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Decaprenylphosphoryl-beta-D-ribose oxidase (EC 1.1.98.3) (Decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase) (Decaprenylphosphoryl-beta-D-ribofuranose 2'-epimerase subunit DprE1) (Decaprenyl-phosphoribose 2'-epimerase subunit 1) (Decaprenylphosphoryl-beta-D-ribofuranose 2'-oxidase) (Decaprenylphosphoryl-beta-D-ribose 2-epimerase flavoprotein subunit) (FAD-dependent decaprenylphosphoryl-beta-D-ribofuranose 2-oxidase)

 DPRE1_MYCTU             Reviewed;         461 AA.
P9WJF1; L0TDT1; P72056; Q7D4V3;
16-APR-2014, integrated into UniProtKB/Swiss-Prot.
16-APR-2014, sequence version 1.
05-DEC-2018, entry version 41.
RecName: Full=Decaprenylphosphoryl-beta-D-ribose oxidase {ECO:0000303|PubMed:19299584, ECO:0000303|PubMed:25427196, ECO:0000303|PubMed:25789990};
EC=1.1.98.3 {ECO:0000269|PubMed:22733761};
AltName: Full=Decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase {ECO:0000303|PubMed:20828197};
AltName: Full=Decaprenylphosphoryl-beta-D-ribofuranose 2'-epimerase subunit DprE1 {ECO:0000305|PubMed:25789990};
Short=Decaprenyl-phosphoribose 2'-epimerase subunit 1 {ECO:0000305|PubMed:25789990};
AltName: Full=Decaprenylphosphoryl-beta-D-ribofuranose 2'-oxidase {ECO:0000305};
AltName: Full=Decaprenylphosphoryl-beta-D-ribose 2-epimerase flavoprotein subunit {ECO:0000303|PubMed:24500695};
AltName: Full=FAD-dependent decaprenylphosphoryl-beta-D-ribofuranose 2-oxidase {ECO:0000303|PubMed:20828197};
Name=dprE1 {ECO:0000303|PubMed:19299584, ECO:0000303|PubMed:20828197};
OrderedLocusNames=Rv3790;
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
Mycobacterium; Mycobacterium tuberculosis complex.
NCBI_TaxID=83332;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 25618 / H37Rv;
PubMed=9634230; DOI=10.1038/31159;
Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M.,
Harris D.E., Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III,
Tekaia F., Badcock K., Basham D., Brown D., Chillingworth T.,
Connor R., Davies R.M., Devlin K., Feltwell T., Gentles S., Hamlin N.,
Holroyd S., Hornsby T., Jagels K., Krogh A., McLean J., Moule S.,
Murphy L.D., Oliver S., Osborne J., Quail M.A., Rajandream M.A.,
Rogers J., Rutter S., Seeger K., Skelton S., Squares S., Squares R.,
Sulston J.E., Taylor K., Whitehead S., Barrell B.G.;
"Deciphering the biology of Mycobacterium tuberculosis from the
complete genome sequence.";
Nature 393:537-544(1998).
[2]
DISRUPTION PHENOTYPE.
STRAIN=ATCC 25618 / H37Rv;
PubMed=12657046; DOI=10.1046/j.1365-2958.2003.03425.x;
Sassetti C.M., Boyd D.H., Rubin E.J.;
"Genes required for mycobacterial growth defined by high density
mutagenesis.";
Mol. Microbiol. 48:77-84(2003).
[3]
FUNCTION IN DPR EPIMERIZATION, AND PATHWAY.
STRAIN=H37Rv;
PubMed=16291675; DOI=10.1128/JB.187.23.8020-8025.2005;
Mikusova K., Huang H., Yagi T., Holsters M., Vereecke D., D'Haeze W.,
Scherman M.S., Brennan P.J., McNeil M.R., Crick D.C.;
"Decaprenylphosphoryl arabinofuranose, the donor of the D-
arabinofuranosyl residues of mycobacterial arabinan, is formed via a
two-step epimerization of decaprenylphosphoryl ribose.";
J. Bacteriol. 187:8020-8025(2005).
[4]
IDENTIFICATION AS A DRUG TARGET [LARGE SCALE ANALYSIS].
PubMed=19099550; DOI=10.1186/1752-0509-2-109;
Raman K., Yeturu K., Chandra N.;
"targetTB: a target identification pipeline for Mycobacterium
tuberculosis through an interactome, reactome and genome-scale
structural analysis.";
BMC Syst. Biol. 2:109-109(2008).
[5]
ACTIVITY REGULATION, AND INHIBITOR SCREENING.
STRAIN=H37Rv;
PubMed=19876393; DOI=10.1371/journal.ppat.1000645;
Christophe T., Jackson M., Jeon H.K., Fenistein D.,
Contreras-Dominguez M., Kim J., Genovesio A., Carralot J.P., Ewann F.,
Kim E.H., Lee S.Y., Kang S., Seo M.J., Park E.J., Skovierova H.,
Pham H., Riccardi G., Nam J.Y., Marsollier L., Kempf M.,
Joly-Guillou M.L., Oh T., Shin W.K., No Z., Nehrbass U., Brosch R.,
Cole S.T., Brodin P.;
"High content screening identifies decaprenyl-phosphoribose 2'
epimerase as a target for intracellular antimycobacterial
inhibitors.";
PLoS Pathog. 5:E1000645-E1000645(2009).
[6]
FUNCTION IN DPR EPIMERIZATION, ACTIVITY REGULATION, DRUG TARGET, AND
BTZ043-RESISTANT VARIANTS NTB1 AND NTB9.
STRAIN=H37Rv;
PubMed=19299584; DOI=10.1126/science.1171583;
Makarov V., Manina G., Mikusova K., Mollmann U., Ryabova O.,
Saint-Joanis B., Dhar N., Pasca M.R., Buroni S., Lucarelli A.P.,
Milano A., De Rossi E., Belanova M., Bobovska A., Dianiskova P.,
Kordulakova J., Sala C., Fullam E., Schneider P., McKinney J.D.,
Brodin P., Christophe T., Waddell S., Butcher P., Albrethsen J.,
Rosenkrands I., Brosch R., Nandi V., Bharath S., Gaonkar S.,
Shandil R.K., Balasubramanian V., Balganesh T., Tyagi S., Grosset J.,
Riccardi G., Cole S.T.;
"Benzothiazinones kill Mycobacterium tuberculosis by blocking arabinan
synthesis.";
Science 324:801-804(2009).
[7]
REVIEW, AND DRUG TARGET.
PubMed=20629622; DOI=10.2174/092986710791959693;
Manina G., Pasca M.R., Buroni S., De Rossi E., Riccardi G.;
"Decaprenylphosphoryl-beta-D-ribose 2'-epimerase from Mycobacterium
tuberculosis is a magic drug target.";
Curr. Med. Chem. 17:3099-3108(2010).
[8]
ACTIVITY REGULATION, MECHANISM OF ACTION OF BENZOTHIAZINONES,
MUTAGENESIS OF CYS-387, AND 3D-STRUCTURE MODELING.
PubMed=20828197; DOI=10.1021/ja106357w;
Trefzer C., Rengifo-Gonzalez M., Hinner M.J., Schneider P.,
Makarov V., Cole S.T., Johnsson K.;
"Benzothiazinones: prodrugs that covalently modify the
decaprenylphosphoryl-beta-D-ribose 2'-epimerase DprE1 of Mycobacterium
tuberculosis.";
J. Am. Chem. Soc. 132:13663-13665(2010).
[9]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
STRAIN=ATCC 25618 / H37Rv;
PubMed=21969609; DOI=10.1074/mcp.M111.011627;
Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B.,
Yadav A.K., Shrivastava P., Marimuthu A., Anand S., Sundaram H.,
Kingsbury R., Harsha H.C., Nair B., Prasad T.S., Chauhan D.S.,
Katoch K., Katoch V.M., Kumar P., Chaerkady R., Ramachandran S.,
Dash D., Pandey A.;
"Proteogenomic analysis of Mycobacterium tuberculosis by high
resolution mass spectrometry.";
Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
[10]
REVIEW, AND DRUG TARGET.
PubMed=24037308; DOI=10.1007/s00253-013-5218-x;
Riccardi G., Pasca M.R., Chiarelli L.R., Manina G., Mattevi A.,
Binda C.;
"The DprE1 enzyme, one of the most vulnerable targets of Mycobacterium
tuberculosis.";
Appl. Microbiol. Biotechnol. 97:8841-8848(2013).
[11]
ACTIVITY REGULATION.
PubMed=24215368; DOI=10.1021/jm401382v;
Shirude P.S., Shandil R., Sadler C., Naik M., Hosagrahara V.,
Hameed S., Shinde V., Bathula C., Humnabadkar V., Kumar N., Reddy J.,
Panduga V., Sharma S., Ambady A., Hegde N., Whiteaker J.,
McLaughlin R.E., Gardner H., Madhavapeddi P., Ramachandran V.,
Kaur P., Narayan A., Guptha S., Awasthy D., Narayan C.,
Mahadevaswamy J., Vishwas K.G., Ahuja V., Srivastava A.,
Prabhakar K.R., Bharath S., Kale R., Ramaiah M., Choudhury N.R.,
Sambandamurthy V.K., Solapure S., Iyer P.S., Narayanan S.,
Chatterji M.;
"Azaindoles: noncovalent DprE1 inhibitors from scaffold morphing
efforts, kill Mycobacterium tuberculosis and are efficacious in
vivo.";
J. Med. Chem. 56:9701-9708(2013).
[12]
REVIEW, AND DRUG TARGET.
PubMed=24245764; DOI=10.2174/138161282027140630122724;
Mikusova K., Makarov V., Neres J.;
"DprE1--from the discovery to the promising tuberculosis drug
target.";
Curr. Pharm. Des. 20:4379-4403(2014).
[13]
ACTIVITY REGULATION.
PubMed=24818517; DOI=10.1021/jm5002937;
Panda M., Ramachandran S., Ramachandran V., Shirude P.S.,
Humnabadkar V., Nagalapur K., Sharma S., Kaur P., Guptha S.,
Narayan A., Mahadevaswamy J., Ambady A., Hegde N., Rudrapatna S.S.,
Hosagrahara V.P., Sambandamurthy V.K., Raichurkar A.;
"Discovery of pyrazolopyridones as a novel class of noncovalent DprE1
inhibitor with potent anti-mycobacterial activity.";
J. Med. Chem. 57:4761-4771(2014).
[14]
DISRUPTION PHENOTYPE, AND PATHWAY.
STRAIN=H37Rv;
PubMed=24517327; DOI=10.1111/mmi.12546;
Kolly G.S., Boldrin F., Sala C., Dhar N., Hartkoorn R.C., Ventura M.,
Serafini A., McKinney J.D., Manganelli R., Cole S.T.;
"Assessing the essentiality of the decaprenyl-phospho-D-
arabinofuranose pathway in Mycobacterium tuberculosis using
conditional mutants.";
Mol. Microbiol. 92:194-211(2014).
[15]
SUBCELLULAR LOCATION.
STRAIN=H37Rv;
PubMed=25906160; DOI=10.1021/acschembio.5b00237;
Brecik M., Centarova I., Mukherjee R., Kolly G.S., Huszar S.,
Bobovska A., Kilacskova E., Mokosova V., Svetlikova Z., Sarkan M.,
Neres J., Kordulakova J., Cole S.T., Mikusova K.;
"DprE1 is a vulnerable tuberculosis drug target due to its cell wall
localization.";
ACS Chem. Biol. 10:1631-1636(2015).
[16]
ACTIVITY REGULATION.
STRAIN=H37Rv;
PubMed=25987616; DOI=10.1128/AAC.00778-15;
Makarov V., Neres J., Hartkoorn R.C., Ryabova O.B., Kazakova E.,
Sarkan M., Huszar S., Piton J., Kolly G.S., Vocat A., Conroy T.M.,
Mikusova K., Cole S.T.;
"The 8-pyrrole-benzothiazinones are noncovalent inhibitors of DprE1
from Mycobacterium tuberculosis.";
Antimicrob. Agents Chemother. 59:4446-4452(2015).
[17]
INTERACTION WITH DPRE2.
PubMed=25789990; DOI=10.1371/journal.pone.0119771;
Bhutani I., Loharch S., Gupta P., Madathil R., Parkesh R.;
"Structure, dynamics, and interaction of Mycobacterium tuberculosis
(Mtb) DprE1 and DprE2 examined by molecular modeling, simulation, and
electrostatic studies.";
PLoS ONE 10:E0119771-E0119771(2015).
[18]
MUTAGENESIS OF CYS-387.
STRAIN=H37Rv;
PubMed=27527085; DOI=10.1128/AAC.01523-16;
Foo C.S., Lechartier B., Kolly G.S., Boy-Roettger S., Neres J.,
Rybniker J., Lupien A., Sala C., Piton J., Cole S.T.;
"Characterization of DprE1-mediated benzothiazinone resistance in
Mycobacterium tuberculosis.";
Antimicrob. Agents Chemother. 60:6451-6459(2016).
[19]
REVIEW, AND ACTIVITY REGULATION.
PubMed=27666194; DOI=10.1016/j.drudis.2016.09.014;
Piton J., Foo C.S., Cole S.T.;
"Structural studies of Mycobacterium tuberculosis DprE1 interacting
with its inhibitors.";
Drug Discov. Today 22:526-533(2017).
[20]
X-RAY CRYSTALLOGRAPHY (2.04 ANGSTROMS) IN COMPLEXES WITH FAD AND
BENZOTHIAZINONE INHIBITORS, FUNCTION, CATALYTIC ACTIVITY, ACTIVITY
REGULATION, AND SUBUNIT.
PubMed=22733761; DOI=10.1073/pnas.1205735109;
Batt S.M., Jabeen T., Bhowruth V., Quill L., Lund P.A., Eggeling L.,
Alderwick L.J., Futterer K., Besra G.S.;
"Structural basis of inhibition of Mycobacterium tuberculosis DprE1 by
benzothiazinone inhibitors.";
Proc. Natl. Acad. Sci. U.S.A. 109:11354-11359(2012).
[21]
X-RAY CRYSTALLOGRAPHY (2.61 ANGSTROMS) IN COMPLEX WITH TCA1 INHIBITOR
AND FAD, INHIBITOR SCREENING, ACTIVITY REGULATION, AND TCA1-RESISTANT
VARIANT CYS-314.
PubMed=23776209; DOI=10.1073/pnas.1309171110;
Wang F., Sambandan D., Halder R., Wang J., Batt S.M., Weinrick B.,
Ahmad I., Yang P., Zhang Y., Kim J., Hassani M., Huszar S.,
Trefzer C., Ma Z., Kaneko T., Mdluli K.E., Franzblau S.,
Chatterjee A.K., Johnsson K., Johnson K., Mikusova K., Besra G.S.,
Futterer K., Robbins S.H., Barnes S.W., Walker J.R., Jacobs W.R. Jr.,
Schultz P.G.;
"Identification of a small molecule with activity against drug-
resistant and persistent tuberculosis.";
Proc. Natl. Acad. Sci. U.S.A. 110:E2510-E2517(2013).
[22]
X-RAY CRYSTALLOGRAPHY (1.88 ANGSTROMS) IN COMPLEX WITH FAD AND THE
BENZOTHIAZINONE PBTZ169 INHIBITOR, AND ACTIVITY REGULATION.
PubMed=24500695; DOI=10.1002/emmm.201303575;
Makarov V., Lechartier B., Zhang M., Neres J., van der Sar A.M.,
Raadsen S.A., Hartkoorn R.C., Ryabova O.B., Vocat A., Decosterd L.A.,
Widmer N., Buclin T., Bitter W., Andries K., Pojer F., Dyson P.J.,
Cole S.T.;
"Towards a new combination therapy for tuberculosis with next
generation benzothiazinones.";
EMBO Mol. Med. 6:372-383(2014).
[23]
X-RAY CRYSTALLOGRAPHY (1.79 ANGSTROMS) IN COMPLEXES WITH FAD AND
DIFFERENT QUINOXALINE INHIBITORS, ACTIVITY REGULATION, INHIBITOR
SCREENING, TY38C-RESISTANT VARIANTS TRC11 AND TRC12, FUNCTION,
BIOPHYSICOCHEMICAL PROPERTIES, AND MUTAGENESIS OF GLY-17 AND LEU-368.
PubMed=25427196; DOI=10.1021/cb5007163;
Neres J., Hartkoorn R.C., Chiarelli L.R., Gadupudi R., Pasca M.R.,
Mori G., Venturelli A., Savina S., Makarov V., Kolly G.S., Molteni E.,
Binda C., Dhar N., Ferrari S., Brodin P., Delorme V., Landry V.,
de Jesus Lopes Ribeiro A.L., Farina D., Saxena P., Pojer F., Carta A.,
Luciani R., Porta A., Zanoni G., De Rossi E., Costi M.P., Riccardi G.,
Cole S.T.;
"2-Carboxyquinoxalines kill Mycobacterium tuberculosis through
noncovalent inhibition of DprE1.";
ACS Chem. Biol. 10:705-714(2015).
-!- FUNCTION: Component of the DprE1-DprE2 complex that catalyzes the
2-step epimerization of decaprenyl-phospho-ribose (DPR) to
decaprenyl-phospho-arabinose (DPA), a key precursor that serves as
the arabinose donor required for the synthesis of cell-wall
arabinans (PubMed:16291675, PubMed:19299584). DprE1 catalyzes the
first step of epimerization, namely FAD-dependent oxidation of the
C2' hydroxyl of DPR to yield the keto intermediate decaprenyl-
phospho-2'-keto-D-arabinose (DPX) (PubMed:22733761). The
intermediate DPX is then transferred to DprE2 subunit of the
epimerase complex, most probably through a 'substrate channel' at
the interface of DprE1-DprE2 complex (PubMed:25789990). Can also
use farnesyl-phosphoryl-beta-D-ribofuranose (FPR) as substrate in
vitro (PubMed:25427196). Appears to be essential for the growth
and survival of M.tuberculosis (PubMed:12657046, PubMed:24517327).
{ECO:0000269|PubMed:12657046, ECO:0000269|PubMed:16291675,
ECO:0000269|PubMed:19299584, ECO:0000269|PubMed:22733761,
ECO:0000269|PubMed:24517327, ECO:0000269|PubMed:25427196,
ECO:0000305|PubMed:25789990}.
-!- FUNCTION: DprE1 is a highly vulnerable and fully validated
tuberculosis drug target. {ECO:0000303|PubMed:20629622,
ECO:0000303|PubMed:24037308, ECO:0000303|PubMed:24245764}.
-!- CATALYTIC ACTIVITY:
Reaction=FAD + H(+) + trans,octa-cis-decaprenylphospho-beta-D-
ribofuranose = FADH2 + trans,octa-cis-decaprenylphospho-beta-D-
erythro-pentofuranosid-2-ulose; Xref=Rhea:RHEA:33899,
ChEBI:CHEBI:15378, ChEBI:CHEBI:57692, ChEBI:CHEBI:58307,
ChEBI:CHEBI:65067, ChEBI:CHEBI:66881; EC=1.1.98.3;
Evidence={ECO:0000269|PubMed:22733761};
-!- ACTIVITY REGULATION: Is inhibited by 8-nitro-benzothiazinones
(BTZs) such as BTZ043 and PBTZ169; BTZs are a new class of
antimycobacterial agents that kill M.tuberculosis in vitro, ex
vivo, and in mouse models of tuberculosis (PubMed:20828197,
PubMed:19299584, PubMed:22733761, PubMed:24500695). Is also
inhibited by dinitrobenzamide derivatives (DNBs), which thus block
formation of both cell-wall lipoarabinomannan and arabinogalactan
via inhibition of decaprenyl-phospho-arabinose (DPA) synthesis;
DNBs show high activity against intracellular growth of
M.tuberculosis inside macrophages, including extensively drug
resistant (XDR) strains (PubMed:19876393). BTZs and DNBs are
suicide inhibitors that act via covalent modification of DprE1;
the essential nitro group of these compounds is reduced by DprE1
to a nitroso group, which then specifically reacts with Cys-387 of
DprE1 to form an irreversible semimercaptal adduct
(PubMed:20828197, PubMed:22733761, PubMed:24500695). Many other
compounds with diverse scaffolds were found to act as either
covalent (e.g. nitroquinoxalines, nitroimidazoles) or non-covalent
(e.g. the benzothiazole derivative TCA1, the 2-carboxyquinoxaline
Ty38C, 8-pyrrole-benzothiazinones, 1,4-azaindoles,
pyrazolopyridones, 4-aminoquinolone piperidine amides) DprE1
inhibitors (PubMed:23776209, PubMed:25427196, PubMed:25987616,
PubMed:24215368, PubMed:24818517, PubMed:27666194).
{ECO:0000269|PubMed:19299584, ECO:0000269|PubMed:19876393,
ECO:0000269|PubMed:20828197, ECO:0000269|PubMed:22733761,
ECO:0000269|PubMed:23776209, ECO:0000269|PubMed:24215368,
ECO:0000269|PubMed:24500695, ECO:0000269|PubMed:24818517,
ECO:0000269|PubMed:25427196, ECO:0000269|PubMed:25987616,
ECO:0000303|PubMed:27666194}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
Note=kcat is 4.1 min(-1) with farnesyl-phosphoryl-beta-D-
ribofuranose as substrate (at pH 8 and 30 degrees Celsius).
{ECO:0000269|PubMed:25427196};
-!- PATHWAY: Cell wall biogenesis; cell wall polysaccharide
biosynthesis. {ECO:0000305|PubMed:16291675,
ECO:0000305|PubMed:24517327}.
-!- SUBUNIT: Monomer. Although forming apparent dimer in crystals,
DprE1 does not dimerize appreciably in solution (PubMed:22733761).
Interacts with DprE2 to form an epimerase complex
(PubMed:25789990). {ECO:0000269|PubMed:22733761,
ECO:0000269|PubMed:25789990}.
-!- SUBCELLULAR LOCATION: Periplasm {ECO:0000269|PubMed:25906160}.
-!- DISRUPTION PHENOTYPE: Traditional knockout mutant with dprE1
disruption could not be achieved, suggesting this gene is
essential (PubMed:24517327). Conditional knock-down mutant of
dprE1 show that down-regulation of DprE1 results in rapid in vitro
growth arrest, swelling of the bacteria, cell wall damage, stop of
cell division or lysis, decreased survival in macrophages and
virulence attenuation (PubMed:24517327). Cells lacking this gene
display impaired growth (PubMed:12657046).
{ECO:0000269|PubMed:12657046, ECO:0000269|PubMed:24517327}.
-!- MISCELLANEOUS: Was identified as a high-confidence drug target.
{ECO:0000269|PubMed:19099550}.
-!- SIMILARITY: Belongs to the DprE1 family. {ECO:0000305}.
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EMBL; AL123456; CCP46619.1; -; Genomic_DNA.
PIR; B70697; B70697.
RefSeq; NP_218307.1; NC_000962.3.
RefSeq; WP_003420630.1; NZ_NVQJ01000009.1.
PDB; 4FDN; X-ray; 2.40 A; A=1-461.
PDB; 4FDO; X-ray; 2.40 A; A=1-461.
PDB; 4FDP; X-ray; 2.23 A; A/B=1-461.
PDB; 4FEH; X-ray; 2.04 A; A=1-461.
PDB; 4FF6; X-ray; 2.60 A; A/B=1-461.
PDB; 4KW5; X-ray; 2.61 A; A/B=1-461.
PDB; 4NCR; X-ray; 1.88 A; A/B=1-461.
PDB; 4P8C; X-ray; 1.95 A; A/B=1-461.
PDB; 4P8H; X-ray; 3.00 A; A/B=1-461.
PDB; 4P8K; X-ray; 2.49 A; A/B=1-461.
PDB; 4P8L; X-ray; 2.02 A; A/B=1-461.
PDB; 4P8M; X-ray; 2.09 A; A/B=1-461.
PDB; 4P8N; X-ray; 1.79 A; A/B=1-461.
PDB; 4P8P; X-ray; 2.20 A; A/B=1-461.
PDB; 4P8T; X-ray; 2.55 A; A/B=1-461.
PDB; 4P8Y; X-ray; 2.01 A; A/B=1-461.
PDB; 4PFA; X-ray; 2.56 A; A/B=1-461.
PDB; 4PFD; X-ray; 2.30 A; A/B=1-461.
PDB; 5OEP; X-ray; 2.35 A; A/B=1-461.
PDB; 5OEQ; X-ray; 2.25 A; A/B=1-461.
PDB; 6HEZ; X-ray; 2.30 A; A/B=1-461.
PDB; 6HF0; X-ray; 2.38 A; A/B=1-461.
PDB; 6HF3; X-ray; 2.20 A; A/B=1-461.
PDB; 6HFV; X-ray; 2.05 A; A/B=1-461.
PDB; 6HFW; X-ray; 2.47 A; A/B=1-461.
PDBsum; 4FDN; -.
PDBsum; 4FDO; -.
PDBsum; 4FDP; -.
PDBsum; 4FEH; -.
PDBsum; 4FF6; -.
PDBsum; 4KW5; -.
PDBsum; 4NCR; -.
PDBsum; 4P8C; -.
PDBsum; 4P8H; -.
PDBsum; 4P8K; -.
PDBsum; 4P8L; -.
PDBsum; 4P8M; -.
PDBsum; 4P8N; -.
PDBsum; 4P8P; -.
PDBsum; 4P8T; -.
PDBsum; 4P8Y; -.
PDBsum; 4PFA; -.
PDBsum; 4PFD; -.
PDBsum; 5OEP; -.
PDBsum; 5OEQ; -.
PDBsum; 6HEZ; -.
PDBsum; 6HF0; -.
PDBsum; 6HF3; -.
PDBsum; 6HFV; -.
PDBsum; 6HFW; -.
ProteinModelPortal; P9WJF1; -.
SMR; P9WJF1; -.
STRING; 83332.Rv3790; -.
BindingDB; P9WJF1; -.
ChEMBL; CHEMBL3804751; -.
PaxDb; P9WJF1; -.
EnsemblBacteria; CCP46619; CCP46619; Rv3790.
GeneID; 886125; -.
KEGG; mtu:Rv3790; -.
TubercuList; Rv3790; -.
eggNOG; ENOG4105IQ5; Bacteria.
eggNOG; COG0277; LUCA.
KO; K16653; -.
OMA; PRGWFLP; -.
PhylomeDB; P9WJF1; -.
BioCyc; MetaCyc:G185E-8086-MONOMER; -.
UniPathway; UPA00963; -.
Proteomes; UP000001584; Chromosome.
GO; GO:0042597; C:periplasmic space; IEA:UniProtKB-SubCell.
GO; GO:0005886; C:plasma membrane; HDA:MTBBASE.
GO; GO:0003885; F:D-arabinono-1,4-lactone oxidase activity; IEA:InterPro.
GO; GO:0071949; F:FAD binding; IEA:InterPro.
GO; GO:0035884; P:arabinan biosynthetic process; IDA:MTBBASE.
GO; GO:0045227; P:capsule polysaccharide biosynthetic process; IEA:UniProtKB-UniPathway.
GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-KW.
GO; GO:0070592; P:cell wall polysaccharide biosynthetic process; IDA:MTBBASE.
GO; GO:0046677; P:response to antibiotic; IEA:UniProtKB-KW.
Gene3D; 3.30.465.10; -; 1.
InterPro; IPR007173; ALO.
InterPro; IPR016166; FAD-bd_PCMH.
InterPro; IPR036318; FAD-bd_PCMH-like_sf.
InterPro; IPR016169; FAD-bd_PCMH_sub2.
InterPro; IPR006094; Oxid_FAD_bind_N.
Pfam; PF04030; ALO; 1.
Pfam; PF01565; FAD_binding_4; 1.
SUPFAM; SSF56176; SSF56176; 1.
PROSITE; PS51387; FAD_PCMH; 1.
1: Evidence at protein level;
3D-structure; Antibiotic resistance; Cell wall biogenesis/degradation;
Complete proteome; FAD; Flavoprotein; Oxidoreductase; Periplasm;
Reference proteome.
CHAIN 1 461 Decaprenylphosphoryl-beta-D-ribose
oxidase.
/FTId=PRO_0000390891.
DOMAIN 19 194 FAD-binding PCMH-type.
{ECO:0000255|PROSITE-ProRule:PRU00718}.
NP_BIND 53 63 FAD. {ECO:0000244|PDB:4FDP,
ECO:0000244|PDB:4NCR,
ECO:0000269|PubMed:22733761,
ECO:0000269|PubMed:23776209,
ECO:0000269|PubMed:24500695,
ECO:0000269|PubMed:25427196}.
NP_BIND 122 125 FAD. {ECO:0000244|PDB:4FDP,
ECO:0000244|PDB:4KW5,
ECO:0000244|PDB:4NCR,
ECO:0000269|PubMed:22733761,
ECO:0000269|PubMed:23776209,
ECO:0000269|PubMed:24500695,
ECO:0000269|PubMed:25427196}.
NP_BIND 129 132 FAD. {ECO:0000244|PDB:4FDP,
ECO:0000244|PDB:4KW5,
ECO:0000244|PDB:4NCR,
ECO:0000269|PubMed:22733761,
ECO:0000269|PubMed:23776209,
ECO:0000269|PubMed:24500695,
ECO:0000269|PubMed:25427196}.
BINDING 117 117 FAD; via amide nitrogen.
{ECO:0000244|PDB:4FDP,
ECO:0000244|PDB:4KW5,
ECO:0000244|PDB:4NCR,
ECO:0000269|PubMed:22733761,
ECO:0000269|PubMed:23776209,
ECO:0000269|PubMed:24500695,
ECO:0000269|PubMed:25427196}.
BINDING 184 184 FAD; via amide nitrogen and carbonyl
oxygen. {ECO:0000244|PDB:4FDP,
ECO:0000244|PDB:4KW5,
ECO:0000244|PDB:4NCR,
ECO:0000269|PubMed:22733761,
ECO:0000269|PubMed:23776209,
ECO:0000269|PubMed:24500695,
ECO:0000269|PubMed:25427196}.
BINDING 415 415 FAD. {ECO:0000244|PDB:4FDP,
ECO:0000244|PDB:4KW5,
ECO:0000244|PDB:4NCR,
ECO:0000269|PubMed:22733761,
ECO:0000269|PubMed:23776209,
ECO:0000269|PubMed:24500695,
ECO:0000269|PubMed:25427196}.
VARIANT 17 17 G -> C (in strain: TRC11; Ty38c-resistant
mutant strain lacking Rv3406, but
sensitive to moxifloxacin).
{ECO:0000269|PubMed:25427196}.
VARIANT 314 314 Y -> C (in a spontaneous TCA1-resistant
mutant strain, but sensitive to BTZ).
{ECO:0000269|PubMed:23776209}.
VARIANT 368 368 L -> P (in strain: TRC12; Ty38c-resistant
mutant strain lacking Rv3406, but
sensitive to moxifloxacin).
{ECO:0000269|PubMed:25427196}.
VARIANT 387 387 C -> G (in strain: NTB9; BTZ043-
resistant).
{ECO:0000269|PubMed:19299584}.
VARIANT 387 387 C -> S (in strain: NTB1; BTZ043-
resistant).
{ECO:0000269|PubMed:19299584}.
MUTAGEN 17 17 G->C: Significantly less susceptible to
Ty38c inhibition. 34-fold reduction in
catalytic activity.
{ECO:0000269|PubMed:25427196}.
MUTAGEN 368 368 L->P: Significantly less susceptible to
Ty38c inhibition. 7-fold reduction in
catalytic activity.
{ECO:0000269|PubMed:25427196}.
MUTAGEN 387 387 C->A,S,T: Confers resistance to BTZ043
and PBTZ169. Decreases M.tuberculosis
cytotoxicity in macrophages. Does not
affect binding affinity of the substrate
to the enzyme, and only slightly affects
catalytic efficiency. Is only partially
inhibited by PBTZ169 at high
concentrations, while totally inhibited
by the non-covalent inhibitor Ty38c.
{ECO:0000269|PubMed:27527085}.
MUTAGEN 387 387 C->G: Confers resistance to BTZ043 and
PBTZ169. Loss of covalent modification
with BTZ043. Decreases M.tuberculosis
cytotoxicity in macrophages. Does not
affect binding affinity of the substrate
to the enzyme, but reduces catalytic
efficiency by 4-fold. Is only partially
inhibited by PBTZ169 at high
concentrations, while nearly totally
inhibited by the non-covalent inhibitor
Ty38c. {ECO:0000269|PubMed:20828197,
ECO:0000269|PubMed:27527085}.
MUTAGEN 387 387 C->N: Confers resistance to BTZ043 and
PBTZ169. Decreases M.tuberculosis
cytotoxicity in macrophages. Does not
affect binding affinity of the substrate
to the enzyme, but reduces catalytic
efficiency by 4-fold. Is only partially
inhibited by PBTZ169 at high
concentrations, while totally inhibited
by the non-covalent inhibitor Ty38c.
{ECO:0000269|PubMed:27527085}.
STRAND 7 13 {ECO:0000244|PDB:4NCR}.
STRAND 22 28 {ECO:0000244|PDB:4NCR}.
HELIX 32 44 {ECO:0000244|PDB:4NCR}.
STRAND 47 49 {ECO:0000244|PDB:4PFA}.
STRAND 51 54 {ECO:0000244|PDB:4NCR}.
STRAND 59 62 {ECO:0000244|PDB:4NCR}.
STRAND 69 73 {ECO:0000244|PDB:4NCR}.
STRAND 80 84 {ECO:0000244|PDB:4NCR}.
TURN 85 87 {ECO:0000244|PDB:4NCR}.
STRAND 89 93 {ECO:0000244|PDB:4NCR}.
HELIX 98 105 {ECO:0000244|PDB:4NCR}.
HELIX 106 108 {ECO:0000244|PDB:4NCR}.
HELIX 123 129 {ECO:0000244|PDB:4NCR}.
HELIX 136 139 {ECO:0000244|PDB:4NCR}.
HELIX 142 145 {ECO:0000244|PDB:4NCR}.
STRAND 146 152 {ECO:0000244|PDB:4NCR}.
STRAND 158 161 {ECO:0000244|PDB:4NCR}.
STRAND 163 165 {ECO:0000244|PDB:4NCR}.
HELIX 168 174 {ECO:0000244|PDB:4NCR}.
TURN 178 181 {ECO:0000244|PDB:4NCR}.
STRAND 183 190 {ECO:0000244|PDB:4NCR}.
STRAND 197 205 {ECO:0000244|PDB:4NCR}.
HELIX 209 217 {ECO:0000244|PDB:4NCR}.
HELIX 220 223 {ECO:0000244|PDB:4NCR}.
STRAND 225 231 {ECO:0000244|PDB:4NCR}.
STRAND 233 235 {ECO:0000244|PDB:6HEZ}.
TURN 237 241 {ECO:0000244|PDB:4NCR}.
STRAND 243 250 {ECO:0000244|PDB:4NCR}.
HELIX 253 255 {ECO:0000244|PDB:4NCR}.
HELIX 258 260 {ECO:0000244|PDB:4NCR}.
STRAND 261 263 {ECO:0000244|PDB:6HEZ}.
HELIX 275 278 {ECO:0000244|PDB:4P8T}.
HELIX 285 288 {ECO:0000244|PDB:4NCR}.
HELIX 291 300 {ECO:0000244|PDB:4NCR}.
STRAND 303 310 {ECO:0000244|PDB:4NCR}.
TURN 311 313 {ECO:0000244|PDB:4NCR}.
TURN 315 322 {ECO:0000244|PDB:4FDO}.
HELIX 324 327 {ECO:0000244|PDB:4FEH}.
TURN 328 330 {ECO:0000244|PDB:4FEH}.
STRAND 332 340 {ECO:0000244|PDB:4NCR}.
HELIX 341 343 {ECO:0000244|PDB:4FDN}.
HELIX 344 356 {ECO:0000244|PDB:4NCR}.
STRAND 365 369 {ECO:0000244|PDB:4NCR}.
STRAND 382 391 {ECO:0000244|PDB:4NCR}.
HELIX 396 409 {ECO:0000244|PDB:4NCR}.
HELIX 416 418 {ECO:0000244|PDB:4NCR}.
HELIX 424 430 {ECO:0000244|PDB:4NCR}.
HELIX 434 444 {ECO:0000244|PDB:4NCR}.
HELIX 453 457 {ECO:0000244|PDB:4NCR}.
SEQUENCE 461 AA; 50163 MW; B9B770002E5FE81C CRC64;
MLSVGATTTA TRLTGWGRTA PSVANVLRTP DAEMIVKAVA RVAESGGGRG AIARGLGRSY
GDNAQNGGGL VIDMTPLNTI HSIDADTKLV DIDAGVNLDQ LMKAALPFGL WVPVLPGTRQ
VTVGGAIACD IHGKNHHSAG SFGNHVRSMD LLTADGEIRH LTPTGEDAEL FWATVGGNGL
TGIIMRATIE MTPTSTAYFI ADGDVTASLD ETIALHSDGS EARYTYSSAW FDAISAPPKL
GRAAVSRGRL ATVEQLPAKL RSEPLKFDAP QLLTLPDVFP NGLANKYTFG PIGELWYRKS
GTYRGKVQNL TQFYHPLDMF GEWNRAYGPA GFLQYQFVIP TEAVDEFKKI IGVIQASGHY
SFLNVFKLFG PRNQAPLSFP IPGWNICVDF PIKDGLGKFV SELDRRVLEF GGRLYTAKDS
RTTAETFHAM YPRVDEWISV RRKVDPLRVF ASDMARRLEL L


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