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Protein

Deoxyribose-phosphate aldolase

Gene

deoC

Organism
Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)
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.1 Publication

Catalytic activityi

2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde.1 Publication

Kineticsi

  1. KM=0.057 mM for 2-deoxy-D-ribose 5-phosphate1 Publication

    pH dependencei

    Optimum pH is 6.5. Is extremely stable over a wide pH range: upon heating at 50 degrees Celsius for 60 minutes, the enzyme does not lose activity at pH 4.5-11.0.1 Publication

    Temperature dependencei

    Extremely thermostable. Retains full activity upon heating at 100 degrees Celsius for 10 minutes and at 80 degrees Celsius for 60 minutes.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.
    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)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei167 – 1671Schiff-base intermediate with acetaldehydeBy similarity
    Active sitei197 – 1971By similarity

    GO - Molecular functioni

    • deoxyribose-phosphate aldolase activity Source: UniProtKB

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Lyase

    Keywords - Ligandi

    Schiff base

    Enzyme and pathway databases

    BioCyciAPER272557:GJD6-1635-MONOMER.
    BRENDAi4.1.2.4. 171.
    UniPathwayiUPA00002; UER00468.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Deoxyribose-phosphate aldolase (EC:4.1.2.4)
    Short name:
    DERA
    Alternative name(s):
    2-deoxy-D-ribose 5-phosphate aldolase
    Phosphodeoxyriboaldolase
    Short name:
    Deoxyriboaldolase
    Gene namesi
    Name:deoC
    Ordered Locus Names:APE_2437.1
    OrganismiAeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)
    Taxonomic identifieri272557 [NCBI]
    Taxonomic lineageiArchaeaCrenarchaeotaThermoproteiDesulfurococcalesDesulfurococcaceaeAeropyrum
    Proteomesi
    • UP000002518 Componenti: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Biotechnological usei

    Its high stability makes the enzyme a potential candidate to be used as a synthetic catalyst in practical application.1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methionineiRemoved1 Publication
    Chaini2 – 235234Deoxyribose-phosphate aldolasePRO_0000057286Add
    BLAST

    Interactioni

    Subunit structurei

    Homotetramer.1 Publication

    Protein-protein interaction databases

    STRINGi272557.APE_2437.1.

    Structurei

    Secondary structure

    1
    235
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi4 – 1411Combined sources
    Helixi18 – 225Combined sources
    Beta strandi25 – 284Combined sources
    Helixi36 – 4914Combined sources
    Beta strandi54 – 563Combined sources
    Helixi58 – 7114Combined sources
    Beta strandi75 – 806Combined sources
    Turni81 – 833Combined sources
    Helixi88 – 10114Combined sources
    Beta strandi105 – 1084Combined sources
    Helixi112 – 1143Combined sources
    Helixi116 – 13217Combined sources
    Beta strandi136 – 1405Combined sources
    Helixi143 – 1453Combined sources
    Helixi148 – 16013Combined sources
    Beta strandi164 – 1685Combined sources
    Beta strandi171 – 1733Combined sources
    Helixi179 – 18911Combined sources
    Helixi190 – 1923Combined sources
    Beta strandi195 – 2017Combined sources
    Helixi205 – 2139Combined sources
    Beta strandi217 – 2215Combined sources
    Helixi224 – 2329Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1N7KX-ray2.00A/B2-235[»]
    ProteinModelPortaliQ9Y948.
    SMRiQ9Y948. Positions 2-235.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9Y948.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiarCOG04320. Archaea.
    COG0274. LUCA.
    HOGENOMiHOG000241645.
    KOiK01619.
    OMAiFFSVCVN.

    Family and domain databases

    CDDicd00959. DeoC. 1 hit.
    Gene3Di3.20.20.70. 1 hit.
    HAMAPiMF_00114. DeoC_type1. 1 hit.
    InterProiIPR013785. Aldolase_TIM.
    IPR011343. DeoC.
    IPR002915. DeoC/FbaB/lacD_aldolase.
    IPR028581. DeoC_typeI.
    [Graphical view]
    PANTHERiPTHR10889. PTHR10889. 1 hit.
    PfamiPF01791. DeoC. 1 hit.
    [Graphical view]
    PIRSFiPIRSF001357. DeoC. 1 hit.
    SMARTiSM01133. DeoC. 1 hit.
    [Graphical view]
    TIGRFAMsiTIGR00126. deoC. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    Q9Y948-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MPSARDILQQ GLDRLGSPED LASRIDSTLL SPRATEEDVR NLVREASDYG
    60 70 80 90 100
    FRCAVLTPVY TVKISGLAEK LGVKLCSVIG FPLGQAPLEV KLVEAQTVLE
    110 120 130 140 150
    AGATELDVVP HLSLGPEAVY REVSGIVKLA KSYGAVVKVI LEAPLWDDKT
    160 170 180 190 200
    LSLLVDSSRR AGADIVKTST GVYTKGGDPV TVFRLASLAK PLGMGVKASG
    210 220 230
    GIRSGIDAVL AVGAGADIIG TSSAVKVLES FKSLV
    Length:235
    Mass (Da):24,529
    Last modified:November 1, 2002 - v2
    Checksum:i64CE582A38DCFD38
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    BA000002 Genomic DNA. Translation: BAA81452.2.
    PIRiD72474.

    Genome annotation databases

    EnsemblBacteriaiBAA81452; BAA81452; APE_2437.1.
    KEGGiape:APE_2437.1.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    BA000002 Genomic DNA. Translation: BAA81452.2.
    PIRiD72474.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1N7KX-ray2.00A/B2-235[»]
    ProteinModelPortaliQ9Y948.
    SMRiQ9Y948. Positions 2-235.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi272557.APE_2437.1.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiBAA81452; BAA81452; APE_2437.1.
    KEGGiape:APE_2437.1.

    Phylogenomic databases

    eggNOGiarCOG04320. Archaea.
    COG0274. LUCA.
    HOGENOMiHOG000241645.
    KOiK01619.
    OMAiFFSVCVN.

    Enzyme and pathway databases

    UniPathwayiUPA00002; UER00468.
    BioCyciAPER272557:GJD6-1635-MONOMER.
    BRENDAi4.1.2.4. 171.

    Miscellaneous databases

    EvolutionaryTraceiQ9Y948.

    Family and domain databases

    CDDicd00959. DeoC. 1 hit.
    Gene3Di3.20.20.70. 1 hit.
    HAMAPiMF_00114. DeoC_type1. 1 hit.
    InterProiIPR013785. Aldolase_TIM.
    IPR011343. DeoC.
    IPR002915. DeoC/FbaB/lacD_aldolase.
    IPR028581. DeoC_typeI.
    [Graphical view]
    PANTHERiPTHR10889. PTHR10889. 1 hit.
    PfamiPF01791. DeoC. 1 hit.
    [Graphical view]
    PIRSFiPIRSF001357. DeoC. 1 hit.
    SMARTiSM01133. DeoC. 1 hit.
    [Graphical view]
    TIGRFAMsiTIGR00126. deoC. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiDEOC_AERPE
    AccessioniPrimary (citable) accession number: Q9Y948
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 30, 2000
    Last sequence update: November 1, 2002
    Last modified: September 7, 2016
    This is version 108 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    The enzyme is also highly resistant to organic solvents such as ethanol, methanol, N,N-dimethylformamide, and Me2SO at 50 degrees Celsius. Loss of activity is not observed in the presence of these reagents even at a concentration as high as 40%.

    Keywords - Technical termi

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