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Protein

Aspartate racemase

Gene

PH0670

Organism
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Catalytic activityi

L-aspartate = D-aspartate.1 Publication

Enzyme regulationi

Weakly inhibited by citrate, but not by asparagine.1 Publication

Kineticsi

  1. KM=0.7 mM for L-aspartate1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei82 – 821Proton donor/acceptor1 Publication
    Binding sitei164 – 1641SubstrateCombined sources1 Publication
    Active sitei194 – 1941Proton donor/acceptor1 Publication

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Isomerase

    Enzyme and pathway databases

    BioCyciPHOR70601:GJWR-661-MONOMER.
    BRENDAi5.1.1.13. 5244.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Aspartate racemase (EC:5.1.1.131 Publication)
    Gene namesi
    Ordered Locus Names:PH0670Imported
    OrganismiPyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)Imported
    Taxonomic identifieri70601 [NCBI]
    Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
    ProteomesiUP000000752 Componenti: Chromosome

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi82 – 821C → A: Abolishes racemase activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 228228Aspartate racemasePRO_0000433135Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi73 – 73InterchainCombined sources1 Publication

    Keywords - PTMi

    Disulfide bond

    Interactioni

    Subunit structurei

    Homodimer. The existence of the interchain disulfide bond seen in the crystal structures is uncertain, but disulfide bonds have been reported for cytoplasmic proteins from thermophiles.Curated2 Publications

    Protein-protein interaction databases

    STRINGi70601.PH0670.

    Structurei

    Secondary structure

    1
    228
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi4 – 85Combined sources
    Helixi12 – 2413Combined sources
    Helixi31 – 333Combined sources
    Beta strandi37 – 415Combined sources
    Helixi48 – 525Combined sources
    Helixi60 – 7314Combined sources
    Beta strandi76 – 794Combined sources
    Helixi84 – 885Combined sources
    Helixi89 – 957Combined sources
    Helixi103 – 11311Combined sources
    Beta strandi117 – 1226Combined sources
    Helixi125 – 1306Combined sources
    Helixi132 – 1398Combined sources
    Beta strandi143 – 1453Combined sources
    Helixi149 – 16012Combined sources
    Helixi163 – 1653Combined sources
    Helixi168 – 18417Combined sources
    Beta strandi188 – 1925Combined sources
    Helixi195 – 2006Combined sources
    Helixi203 – 2053Combined sources
    Helixi213 – 22614Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1IU9X-ray2.04A103-213[»]
    1JFLX-ray1.90A/B1-228[»]
    2DX7X-ray2.00A/B1-228[»]
    ProteinModelPortaliO58403.
    SMRiO58403. Positions 1-228.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO58403.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni47 – 493Substrate bindingCombined sources1 Publication
    Regioni83 – 853Substrate bindingCombined sources1 Publication

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG1794.
    HOGENOMiHOG000262147.
    KOiK01779.
    OMAiDFIIMPC.

    Family and domain databases

    Gene3Di3.40.50.1860. 2 hits.
    InterProiIPR015942. Asp/Glu/hydantoin_racemase.
    IPR001920. Asp/Glu_race.
    IPR018187. Asp/Glu_racemase_AS.
    IPR004380. Asp_race.
    [Graphical view]
    PfamiPF01177. Asp_Glu_race. 1 hit.
    [Graphical view]
    SUPFAMiSSF53681. SSF53681. 2 hits.
    TIGRFAMsiTIGR00035. asp_race. 1 hit.
    PROSITEiPS00923. ASP_GLU_RACEMASE_1. 1 hit.
    PS00924. ASP_GLU_RACEMASE_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    O58403-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MKTIGILGGM GPLATAELFR RIVIKTPAKR DQEHPKVIIF NNPQIPDRTA
    60 70 80 90 100
    YILGKGEDPR PQLIWTAKRL EECGADFIIM PCNTAHAFVE DIRKAIKIPI
    110 120 130 140 150
    ISMIEETAKK VKELGFKKAG LLATTGTIVS GVYEKEFSKY GVEIMTPTED
    160 170 180 190 200
    EQKDVMRGIY EGVKAGNLKL GRELLLKTAK ILEERGAECI IAGCTEVSVV
    210 220
    LKQDDLKVPL IDPMDVIAEV AVKVALEK
    Length:228
    Mass (Da):25,158
    Last modified:August 1, 1998 - v1
    Checksum:iDDAA2CBEB39682CF
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    BA000001 Genomic DNA. Translation: BAA29761.1.
    PIRiG71112.
    RefSeqiNP_142620.1. NC_000961.1.
    WP_010884762.1. NC_000961.1.

    Genome annotation databases

    EnsemblBacteriaiBAA29761; BAA29761; BAA29761.
    GeneIDi1442997.
    KEGGipho:PH0670.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    BA000001 Genomic DNA. Translation: BAA29761.1.
    PIRiG71112.
    RefSeqiNP_142620.1. NC_000961.1.
    WP_010884762.1. NC_000961.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1IU9X-ray2.04A103-213[»]
    1JFLX-ray1.90A/B1-228[»]
    2DX7X-ray2.00A/B1-228[»]
    ProteinModelPortaliO58403.
    SMRiO58403. Positions 1-228.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi70601.PH0670.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiBAA29761; BAA29761; BAA29761.
    GeneIDi1442997.
    KEGGipho:PH0670.

    Phylogenomic databases

    eggNOGiCOG1794.
    HOGENOMiHOG000262147.
    KOiK01779.
    OMAiDFIIMPC.

    Enzyme and pathway databases

    BioCyciPHOR70601:GJWR-661-MONOMER.
    BRENDAi5.1.1.13. 5244.

    Miscellaneous databases

    EvolutionaryTraceiO58403.

    Family and domain databases

    Gene3Di3.40.50.1860. 2 hits.
    InterProiIPR015942. Asp/Glu/hydantoin_racemase.
    IPR001920. Asp/Glu_race.
    IPR018187. Asp/Glu_racemase_AS.
    IPR004380. Asp_race.
    [Graphical view]
    PfamiPF01177. Asp_Glu_race. 1 hit.
    [Graphical view]
    SUPFAMiSSF53681. SSF53681. 2 hits.
    TIGRFAMsiTIGR00035. asp_race. 1 hit.
    PROSITEiPS00923. ASP_GLU_RACEMASE_1. 1 hit.
    PS00924. ASP_GLU_RACEMASE_2. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3Imported.
    2. "Structural insight into gene duplication, gene fusion and domain swapping in the evolution of PLP-independent amino acid racemases."
      Liu L., Iwata K., Yohda M., Miki K.
      FEBS Lett. 528:114-118(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.04 ANGSTROMS) OF 103-213.
    3. "Crystal structure of aspartate racemase from Pyrococcus horikoshii OT3 and its implications for molecular mechanism of PLP-independent racemization."
      Liu L., Iwata K., Kita A., Kawarabayasi Y., Yohda M., Miki K.
      J. Mol. Biol. 319:479-489(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS), SUBUNIT, DISULFIDE BOND.
    4. "Structure of aspartate racemase complexed with a dual substrate analogue, citric acid, and implications for the reaction mechanism."
      Ohtaki A., Nakano Y., Iizuka R., Arakawa T., Yamada K., Odaka M., Yohda M.
      Proteins 70:1167-1174(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) OF MUTANT ALA-82 IN COMPLEX WITH THE SUBSTRATE ANALOG CITRATE, DISULFIDE BOND, ACTIVE SITE, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION, MUTAGENESIS OF CYS-82.

    Entry informationi

    Entry nameiRACD_PYRHO
    AccessioniPrimary (citable) accession number: O58403
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 27, 2015
    Last sequence update: August 1, 1998
    Last modified: July 22, 2015
    This is version 101 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. 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.