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Protein

Decaprenylphosphoryl-beta-D-ribose 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

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).By similarity3 Publications

Catalytic activityi

Trans,octacis-decaprenylphospho-beta-D-ribofuranose + FAD = trans,octacis-decaprenylphospho-beta-D-erythro-pentofuranosid-2-ulose + FADH2.1 Publication

Enzyme regulationi

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).3 Publications

Kineticsi

kcat is 12.7 min(-1) for epimerase activity with FPR as substrate (at pH 8.5 and 25 degrees Celsius).1 Publication
  1. KM=0.11 mM for FPR (at pH 8.5 and 25 degrees Celsius)1 Publication

    Pathwayi: cell wall polysaccharide biosynthesis

    This protein is involved in the pathway cell wall polysaccharide biosynthesis, which is part of Cell wall biogenesis.1 Publication
    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)DescriptionActionsGraphical viewLength
    Binding sitei116FAD; via amide nitrogenCombined sources1 Publication1
    Binding sitei183FAD; via amide nitrogen and carbonyl oxygenCombined sources1 Publication1
    Binding sitei414FADCombined sources1 Publication1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi52 – 62FADCombined sources1 PublicationAdd BLAST11
    Nucleotide bindingi121 – 124FADCombined sources1 Publication4
    Nucleotide bindingi128 – 131FADCombined sources1 Publication4

    GO - Molecular functioni

    GO - Biological processi

    Keywordsi

    Molecular functionOxidoreductase
    Biological processAntibiotic resistance, Cell wall biogenesis/degradation
    LigandFAD, Flavoprotein, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-17534.
    BRENDAi1.1.98.3. 3512.
    UniPathwayiUPA00963.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Decaprenylphosphoryl-beta-D-ribose oxidaseCurated (EC:1.1.98.31 Publication)
    Alternative name(s):
    Decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase1 Publication
    Decaprenylphosphoryl-beta-D-ribofuranose 2'-epimerase subunit DprE11 Publication
    Short name:
    Decaprenyl-phosphoribose 2'-epimerase subunit 11 Publication
    Decaprenylphosphoryl-beta-D-ribofuranose 2'-oxidase1 Publication
    Decaprenylphosphoryl-beta-D-ribose 2-epimerase flavoprotein subunitCurated
    FAD-dependent decaprenylphosphoryl-beta-D-ribofuranose 2-oxidase1 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
    Proteomesi
    • UP000006158 Componenti: Chromosome
    • UP000000757 Componenti: Chromosome

    Subcellular locationi

    • Periplasm By similarity

    GO - Cellular componenti

    Keywords - Cellular componenti

    Periplasm

    Pathology & Biotechi

    Disruption phenotypei

    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.1 Publication

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi335Q → A: 10-fold decrease in catalytic efficiency. 1 Publication1
    Mutagenesisi386C → G: 14-fold decrease in catalytic efficiency. Reduces BTZs to inert metabolites while avoiding covalent inactivation. 2 Publications1
    Mutagenesisi417K → A: Loss of catalytic activity. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00004324711 – 460Decaprenylphosphoryl-beta-D-ribose oxidaseAdd BLAST460

    Interactioni

    Subunit structurei

    Monomer (PubMed:22956199). Interacts with DprE2 to form an epimerase complex (By similarity).By similarity1 Publication

    Protein-protein interaction databases

    STRINGi246196.MSMEG_6382.

    Structurei

    Secondary structure

    1460
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi8 – 13Combined sources6
    Beta strandi22 – 27Combined sources6
    Helixi32 – 40Combined sources9
    Helixi42 – 45Combined sources4
    Beta strandi50 – 55Combined sources6
    Beta strandi58 – 61Combined sources4
    Beta strandi68 – 72Combined sources5
    Helixi73 – 75Combined sources3
    Beta strandi79 – 83Combined sources5
    Turni84 – 87Combined sources4
    Beta strandi88 – 92Combined sources5
    Helixi97 – 104Combined sources8
    Helixi105 – 107Combined sources3
    Helixi122 – 127Combined sources6
    Helixi135 – 138Combined sources4
    Helixi141 – 144Combined sources4
    Beta strandi145 – 151Combined sources7
    Beta strandi157 – 160Combined sources4
    Beta strandi162 – 164Combined sources3
    Helixi167 – 173Combined sources7
    Turni177 – 180Combined sources4
    Beta strandi182 – 189Combined sources8
    Beta strandi196 – 204Combined sources9
    Helixi208 – 216Combined sources9
    Helixi219 – 222Combined sources4
    Beta strandi224 – 230Combined sources7
    Beta strandi232 – 234Combined sources3
    Turni236 – 240Combined sources5
    Beta strandi242 – 249Combined sources8
    Helixi252 – 254Combined sources3
    Helixi257 – 261Combined sources5
    Beta strandi302 – 308Combined sources7
    Helixi309 – 313Combined sources5
    Turni314 – 317Combined sources4
    Beta strandi331 – 339Combined sources9
    Helixi343 – 356Combined sources14
    Beta strandi361 – 368Combined sources8
    Beta strandi381 – 390Combined sources10
    Helixi395 – 408Combined sources14
    Helixi415 – 417Combined sources3
    Helixi423 – 429Combined sources7
    Helixi433 – 443Combined sources11
    Helixi452 – 456Combined sources5

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    4AUTX-ray2.10A1-460[»]
    4F4QX-ray2.62A1-460[»]
    4G3TX-ray2.35A58-460[»]
    4G3UX-ray2.69A/B58-460[»]
    SMRiA0R607.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini19 – 193FAD-binding PCMH-typePROSITE-ProRule annotationAdd BLAST175

    Sequence similaritiesi

    Belongs to the DprE1 family.Curated

    Phylogenomic databases

    eggNOGiENOG4105IQ5. Bacteria.
    COG0277. LUCA.
    HOGENOMiHOG000010204.
    KOiK16653.
    OrthoDBiPOG091H08SQ.

    Family and domain databases

    Gene3Di3.30.465.10. 1 hit.
    InterProiView protein in InterPro
    IPR007173. ALO.
    IPR016169. CO_DH_flavot_FAD-bd_sub2.
    IPR016166. FAD-bd_2.
    IPR006094. Oxid_FAD_bind_N.
    PfamiView protein in Pfam
    PF04030. ALO. 1 hit.
    PF01565. FAD_binding_4. 1 hit.
    SUPFAMiSSF56176. SSF56176. 1 hit.
    PROSITEiView protein in PROSITE
    PS51387. FAD_PCMH. 1 hit.

    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 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

    Natural variant

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Natural varianti386C → G in strain: MN47; BTZ043-resistant. 1 Publication1
    Natural varianti386C → S in strain: MN84; BTZ043-resistant. 1 Publication1

    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.
    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.
    YP_890595.1. NC_008596.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    4AUTX-ray2.10A1-460[»]
    4F4QX-ray2.62A1-460[»]
    4G3TX-ray2.35A58-460[»]
    4G3UX-ray2.69A/B58-460[»]
    SMRiA0R607.
    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

    eggNOGiENOG4105IQ5. Bacteria.
    COG0277. LUCA.
    HOGENOMiHOG000010204.
    KOiK16653.
    OrthoDBiPOG091H08SQ.

    Enzyme and pathway databases

    UniPathwayiUPA00963.
    BioCyciMetaCyc:MONOMER-17534.
    BRENDAi1.1.98.3. 3512.

    Family and domain databases

    Gene3Di3.30.465.10. 1 hit.
    InterProiView protein in InterPro
    IPR007173. ALO.
    IPR016169. CO_DH_flavot_FAD-bd_sub2.
    IPR016166. FAD-bd_2.
    IPR006094. Oxid_FAD_bind_N.
    PfamiView protein in Pfam
    PF04030. ALO. 1 hit.
    PF01565. FAD_binding_4. 1 hit.
    SUPFAMiSSF56176. SSF56176. 1 hit.
    PROSITEiView protein in PROSITE
    PS51387. FAD_PCMH. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiDPRE1_MYCS2
    AccessioniPrimary (citable) accession number: A0R607
    Secondary accession number(s): I7FMU1
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 1, 2015
    Last sequence update: April 1, 2015
    Last modified: March 15, 2017
    This is version 77 of the entry and version 2 of the sequence. See 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

    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 one 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.