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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_MYCS2             Reviewed;         460 AA.
A0R607; I7FMU1;
01-APR-2015, integrated into UniProtKB/Swiss-Prot.
01-APR-2015, sequence version 2.
28-MAR-2018, entry version 84.
RecName: Full=Decaprenylphosphoryl-beta-D-ribose oxidase {ECO:0000305};
EC=1.1.98.3 {ECO:0000269|PubMed:22188377};
AltName: Full=Decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase {ECO:0000305|PubMed:22956199};
AltName: Full=Decaprenylphosphoryl-beta-D-ribofuranose 2'-epimerase subunit DprE1 {ECO:0000305|PubMed:22188377};
Short=Decaprenyl-phosphoribose 2'-epimerase subunit 1 {ECO:0000305|PubMed:22188377};
AltName: Full=Decaprenylphosphoryl-beta-D-ribofuranose 2'-oxidase {ECO:0000303|PubMed:22188377};
AltName: Full=Decaprenylphosphoryl-beta-D-ribose 2-epimerase flavoprotein subunit {ECO:0000305};
AltName: Full=FAD-dependent decaprenylphosphoryl-beta-D-ribofuranose 2-oxidase {ECO:0000305|PubMed:22188377};
Name=dprE1 {ECO:0000303|PubMed:22188377};
OrderedLocusNames=MSMEG_6382, MSMEI_6214; ORFNames=LJ00_31545;
Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155).
Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
Mycobacterium.
NCBI_TaxID=246196;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 700084 / mc(2)155;
Fleischmann R.D., Dodson R.J., Haft D.H., Merkel J.S., Nelson W.C.,
Fraser C.M.;
Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases.
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 700084 / mc(2)155;
PubMed=17295914; DOI=10.1186/gb-2007-8-2-r20;
Deshayes C., Perrodou E., Gallien S., Euphrasie D., Schaeffer C.,
Van-Dorsselaer A., Poch O., Lecompte O., Reyrat J.-M.;
"Interrupted coding sequences in Mycobacterium smegmatis: authentic
mutations or sequencing errors?";
Genome Biol. 8:R20.1-R20.9(2007).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 700084 / mc(2)155;
PubMed=18955433; DOI=10.1101/gr.081901.108;
Gallien S., Perrodou E., Carapito C., Deshayes C., Reyrat J.-M.,
Van Dorsselaer A., Poch O., Schaeffer C., Lecompte O.;
"Ortho-proteogenomics: multiple proteomes investigation through
orthology and a new MS-based protocol.";
Genome Res. 19:128-135(2009).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 700084 / mc(2)155;
PubMed=25657281; DOI=10.1128/genomeA.01520-14;
Mohan A., Padiadpu J., Baloni P., Chandra N.;
"Complete genome sequences of a Mycobacterium smegmatis laboratory
strain (MC2 155) and isoniazid-resistant (4XR1/R2) mutant strains.";
Genome Announc. 3:E01520-E01520(2015).
[5]
ENZYME REGULATION, DRUG TARGET, AND BTZ043-RESISTANT VARIANTS MN47 AND
MN84.
STRAIN=ATCC 700084 / mc(2)155;
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).
[6]
DISRUPTION PHENOTYPE, AND PATHWAY.
STRAIN=ATCC 700084 / mc(2)155;
PubMed=21346818; DOI=10.1371/journal.pone.0016869;
Crellin P.K., Brammananth R., Coppel R.L.;
"Decaprenylphosphoryl-beta-D-ribose 2'-epimerase, the target of
benzothiazinones and dinitrobenzamides, is an essential enzyme in
Mycobacterium smegmatis.";
PLoS ONE 6:E16869-E16869(2011).
[7]
FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF CYS-386, ENZYME
REGULATION, AND SUBSTRATE SPECIFICITY.
STRAIN=ATCC 700084 / mc(2)155;
PubMed=22188377; DOI=10.1021/ja211042r;
Trefzer C., Skovierova H., Buroni S., Bobovska A., Nenci S.,
Molteni E., Pojer F., Pasca M.R., Makarov V., Cole S.T., Riccardi G.,
Mikusova K., Johnsson K.;
"Benzothiazinones are suicide inhibitors of mycobacterial
decaprenylphosphoryl-beta-D-ribofuranose 2'-oxidase DprE1.";
J. Am. Chem. Soc. 134:912-915(2012).
[8]
X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) IN COMPLEXES WITH FAD AND THE
BENZOTHIAZINONE BTZ043 INHIBITOR, FUNCTION, BIOPHYSICOCHEMICAL
PROPERTIES, MUTAGENESIS OF GLN-335; CYS-386 AND LYS-417, ENZYME
REGULATION, AND SUBUNIT.
STRAIN=ATCC 700084 / mc(2)155;
PubMed=22956199; DOI=10.1126/scitranslmed.3004395;
Neres J., Pojer F., Molteni E., Chiarelli L.R., Dhar N.,
Boy-Rottger S., Buroni S., Fullam E., Degiacomi G., Lucarelli A.P.,
Read R.J., Zanoni G., Edmondson D.E., De Rossi E., Pasca M.R.,
McKinney J.D., Dyson P.J., Riccardi G., Mattevi A., Cole S.T.,
Binda C.;
"Structural basis for benzothiazinone-mediated killing of
Mycobacterium tuberculosis.";
Sci. Transl. Med. 4:150RA121-150RA121(2012).
[9]
X-RAY CRYSTALLOGRAPHY (2.35 ANGSTROMS) OF 58-460.
STRAIN=ATCC 607 / DSM 43465 / JCM 20379 / NBRC 3207 / NRRL B-692;
PubMed=23184707; DOI=10.1002/prot.24220;
Li H., Jogl G.;
"Crystal structure of decaprenylphosphoryl-beta- D-ribose 2'-epimerase
from Mycobacterium smegmatis.";
Proteins 81:538-543(2013).
-!- 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:22188377). 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:22188377). 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 (By similarity). Can also use farnesyl-phosphoryl-
beta-D-ribofuranose (FPR) as substrate in vitro (PubMed:22188377,
PubMed:22956199). Appears to be essential for the growth of
M.smegmatis (PubMed:21346818). {ECO:0000250|UniProtKB:P9WJF1,
ECO:0000269|PubMed:21346818, ECO:0000269|PubMed:22188377,
ECO:0000269|PubMed:22956199}.
-!- CATALYTIC ACTIVITY: Trans,octacis-decaprenylphospho-beta-D-
ribofuranose + FAD = trans,octacis-decaprenylphospho-beta-D-
erythro-pentofuranosid-2-ulose + FADH(2).
{ECO:0000269|PubMed:22188377}.
-!- ENZYME REGULATION: Is inhibited by 8-nitro-benzothiazinones (BTZs)
such as BTZ043; BTZs are a new class of antimycobacterial agents
that block formation of both cell-wall lipoarabinomannan and
arabinogalactan via inhibition of decaprenyl-phospho-arabinose
(DPA) synthesis (PubMed:19299584, PubMed:22188377). BTZs 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-386 of
DprE1 to form an irreversible semimercaptal adduct
(PubMed:22188377, PubMed:22956199). Other compounds with diverse
scaffolds (dinitrobenzamides and nitrobenzoquinoxalines) also act
as covalent DprE1 inhibitors (PubMed:22956199).
{ECO:0000269|PubMed:19299584, ECO:0000269|PubMed:22188377,
ECO:0000269|PubMed:22956199}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=0.11 mM for FPR (at pH 8.5 and 25 degrees Celsius)
{ECO:0000269|PubMed:22956199};
Note=kcat is 12.7 min(-1) for epimerase activity with FPR as
substrate (at pH 8.5 and 25 degrees Celsius).
{ECO:0000269|PubMed:22956199};
-!- PATHWAY: Cell wall biogenesis; cell wall polysaccharide
biosynthesis. {ECO:0000305|PubMed:21346818}.
-!- SUBUNIT: Monomer (PubMed:22956199). Interacts with DprE2 to form
an epimerase complex (By similarity).
{ECO:0000250|UniProtKB:P9WJF1, ECO:0000269|PubMed:22956199}.
-!- SUBCELLULAR LOCATION: Periplasm {ECO:0000250|UniProtKB:P9WJF1}.
-!- DISRUPTION PHENOTYPE: Disruption of this gene is only possible in
the presence of a plasmid-encoded copy of the gene. Curing of this
'rescue' plasmid from the bacterial population results in a
cessation of growth, demonstrating gene essentiality.
{ECO:0000269|PubMed:21346818}.
-!- SIMILARITY: Belongs to the DprE1 family. {ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=ABK72795.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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EMBL; CP000480; ABK72795.1; ALT_INIT; Genomic_DNA.
EMBL; CP001663; AFP42640.1; -; Genomic_DNA.
EMBL; CP009494; AIU11363.1; -; Genomic_DNA.
RefSeq; YP_890595.1; NC_008596.1.
PDB; 4AUT; X-ray; 2.10 A; A=1-460.
PDB; 4F4Q; X-ray; 2.62 A; A=1-460.
PDB; 4G3T; X-ray; 2.35 A; A=58-460.
PDB; 4G3U; X-ray; 2.69 A; A/B=58-460.
PDBsum; 4AUT; -.
PDBsum; 4F4Q; -.
PDBsum; 4G3T; -.
PDBsum; 4G3U; -.
SMR; A0R607; -.
STRING; 246196.MSMEG_6382; -.
ChEMBL; CHEMBL3797019; -.
EnsemblBacteria; ABK72795; ABK72795; MSMEG_6382.
EnsemblBacteria; AFP42640; AFP42640; MSMEI_6214.
EnsemblBacteria; AIU11363; AIU11363; LJ00_31545.
GeneID; 4532115; -.
KEGG; msb:LJ00_31545; -.
KEGG; msg:MSMEI_6214; -.
KEGG; msm:MSMEG_6382; -.
PATRIC; fig|246196.19.peg.6209; -.
eggNOG; ENOG4105IQ5; Bacteria.
eggNOG; COG0277; LUCA.
HOGENOM; HOG000010204; -.
KO; K16653; -.
OrthoDB; POG091H08SQ; -.
BioCyc; MetaCyc:MONOMER-17534; -.
BRENDA; 1.1.98.3; 3512.
UniPathway; UPA00963; -.
Proteomes; UP000000757; Chromosome.
Proteomes; UP000006158; Chromosome.
GO; GO:0016020; C:membrane; IEA:InterPro.
GO; GO:0042597; C:periplasmic space; IEA:UniProtKB-SubCell.
GO; GO:0003885; F:D-arabinono-1,4-lactone oxidase activity; IEA:InterPro.
GO; GO:0050660; F:flavin adenine dinucleotide binding; IEA:InterPro.
GO; GO:0045227; P:capsule polysaccharide biosynthetic process; IEA:UniProtKB-UniPathway.
GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-KW.
GO; GO:0046677; P:response to antibiotic; IEA:UniProtKB-KW.
Gene3D; 3.30.43.10; -; 1.
InterPro; IPR007173; ALO.
InterPro; IPR016166; FAD-bd_2.
InterPro; IPR036318; FAD-bd_2-like_sf.
InterPro; IPR016167; FAD-bd_2_sub1.
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; Nucleotide-binding;
Oxidoreductase; Periplasm; Reference proteome.
CHAIN 1 460 Decaprenylphosphoryl-beta-D-ribose
oxidase.
/FTId=PRO_0000432471.
DOMAIN 19 193 FAD-binding PCMH-type.
{ECO:0000255|PROSITE-ProRule:PRU00718}.
NP_BIND 52 62 FAD. {ECO:0000244|PDB:4AUT,
ECO:0000244|PDB:4F4Q,
ECO:0000269|PubMed:22956199}.
NP_BIND 121 124 FAD. {ECO:0000244|PDB:4AUT,
ECO:0000244|PDB:4F4Q,
ECO:0000269|PubMed:22956199}.
NP_BIND 128 131 FAD. {ECO:0000244|PDB:4AUT,
ECO:0000244|PDB:4F4Q,
ECO:0000269|PubMed:22956199}.
BINDING 116 116 FAD; via amide nitrogen.
{ECO:0000244|PDB:4AUT,
ECO:0000244|PDB:4F4Q,
ECO:0000269|PubMed:22956199}.
BINDING 183 183 FAD; via amide nitrogen and carbonyl
oxygen. {ECO:0000244|PDB:4AUT,
ECO:0000244|PDB:4F4Q,
ECO:0000269|PubMed:22956199}.
BINDING 414 414 FAD. {ECO:0000244|PDB:4AUT,
ECO:0000244|PDB:4F4Q,
ECO:0000269|PubMed:22956199}.
VARIANT 386 386 C -> G (in strain: MN47; BTZ043-
resistant).
{ECO:0000269|PubMed:19299584}.
VARIANT 386 386 C -> S (in strain: MN84; BTZ043-
resistant).
{ECO:0000269|PubMed:19299584}.
MUTAGEN 335 335 Q->A: 10-fold decrease in catalytic
efficiency.
{ECO:0000269|PubMed:22956199}.
MUTAGEN 386 386 C->G: 14-fold decrease in catalytic
efficiency. Reduces BTZs to inert
metabolites while avoiding covalent
inactivation.
{ECO:0000269|PubMed:22188377,
ECO:0000269|PubMed:22956199}.
MUTAGEN 417 417 K->A: Loss of catalytic activity.
{ECO:0000269|PubMed:22956199}.
STRAND 8 13 {ECO:0000244|PDB:4AUT}.
STRAND 22 27 {ECO:0000244|PDB:4AUT}.
HELIX 32 40 {ECO:0000244|PDB:4AUT}.
HELIX 42 45 {ECO:0000244|PDB:4AUT}.
STRAND 50 55 {ECO:0000244|PDB:4AUT}.
STRAND 58 61 {ECO:0000244|PDB:4AUT}.
STRAND 68 72 {ECO:0000244|PDB:4AUT}.
HELIX 73 75 {ECO:0000244|PDB:4AUT}.
STRAND 79 83 {ECO:0000244|PDB:4AUT}.
TURN 84 87 {ECO:0000244|PDB:4AUT}.
STRAND 88 92 {ECO:0000244|PDB:4AUT}.
HELIX 97 104 {ECO:0000244|PDB:4AUT}.
HELIX 105 107 {ECO:0000244|PDB:4AUT}.
HELIX 122 127 {ECO:0000244|PDB:4AUT}.
HELIX 135 138 {ECO:0000244|PDB:4AUT}.
HELIX 141 144 {ECO:0000244|PDB:4AUT}.
STRAND 145 151 {ECO:0000244|PDB:4AUT}.
STRAND 157 160 {ECO:0000244|PDB:4AUT}.
STRAND 162 164 {ECO:0000244|PDB:4AUT}.
HELIX 167 173 {ECO:0000244|PDB:4AUT}.
TURN 177 180 {ECO:0000244|PDB:4AUT}.
STRAND 182 189 {ECO:0000244|PDB:4AUT}.
STRAND 196 204 {ECO:0000244|PDB:4AUT}.
HELIX 208 216 {ECO:0000244|PDB:4AUT}.
HELIX 219 222 {ECO:0000244|PDB:4AUT}.
STRAND 224 230 {ECO:0000244|PDB:4AUT}.
STRAND 232 234 {ECO:0000244|PDB:4G3T}.
TURN 236 240 {ECO:0000244|PDB:4AUT}.
STRAND 242 249 {ECO:0000244|PDB:4AUT}.
HELIX 252 254 {ECO:0000244|PDB:4AUT}.
HELIX 257 261 {ECO:0000244|PDB:4AUT}.
STRAND 302 308 {ECO:0000244|PDB:4AUT}.
HELIX 309 313 {ECO:0000244|PDB:4AUT}.
TURN 314 317 {ECO:0000244|PDB:4AUT}.
STRAND 331 339 {ECO:0000244|PDB:4AUT}.
HELIX 343 356 {ECO:0000244|PDB:4AUT}.
STRAND 361 368 {ECO:0000244|PDB:4AUT}.
STRAND 381 390 {ECO:0000244|PDB:4AUT}.
HELIX 395 408 {ECO:0000244|PDB:4AUT}.
HELIX 415 417 {ECO:0000244|PDB:4AUT}.
HELIX 423 429 {ECO:0000244|PDB:4AUT}.
HELIX 433 443 {ECO:0000244|PDB:4AUT}.
HELIX 452 456 {ECO:0000244|PDB:4AUT}.
SEQUENCE 460 AA; 50377 MW; 2F19107D18638FC0 CRC64;
MSTTEFPTTT KRLMGWGRTA PTVASVLSTS DPEVIVRAVT RAAEEGGRGV IARGLGRSYG
DNAQNGGGLV IDMPALNRIH SIDSGTRLVD VDAGVSLDQL MKAALPHGLW VPVLPGTRQV
TVGGAIGCDI HGKNHHSAGS FGNHVRSMEL LTANGEVRHL TPAGPDSDLF WATVGGNGLT
GIILRATIEM TPTETAYFIA DGDVTGSLDE TIAFHSDGSE ANYTYSSAWF DAISKPPKLG
RAAISRGSLA KLDQLPSKLQ KDPLKFDAPQ LLTLPDIFPN GLANKFTFMP IGELWYRKSG
TYRNKVQNLT QFYHPLDMFG EWNRAYGSAG FLQYQFVVPT EAVEEFKSII VDIQRSGHYS
FLNVFKLFGP GNQAPLSFPI PGWNVCVDFP IKAGLHEFVT ELDRRVLEFG GRLYTAKDSR
TTAETFHAMY PRIDEWIRIR RSVDPDGVFA SDMARRLQLL


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