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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

Pathwayi

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

  1. D-arabinono-1,4-lactone oxidase activity Source: InterPro
  2. flavin adenine dinucleotide binding Source: InterPro
  3. UDP-N-acetylmuramate dehydrogenase activity Source: InterPro

GO - Biological processi

  1. capsule polysaccharide biosynthetic process Source: UniProtKB-UniPathway
  2. cell wall organization Source: UniProtKB-KW
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 lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesCorynebacterineaeMycobacteriaceaeMycobacterium
ProteomesiUP000006158 Componenti: Chromosome UP000000757 Componenti: Chromosome

Subcellular locationi

  1. Cytoplasm 1 Publication

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
  2. membrane Source: InterPro
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

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[»]
ProteinModelPortaliA0R607.
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.
OMAiAADVHGK.
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.
RefSeqiYP_006570935.1. NC_018289.1.
YP_890595.1. NC_008596.1.

Genome annotation databases

EnsemblBacteriaiABK72795; ABK72795; MSMEG_6382.
GeneIDi4532115.
KEGGimsm: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.
RefSeqiYP_006570935.1. NC_018289.1.
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[»]
ProteinModelPortaliA0R607.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi246196.MSMEG_6382.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABK72795; ABK72795; MSMEG_6382.
GeneIDi4532115.
KEGGimsm:MSMEG_6382.
PATRICi18084993. VBIMycSme59918_6209.

Phylogenomic databases

eggNOGiCOG0277.
HOGENOMiHOG000010204.
KOiK16653.
OMAiAADVHGK.
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 sequence of Mycobacterium smegmatis laboratory strains (INHwt) and isoniazid resistant (INHR1/R2) mutant strains."
    Mohan A., Padiadpu J., Baloni P., Chandra N.
    Submitted (SEP-2014) to the EMBL/GenBank/DDBJ databases
    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: April 29, 2015
This is version 61 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.