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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

Manual assertion based on experiment ini

  1. KM=0.11 mM for FPR (with DCPIP as electron acceptor 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.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)DescriptionActionsGraphical viewLength
    Binding sitei116FAD; via amide nitrogen1 Publication1
    Binding sitei133SubstrateBy similarity1
    Binding sitei177FAD; via carbonyl oxygen1 Publication1
    Binding sitei183FAD; via amide nitrogen and carbonyl oxygen1 Publication1
    Binding sitei414FAD1 Publication1
    Binding sitei417Substrate1 Publication1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi52 – 62FAD1 PublicationAdd BLAST11
    Nucleotide bindingi121 – 124FAD1 Publication4
    Nucleotide bindingi128 – 131FAD1 Publication4

    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.
    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
    Proteomesi
    • UP000006158 Componenti: Chromosome
    • UP000000757 Componenti: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi335Q → A: 10-fold decrease in the catalytic efficiency. 1 Publication1
    Mutagenesisi386C → G: 4-fold decrease in the catalytic efficiency. 1 Publication1
    Mutagenesisi386C → G: Resistance toward BTZs. Reduces BTZs to inert metabolites while avoiding covalent inactivation. 1 Publication1
    Mutagenesisi417K → A: Loss of epimerase activity. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00004324711 – 460FAD-dependent decaprenylphosphoryl-beta-D-ribofuranose 2-oxidaseAdd BLAST460

    Interactioni

    Subunit structurei

    Homodimer.2 Publications

    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

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni384 – 386Substrate binding1 Publication3

    Sequence similaritiesi

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

    Phylogenomic databases

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

    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 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
    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.
    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...

    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: November 30, 2016
    This is version 74 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

    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.