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Protein

Deoxyribose-phosphate aldolase

Gene

deoC

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate.UniRule annotation3 Publications

Catalytic activityi

2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde.UniRule annotation3 Publications

Kineticsi

  1. KM=0.23 mM for 2-deoxy-D-ribose 5-phosphate1 Publication

    pH dependencei

    Optimum pH is 7.5 for 2-deoxy-D-ribose 5-phosphate cleavage.1 Publication

    Pathwayi: 2-deoxy-D-ribose 1-phosphate degradation

    This protein is involved in step 2 of the subpathway that synthesizes D-glyceraldehyde 3-phosphate and acetaldehyde from 2-deoxy-alpha-D-ribose 1-phosphate.UniRule annotationCurated
    Proteins known to be involved in the 2 steps of the subpathway in this organism are:
    1. no protein annotated in this organism
    2. Deoxyribose-phosphate aldolase (deoC)
    This subpathway is part of the pathway 2-deoxy-D-ribose 1-phosphate degradation, which is itself part of Carbohydrate degradation.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes D-glyceraldehyde 3-phosphate and acetaldehyde from 2-deoxy-alpha-D-ribose 1-phosphate, the pathway 2-deoxy-D-ribose 1-phosphate degradation and in Carbohydrate degradation.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Active sitei102Proton donor/acceptorUniRule annotation1 Publication1
    Active sitei167Schiff-base intermediate with acetaldehydeUniRule annotation1 Publication1 Publication1
    Active sitei201Proton donor/acceptorUniRule annotation2 Publications1

    GO - Molecular functioni

    • deoxyribose-phosphate aldolase activity Source: EcoCyc
    • lyase activity Source: EcoliWiki

    GO - Biological processi

    • carbohydrate catabolic process Source: EcoliWiki
    • cellular response to DNA damage stimulus Source: EcoliWiki
    • deoxyribonucleotide catabolic process Source: EcoliWiki
    • deoxyribose phosphate catabolic process Source: UniProtKB-UniPathway
    • nucleobase-containing small molecule interconversion Source: EcoliWiki

    Keywordsi

    Molecular functionLyase
    LigandSchiff base

    Enzyme and pathway databases

    BioCyciEcoCyc:DEOXYRIBOSE-P-ALD-MONOMER.
    MetaCyc:DEOXYRIBOSE-P-ALD-MONOMER.
    BRENDAi4.1.2.4. 2026.
    SABIO-RKiP0A6L0.
    UniPathwayiUPA00002; UER00468.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Deoxyribose-phosphate aldolaseUniRule annotationCurated (EC:4.1.2.4UniRule annotation3 Publications)
    Short name:
    DERA1 PublicationUniRule annotation
    Alternative name(s):
    2-deoxy-D-ribose 5-phosphate aldolase1 PublicationUniRule annotationCurated
    PhosphodeoxyriboaldolaseUniRule annotationCurated
    Short name:
    DeoxyriboaldolaseUniRule annotationCurated
    Gene namesi
    Name:deoC1 PublicationUniRule annotation
    Synonyms:dra, thyR
    Ordered Locus Names:b4381, JW4344
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG10221. deoC.

    Subcellular locationi

    • Cytoplasm UniRule annotationCurated

    GO - Cellular componenti

    • cytosol Source: UniProtKB
    • membrane Source: UniProtKB

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi47C → A or S: 3-fold decrease in catalytic efficiency. 1 Publication1
    Mutagenesisi102D → E: 44-fold decrease in catalytic efficiency. 1 Publication1
    Mutagenesisi102D → L: 2000-fold decrease in catalytic efficiency. 1 Publication1
    Mutagenesisi102D → N: 1500-fold decrease in catalytic efficiency. 1 Publication1
    Mutagenesisi137K → L: 20-fold decrease in catalytic efficiency. 1 Publication1
    Mutagenesisi167K → L: 1000-fold decrease in catalytic efficiency. 1 Publication1
    Mutagenesisi167K → R: 20-fold decrease in catalytic efficiency. 1 Publication1
    Mutagenesisi201K → L: 1500-fold decrease in catalytic efficiency. 1 Publication1
    Mutagenesisi201K → R: 1000-fold decrease in catalytic efficiency. 1 Publication1
    Mutagenesisi259Y → F: 200-fold decrease in catalytic efficiency. 1 Publication1

    Chemistry databases

    DrugBankiDB04087. Open Form of 2'-Deoxy-Ribofuranose-5'-Phosphate.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00000572961 – 259Deoxyribose-phosphate aldolaseAdd BLAST259

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei167N6-acetyllysine1 Publication1

    Keywords - PTMi

    Acetylation

    Proteomic databases

    PaxDbiP0A6L0.
    PRIDEiP0A6L0.

    2D gel databases

    SWISS-2DPAGEiP0A6L0.

    PTM databases

    iPTMnetiP0A6L0.

    Interactioni

    Subunit structurei

    Monomer and homodimer.2 Publications

    Protein-protein interaction databases

    BioGridi4263350. 9 interactors.
    IntActiP0A6L0. 8 interactors.
    STRINGi316385.ECDH10B_4539.

    Structurei

    Secondary structure

    1259
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi3 – 12Combined sources10
    Beta strandi15 – 18Combined sources4
    Helixi26 – 35Combined sources10
    Beta strandi44 – 47Combined sources4
    Helixi50 – 52Combined sources3
    Helixi53 – 62Combined sources10
    Beta strandi68 – 75Combined sources8
    Turni76 – 78Combined sources3
    Helixi83 – 96Combined sources14
    Beta strandi99 – 104Combined sources6
    Helixi107 – 111Combined sources5
    Helixi116 – 131Combined sources16
    Beta strandi135 – 139Combined sources5
    Helixi142 – 145Combined sources4
    Helixi148 – 160Combined sources13
    Beta strandi164 – 167Combined sources4
    Beta strandi171 – 174Combined sources4
    Helixi179 – 192Combined sources14
    Turni195 – 197Combined sources3
    Beta strandi199 – 201Combined sources3
    Beta strandi203 – 205Combined sources3
    Helixi209 – 223Combined sources15
    Turni230 – 232Combined sources3
    Beta strandi235 – 238Combined sources4
    Helixi240 – 248Combined sources9

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1JCJX-ray1.10A/B1-259[»]
    1JCLX-ray1.05A/B1-259[»]
    1KTNX-ray1.40A/B1-250[»]
    1P1XX-ray0.99A/B1-259[»]
    5EKYX-ray1.10A1-259[»]
    5EL1X-ray1.25A1-259[»]
    5EMUX-ray1.50A1-259[»]
    ProteinModelPortaliP0A6L0.
    SMRiP0A6L0.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP0A6L0.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the DeoC/FbaB aldolase family. DeoC type 2 subfamily.UniRule annotationCurated

    Phylogenomic databases

    eggNOGiENOG4105FCI. Bacteria.
    COG0274. LUCA.
    HOGENOMiHOG000241644.
    InParanoidiP0A6L0.
    KOiK01619.
    PhylomeDBiP0A6L0.

    Family and domain databases

    CDDicd00959. DeoC. 1 hit.
    Gene3Di3.20.20.70. 1 hit.
    HAMAPiMF_00592. DeoC_type2. 1 hit.
    InterProiView protein in InterPro
    IPR013785. Aldolase_TIM.
    IPR011343. DeoC.
    IPR002915. DeoC/FbaB/lacD_aldolase.
    IPR023649. DeoC_typeII.
    PANTHERiPTHR10889. PTHR10889. 1 hit.
    PfamiView protein in Pfam
    PF01791. DeoC. 1 hit.
    PIRSFiPIRSF001357. DeoC. 1 hit.
    SMARTiView protein in SMART
    SM01133. DeoC. 1 hit.
    TIGRFAMsiTIGR00126. deoC. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P0A6L0-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MTDLKASSLR ALKLMDLTTL NDDDTDEKVI ALCHQAKTPV GNTAAICIYP
    60 70 80 90 100
    RFIPIARKTL KEQGTPEIRI ATVTNFPHGN DDIDIALAET RAAIAYGADE
    110 120 130 140 150
    VDVVFPYRAL MAGNEQVGFD LVKACKEACA AANVLLKVII ETGELKDEAL
    160 170 180 190 200
    IRKASEISIK AGADFIKTST GKVAVNATPE SARIMMEVIR DMGVEKTVGF
    210 220 230 240 250
    KPAGGVRTAE DAQKYLAIAD ELFGADWADA RHYRFGASSL LASLLKALGH

    GDGKSASSY
    Length:259
    Mass (Da):27,734
    Last modified:March 29, 2005 - v1
    Checksum:iABA50C625195D494
    GO

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti18T → N in CAA26974 (PubMed:6749498).Curated1

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X03224 Genomic DNA. Translation: CAA26974.1.
    U14003 Genomic DNA. Translation: AAA97277.1.
    U00096 Genomic DNA. Translation: AAC77334.1.
    AP009048 Genomic DNA. Translation: BAE78370.1.
    PIRiA01102. ADECD.
    RefSeqiNP_418798.1. NC_000913.3.
    WP_001298497.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC77334; AAC77334; b4381.
    BAE78370; BAE78370; BAE78370.
    GeneIDi948902.
    KEGGiecj:JW4344.
    eco:b4381.
    PATRICifig|1411691.4.peg.2304.

    Similar proteinsi

    Entry informationi

    Entry nameiDEOC_ECOLI
    AccessioniPrimary (citable) accession number: P0A6L0
    Secondary accession number(s): P00882, Q2M5T6
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 21, 1986
    Last sequence update: March 29, 2005
    Last modified: October 25, 2017
    This is version 110 of the entry and version 1 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families