction of
CC quinones to dihydroquinones, thereby preventing the formation of
CC cytotoxic semiquinones obtained by the one-electron reduction pathway
CC (PubMed:23240649). In vitro, catalyzes the reduction of both
CC benzoquinone and naphthoquinone analogs; since menaquinone is the sole
CC quinone electron carrier in the respiratory chain in M.tuberculosis,
CC the physiological electron acceptor for Fqr-mediated F420H(2) oxidation
CC is therefore likely to be the endogenous menaquinone found in the
CC membrane fraction of M.tuberculosis (PubMed:23240649). Is able to use
CC F420 species with two and five glutamate residues in its polyglutamate
CC tail (PubMed:22023140). Cannot use NADH or NADPH instead of F420H(2) as
CC the electron donor (PubMed:23240649). {ECO:0000269|PubMed:22023140,
CC ECO:0000269|PubMed:23240649}.
CC -!- FUNCTION: Is involved in the bioreductive activation of bicyclic 4-
CC nitroimidazole prodrugs such as PA-824 and delamanid developed for
CC anti-tuberculosis therapy against both replicating and persistent
CC bacteria. It converts PA-824 into three primary metabolites resulting
CC from reduction of the imidazole ring at C-3; the major one is the
CC corresponding des-nitroimidazole that generates lethal reactive
CC nitrogen species, including nitric oxide (NO), which appears to be
CC responsible for the anaerobic killing activity. Ddn uses the reduced
CC F420 produced by FGD1 to activate PA-824. Delamanid (OPC-67683) is also
CC reduced by Ddn to its des-nitro form. {ECO:0000269|PubMed:16387854,
CC ECO:0000269|PubMed:19039139, ECO:0000269|PubMed:22023140,
CC ECO:0000269|PubMed:22244759}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a quinol + H(+) + oxidized coenzyme F420-(gamma-L-Glu)(n) = a
CC quinone + reduced coenzyme F420-(gamma-L-Glu)(n);
CC Xref=Rhea:RHEA:39663, Rhea:RHEA-COMP:12939, Rhea:RHEA-COMP:14378,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:24646, ChEBI:CHEBI:132124,
CC ChEBI:CHEBI:133980, ChEBI:CHEBI:139511;
CC Evidence={ECO:0000269|PubMed:23240649};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=3.4 uM for menadione {ECO:0000269|PubMed:23240649};
CC KM=2.17 uM for plumbagin {ECO:0000269|PubMed:23240649};
CC KM=2.23 uM for 1,4-naphthoquinone {ECO:0000269|PubMed:23240649};
CC KM=2.21 uM for 2,3-dimethyl-naphthoquinone
CC {ECO:0000269|PubMed:23240649};
CC KM=12.35 uM for Co-Q(0) {ECO:0000269|PubMed:23240649};
CC KM=10.12 uM for Co-Q(1) {ECO:0000269|PubMed:23240649};
CC KM=3.14 uM for Co-Q(2) {ECO:0000269|PubMed:23240649};
CC KM=26 uM for reduced F(420)-2 {ECO:0000269|PubMed:22023140};
CC KM=29 uM for reduced F(420)-5 {ECO:0000269|PubMed:22023140};
CC KM=28.6 uM for PA-824 {ECO:0000269|PubMed:22023140};
CC KM=207.2 uM for (S)-CGI-17341 {ECO:0000269|PubMed:22023140};
CC KM=123.2 uM for (R)-CGI-17341 {ECO:0000269|PubMed:22023140};
CC KM=67.8 uM for (S)-phenyloxazole {ECO:0000269|PubMed:22023140};
CC KM=83.6 uM for (R)-phenyloxazole {ECO:0000269|PubMed:22023140};
CC KM=12.9 uM for aza-PA-824 {ECO:0000269|PubMed:22023140};
CC Note=kcat is 17.7 min(-1) for the reduction of menadione. kcat is
CC 5.03 min(-1) for the reduction of plumbagin. kcat is 17.2 min(-1) for
CC the reduction of 1,4-naphthoquinone. kcat is 5.37 min(-1) for the
CC reduction of 2,3-dimethyl-naphthoquinone. kcat is 1.23 min(-1) for
CC the reduction of Co-Q(0). kcat is 2.15 min(-1) for the reduction of
CC Co-Q(1). kcat is 5.43 min(-1) for the reduction of Co-Q(2)
CC (PubMed:23240649). kcat is 4.7 min(-1) for the reduction of PA-824.
CC kcat is 2.4 min(-1) for the reduction of (S)-CGI-17341. kcat is 2.2
CC min(-1) for the reduction of (R)-CGI-17341. kcat is 2.7 min(-1) for
CC the reduction of (S)-phenyloxazole. kcat is 4.8 min(-1) for the
CC reduction of (R)-phenyloxazole. kcat is 1.6 min(-1) for the reduction
CC of aza-PA-824 (PubMed:22023140). Is not able to reduce the enantiomer
CC (R)-PA-824 (the drug PA-824 is defined as the (S) isomer), and
CC metronidazole (Mtz) (PubMed:22023140). {ECO:0000269|PubMed:22023140,
CC ECO:0000269|PubMed:23240649};
CC pH dependence:
CC Optimum pH is 7.0-8.0. {ECO:0000269|PubMed:22023140};
CC -!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000269|PubMed:16000731};
CC Peripheral membrane protein {ECO:0000269|PubMed:16000731}.
CC -!- SIMILARITY: Belongs to the F420H(2)-dependent quinone reductase family.
CC {ECO:0000305}.
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DR EMBL; AL123456; CCP46369.1; -; Genomic_DNA.
DR PIR; D70677; D70677.
DR RefSeq; NP_218064.1; NC_000962.3.
DR RefSeq; WP_003419309.1; NZ_NVQJ01000014.1.
DR PDB; 3R5L; X-ray; 1.55 A; A=31-151.
DR PDB; 3R5P; X-ray; 1.85 A; A=34-151.
DR PDB; 3R5R; X-ray; 2.10 A; A/B/C/D/E=41-151.
DR PDB; 3R5W; X-ray; 1.79 A; A/B/C/D/E/K/L/M/N/O=41-151.
DR PDBsum; 3R5L; -.
DR PDBsum; 3R5P; -.
DR PDBsum; 3R5R; -.
DR PDBsum; 3R5W; -.
DR AlphaFoldDB; P9WP15; -.
DR SMR; P9WP15; -.
DR STRING; 83332.Rv3547; -.
DR ChEMBL; CHEMBL5663; -.
DR DrugBank; DB11637; Delamanid.
DR DrugBank; DB05154; Pretomanid.
DR PaxDb; P9WP15; -.
DR DNASU; 887496; -.
DR GeneID; 45427531; -.
DR GeneID; 887496; -.
DR KEGG; mtu:Rv3547; -.
DR TubercuList; Rv3547; -.
DR eggNOG; COG0748; Bacteria.
DR OMA; PKLDAMY; -.
DR PhylomeDB; P9WP15; -.
DR PRO; PR:P9WP15; -.
DR Proteomes; UP000001584; Chromosome.
DR GO; GO:0009274; C:peptidoglycan-based cell wall; HDA:UniProtKB.
DR GO; GO:0005886; C:plasma membrane; HDA:MTBBASE.
DR GO; GO:0070967; F:coenzyme F420 binding; IMP:MTBBASE.
DR GO; GO:0016491; F:oxidoreductase activity; IEA:UniProtKB-KW.
DR Gene3D; 2.30.110.10; -; 1.
DR InterPro; IPR004378; F420H2_quin_Rdtase.
DR InterPro; IPR012349; Split_barrel_FMN-bd.
DR Pfam; PF04075; F420H2_quin_red; 1.
DR TIGRFAMs; TIGR00026; hi_GC_TIGR00026; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cell membrane; Membrane; Oxidoreductase; Reference proteome.
FT CHAIN 1..151
FT /note="Deazaflavin-dependent nitroreductase"
FT /id="PRO_0000399507"
FT BINDING 54..56
FT /ligand="coenzyme F420-(gamma-Glu)n"
FT /ligand_id="ChEBI:CHEBI:133980"
FT /evidence="ECO:0000305|PubMed:22244759,
FT ECO:0007744|PDB:3R5W"
FT BINDING 60..65
FT /ligand="coenzyme F420-(gamma-Glu)n"
FT /ligand_id="ChEBI:CHEBI:133980"
FT /evidence="ECO:0000305|PubMed:22244759,
FT ECO:0007744|PDB:3R5W"
FT BINDING 76..79
FT /ligand="coenzyme F420-(gamma-Glu)n"
FT /ligand_id="ChEBI:CHEBI:133980"
FT /evidence="ECO:0000305|PubMed:22244759,
FT ECO:0007744|PDB:3R5W"
FT BINDING 87..91
FT /ligand="coenzyme F420-(gamma-Glu)n"
FT /ligand_id="ChEBI:CHEBI:133980"
FT /evidence="ECO:0000305|PubMed:22244759,
FT ECO:0007744|PDB:3R5W"
FT BINDING 133
FT /ligand="coenzyme F420-(gamma-Glu)n"
FT /ligand_id="ChEBI:CHEBI:133980"
FT /evidence="ECO:0000305|PubMed:22244759,
FT ECO:0007744|PDB:3R5W"
FT MUTAGEN 65
FT /note="Y->A,L: Loss of PA-824 and menadione reductase
FT activity."
FT /evidence="ECO:0000269|PubMed:22244759,
FT ECO:0000269|PubMed:23240649"
FT MUTAGEN 76
FT /note="A->G: Loss of PA-824 reductase activity."
FT /evidence="ECO:0000269|PubMed:22244759"
FT MUTAGEN 78
FT /note="S->A: Loss of PA-824 reductase activity."
FT /evidence="ECO:0000269|PubMed:22244759"
FT MUTAGEN 79
FT /note="K->L: Loss of PA-824 reductase activity."
FT /evidence="ECO:0000269|PubMed:22244759"
FT MUTAGEN 130
FT /note="Y->A,L: Loss of PA-824 reductase activity."
FT /evidence="ECO:0000269|PubMed:22244759"
FT MUTAGEN 133
FT /note="Y->A,F,L: Loss of PA-824 reductase activity."
FT /evidence="ECO:0000269|PubMed:22244759"
FT MUTAGEN 136
FT /note="Y->L,V: Loss of PA-824 reductase activity."
FT /evidence="ECO:0000269|PubMed:22244759"
FT MUTAGEN 142
FT /note="R->A,L: Loss of PA-824 reductase activity."
FT /evidence="ECO:0000269|PubMed:22244759"
FT MUTAGEN 144
FT /note="I->A,G: Loss of PA-824 reductase activity."
FT /evidence="ECO:0000269|PubMed:22244759"
FT STRAND 47..52
FT /evidence="ECO:0007829|PDB:3R5L"
FT TURN 54..56
FT /evidence="ECO:0007829|PDB:3R5L"
FT STRAND 58..69
FT /evidence="ECO:0007829|PDB:3R5L"
FT STRAND 72..76
FT /evidence="ECO:0007829|PDB:3R5L"
FT HELIX 81..83
FT /evidence="ECO:0007829|PDB:3R5L"
FT HELIX 87..94
FT /evidence="ECO:0007829|PDB:3R5L"
FT STRAND 97..102
FT /evidence="ECO:0007829|PDB:3R5L"
FT STRAND 105..113
FT /evidence="ECO:0007829|PDB:3R5L"
FT HELIX 116..129
FT /evidence="ECO:0007829|PDB:3R5L"
FT HELIX 131..135
FT /evidence="ECO:0007829|PDB:3R5P"
FT HELIX 138..140
FT /evidence="ECO:0007829|PDB:3R5L"
FT STRAND 146..150
FT /evidence="ECO:0007829|PDB:3R5L"
SQ SEQUENCE 151 AA; 17371 MW; 41534E55D948FB52 CRC64;
MPKSPPRFLN SPLSDFFIKW MSRINTWMYR RNDGEGLGGT FQKIPVALLT TTGRKTGQPR
VNPLYFLRDG GRVIVAASKG GAEKNPMWYL NLKANPKVQV QIKKEVLDLT ARDATDEERA
EYWPQLVTMY PSYQDYQSWT DRTIPIVVCE P
