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Protein

FAD-dependent decaprenylphosphoryl-beta-D-ribofuranose 2-oxidase

Gene

dprE1

Organism
Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Dpre1 and DprE2 are involved in the epimerization of decaprenylphosphoryl-beta-D-ribofuranose (DPR) to decaprenylphosphoryl-beta-D-arabinofuranose (DPA), the arabinosyl donor for the biosynthesis of mycobacterial cell wall arabinan polymers. The reaction proceeds via the keto intermediate decaprenylphosphoryl-D-2-keto-erythro-pentofuranose (DPX). DprE1 catalyzes the FAD-dependent oxidation at the C-2 of DPR to yield DPX. It can also use farnesylphosphoryl-beta-D-ribofuranose (FPR) as substrate and 2,6-dichlorophenolindophenol (DCPIP) as electron acceptor.2 Publications

Catalytic activityi

Trans,octacis-decaprenylphospho-beta-D-ribofuranose + FAD = trans,octacis-decaprenylphospho-beta-D-erythro-pentofuranosid-2-ulose + FADH2.2 Publications

Enzyme regulationi

Inhibited by dinitrobenzamide, nitrobenzoquinoxaline VI-9376 and 1,3-benzothiazin-4-ones (BTZs) such as BTZ043. The reaction involves the reduction of the essential nitro group of the inhibitors to a nitroso group that then reacts with Cys-386 of DprE1 to form a stable and irreversible semimercaptal (covalent).2 Publications

Kineticsi

Kcat is 12.7 min(-1) for epimerase activity with FPR as substrate (with DCPIP as electron acceptor at pH 8.5 and 25 degrees Celsius).1 Publication

  1. KM=0.11 mM for FPR (with DCPIP as electron acceptor at pH 8.5 and 25 degrees Celsius)1 Publication

    Pathway:icell wall polysaccharide biosynthesis

    This protein is involved in the pathway cell wall polysaccharide biosynthesis, which is part of Cell wall biogenesis.By similarity
    View all proteins of this organism that are known to be involved in the pathway cell wall polysaccharide biosynthesis and in Cell wall biogenesis.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei116 – 1161FAD; via amide nitrogen1 Publication
    Binding sitei133 – 1331SubstrateBy similarity
    Binding sitei177 – 1771FAD; via carbonyl oxygen1 Publication
    Binding sitei183 – 1831FAD; via amide nitrogen and carbonyl oxygen1 Publication
    Binding sitei414 – 4141FAD1 Publication
    Binding sitei417 – 4171Substrate1 Publication

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi52 – 6211FAD1 PublicationAdd
    BLAST
    Nucleotide bindingi121 – 1244FAD1 Publication
    Nucleotide bindingi128 – 1314FAD1 Publication

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Cell wall biogenesis/degradation

    Keywords - Ligandi

    FAD, Flavoprotein, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-17534.
    MSME246196:GJ4Y-6381-MONOMER.
    BRENDAi1.1.98.3. 3512.
    UniPathwayiUPA00963.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    FAD-dependent decaprenylphosphoryl-beta-D-ribofuranose 2-oxidase1 Publication (EC:1.1.98.32 Publications)
    Alternative name(s):
    Decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase1 Publication
    Decaprenylphosphoryl-beta-D-ribofuranose 2'-epimerase 11 Publication
    Short name:
    DprE11 Publication
    Gene namesi
    Name:dprE11 Publication
    Ordered Locus Names:MSMEG_6382, MSMEI_6214
    ORF Names:LJ00_31545
    OrganismiMycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
    Taxonomic identifieri246196 [NCBI]
    Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesMycobacteriaceaeMycobacterium
    ProteomesiUP000006158 Componenti: Chromosome UP000000757 Componenti: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi335 – 3351Q → A: 10-fold decrease in the catalytic efficiency. 1 Publication
    Mutagenesisi386 – 3861C → G: 4-fold decrease in the catalytic efficiency. 1 Publication
    Mutagenesisi386 – 3861C → G: Resistance toward BTZs. Reduces BTZs to inert metabolites while avoiding covalent inactivation. 1 Publication
    Mutagenesisi417 – 4171K → A: Loss of epimerase activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 460460FAD-dependent decaprenylphosphoryl-beta-D-ribofuranose 2-oxidasePRO_0000432471Add
    BLAST

    Interactioni

    Subunit structurei

    Homodimer.2 Publications

    Protein-protein interaction databases

    STRINGi246196.MSMEG_6382.

    Structurei

    Secondary structure

    1
    460
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi8 – 136Combined sources
    Beta strandi22 – 276Combined sources
    Helixi32 – 409Combined sources
    Helixi42 – 454Combined sources
    Beta strandi50 – 556Combined sources
    Beta strandi58 – 614Combined sources
    Beta strandi68 – 725Combined sources
    Helixi73 – 753Combined sources
    Beta strandi79 – 835Combined sources
    Turni84 – 874Combined sources
    Beta strandi88 – 925Combined sources
    Helixi97 – 1048Combined sources
    Helixi105 – 1073Combined sources
    Helixi122 – 1276Combined sources
    Helixi135 – 1384Combined sources
    Helixi141 – 1444Combined sources
    Beta strandi145 – 1517Combined sources
    Beta strandi157 – 1604Combined sources
    Beta strandi162 – 1643Combined sources
    Helixi167 – 1737Combined sources
    Turni177 – 1804Combined sources
    Beta strandi182 – 1898Combined sources
    Beta strandi196 – 2049Combined sources
    Helixi208 – 2169Combined sources
    Helixi219 – 2224Combined sources
    Beta strandi224 – 2307Combined sources
    Beta strandi232 – 2343Combined sources
    Turni236 – 2405Combined sources
    Beta strandi242 – 2498Combined sources
    Helixi252 – 2543Combined sources
    Helixi257 – 2615Combined sources
    Beta strandi302 – 3087Combined sources
    Helixi309 – 3135Combined sources
    Turni314 – 3174Combined sources
    Beta strandi331 – 3399Combined sources
    Helixi343 – 35614Combined sources
    Beta strandi361 – 3688Combined sources
    Beta strandi381 – 39010Combined sources
    Helixi395 – 40814Combined sources
    Helixi415 – 4173Combined sources
    Helixi423 – 4297Combined sources
    Helixi433 – 44311Combined sources
    Helixi452 – 4565Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4AUTX-ray2.10A1-460[»]
    4F4QX-ray2.62A1-460[»]
    4G3TX-ray2.35A58-460[»]
    4G3UX-ray2.69A/B58-460[»]
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini19 – 193175FAD-binding PCMH-typePROSITE-ProRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni384 – 3863Substrate binding1 Publication

    Sequence similaritiesi

    Contains 1 FAD-binding PCMH-type domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiCOG0277.
    HOGENOMiHOG000010204.
    KOiK16653.
    OMAiADVHGKN.
    OrthoDBiEOG69WFG8.

    Family and domain databases

    Gene3Di3.30.465.10. 1 hit.
    InterProiIPR007173. ALO.
    IPR016169. CO_DH_flavot_FAD-bd_sub2.
    IPR016166. FAD-bd_2.
    IPR006094. Oxid_FAD_bind_N.
    [Graphical view]
    PfamiPF04030. ALO. 1 hit.
    PF01565. FAD_binding_4. 1 hit.
    [Graphical view]
    SUPFAMiSSF56176. SSF56176. 1 hit.
    PROSITEiPS51387. FAD_PCMH. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    A0R607-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSTTEFPTTT KRLMGWGRTA PTVASVLSTS DPEVIVRAVT RAAEEGGRGV
    60 70 80 90 100
    IARGLGRSYG DNAQNGGGLV IDMPALNRIH SIDSGTRLVD VDAGVSLDQL
    110 120 130 140 150
    MKAALPHGLW VPVLPGTRQV TVGGAIGCDI HGKNHHSAGS FGNHVRSMEL
    160 170 180 190 200
    LTANGEVRHL TPAGPDSDLF WATVGGNGLT GIILRATIEM TPTETAYFIA
    210 220 230 240 250
    DGDVTGSLDE TIAFHSDGSE ANYTYSSAWF DAISKPPKLG RAAISRGSLA
    260 270 280 290 300
    KLDQLPSKLQ KDPLKFDAPQ LLTLPDIFPN GLANKFTFMP IGELWYRKSG
    310 320 330 340 350
    TYRNKVQNLT QFYHPLDMFG EWNRAYGSAG FLQYQFVVPT EAVEEFKSII
    360 370 380 390 400
    VDIQRSGHYS FLNVFKLFGP GNQAPLSFPI PGWNVCVDFP IKAGLHEFVT
    410 420 430 440 450
    ELDRRVLEFG GRLYTAKDSR TTAETFHAMY PRIDEWIRIR RSVDPDGVFA
    460
    SDMARRLQLL
    Length:460
    Mass (Da):50,377
    Last modified:April 1, 2015 - v2
    Checksum:i2F19107D18638FC0
    GO

    Sequence cautioni

    The sequence ABK72795.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    CP000480 Genomic DNA. Translation: ABK72795.1. Different initiation.
    CP001663 Genomic DNA. Translation: AFP42640.1.
    CP009494 Genomic DNA. Translation: AIU11363.1.
    RefSeqiWP_003897792.1. NZ_CP009494.1.
    WP_011731248.1. NC_008596.1.
    YP_890595.1. NC_008596.1.

    Genome annotation databases

    EnsemblBacteriaiABK72795; ABK72795; MSMEG_6382.
    AFP42640; AFP42640; MSMEI_6214.
    AIU11363; AIU11363; LJ00_31545.
    GeneIDi4532115.
    KEGGimsb:LJ00_31545.
    msg:MSMEI_6214.
    msm:MSMEG_6382.
    PATRICi18084993. VBIMycSme59918_6209.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    CP000480 Genomic DNA. Translation: ABK72795.1. Different initiation.
    CP001663 Genomic DNA. Translation: AFP42640.1.
    CP009494 Genomic DNA. Translation: AIU11363.1.
    RefSeqiWP_003897792.1. NZ_CP009494.1.
    WP_011731248.1. NC_008596.1.
    YP_890595.1. NC_008596.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4AUTX-ray2.10A1-460[»]
    4F4QX-ray2.62A1-460[»]
    4G3TX-ray2.35A58-460[»]
    4G3UX-ray2.69A/B58-460[»]
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi246196.MSMEG_6382.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiABK72795; ABK72795; MSMEG_6382.
    AFP42640; AFP42640; MSMEI_6214.
    AIU11363; AIU11363; LJ00_31545.
    GeneIDi4532115.
    KEGGimsb:LJ00_31545.
    msg:MSMEI_6214.
    msm:MSMEG_6382.
    PATRICi18084993. VBIMycSme59918_6209.

    Phylogenomic databases

    eggNOGiCOG0277.
    HOGENOMiHOG000010204.
    KOiK16653.
    OMAiADVHGKN.
    OrthoDBiEOG69WFG8.

    Enzyme and pathway databases

    UniPathwayiUPA00963.
    BioCyciMetaCyc:MONOMER-17534.
    MSME246196:GJ4Y-6381-MONOMER.
    BRENDAi1.1.98.3. 3512.

    Family and domain databases

    Gene3Di3.30.465.10. 1 hit.
    InterProiIPR007173. ALO.
    IPR016169. CO_DH_flavot_FAD-bd_sub2.
    IPR016166. FAD-bd_2.
    IPR006094. Oxid_FAD_bind_N.
    [Graphical view]
    PfamiPF04030. ALO. 1 hit.
    PF01565. FAD_binding_4. 1 hit.
    [Graphical view]
    SUPFAMiSSF56176. SSF56176. 1 hit.
    PROSITEiPS51387. FAD_PCMH. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. 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
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 700084 / mc(2)155.
    2. "Interrupted coding sequences in Mycobacterium smegmatis: authentic mutations or sequencing errors?"
      Deshayes C., Perrodou E., Gallien S., Euphrasie D., Schaeffer C., Van-Dorsselaer A., Poch O., Lecompte O., Reyrat J.-M.
      Genome Biol. 8:R20.1-R20.9(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 700084 / mc(2)155.
    3. "Ortho-proteogenomics: multiple proteomes investigation through orthology and a new MS-based protocol."
      Gallien S., Perrodou E., Carapito C., Deshayes C., Reyrat J.-M., Van Dorsselaer A., Poch O., Schaeffer C., Lecompte O.
      Genome Res. 19:128-135(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 700084 / mc(2)155.
    4. "Complete genome sequences of a Mycobacterium smegmatis laboratory strain (MC2 155) and isoniazid-resistant (4XR1/R2) mutant strains."
      Mohan A., Padiadpu J., Baloni P., Chandra N.
      Genome Announc. 3:E01520-E01520(2015) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 700084 / mc(2)155.
    5. "Benzothiazinones are suicide inhibitors of mycobacterial decaprenylphosphoryl-beta-D-ribofuranose 2'-oxidase DprE1."
      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.
      J. Am. Chem. Soc. 134:912-915(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF CYS-386, ENZYME REGULATION, SUBSTRATE SPECIFICITY.
      Strain: ATCC 700084 / mc(2)155.
    6. Cited for: X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG AND FAD, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF GLN-335; CYS-386 AND LYS-417, ENZYME REGULATION, SUBCELLULAR LOCATION, SUBSTRATE SPECIFICITY, SUBUNIT.
      Strain: ATCC 700084 / mc(2)155.
    7. "Crystal structure of decaprenylphosphoryl-beta- D-ribose 2'-epimerase from Mycobacterium smegmatis."
      Li H., Jogl G.
      Proteins 81:538-543(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.35 ANGSTROMS) OF 58-460, SUBUNIT.

    Entry informationi

    Entry nameiDPRE1_MYCS2
    AccessioniPrimary (citable) accession number: A0R607
    Secondary accession number(s): I7FMU1
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 1, 2015
    Last sequence update: April 1, 2015
    Last modified: July 22, 2015
    This is version 64 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.