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Protein

4-hydroxy-4-methyl-2-oxoglutarate aldolase

Gene

YER010C

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the aldol cleavage of 4-hydroxy-4-methyl-2-oxoglutarate (HMG) into 2 molecules of pyruvate. Also contains a secondary oxaloacetate (OAA) decarboxylase activity due to the common pyruvate enolate transition state formed following C-C bond cleavage in the retro-aldol and decarboxylation reactions.1 Publication

Catalytic activityi

4-hydroxy-4-methyl-2-oxoglutarate = 2 pyruvate.1 Publication
Oxaloacetate = pyruvate + CO2.1 Publication

Cofactori

Ni2+1 Publication, Co2+1 Publication, Zn2+1 PublicationNote: Divalent metal cation. Has preference for nickel ions for the HMG aldolase activity. Has preference for cobalt and zinc ions for the OAA decarboxylase activity.1 Publication

Enzyme regulationi

Competitively inhibited by oxalate, a pyruvate enolate analog.1 Publication

Kineticsi

kcat is 0.0276 sec(-1) with 4-hydroxy-4-methyl-2-oxoglutarate as substrate and 3.91 sec(-1) with oxaloacetate as substrate.

  1. KM=126.5 µM for 4-hydroxy-4-methyl-2-oxoglutarate1 Publication
  2. KM=132.5 µM for oxaloacetate1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei122 – 1221SubstrateBy similarity
    Metal bindingi123 – 1231Divalent metal cationBy similarity

    GO - Molecular functioni

    • 4-hydroxy-4-methyl-2-oxoglutarate aldolase activity Source: SGD
    • metal ion binding Source: UniProtKB-KW
    • oxaloacetate decarboxylase activity Source: SGD

    GO - Biological processi

    • protocatechuate catabolic process Source: SGD
    Complete GO annotation...

    Keywords - Molecular functioni

    Lyase

    Keywords - Ligandi

    Metal-binding

    Enzyme and pathway databases

    BioCyciYEAST:G3O-30197-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    4-hydroxy-4-methyl-2-oxoglutarate aldolase (EC:4.1.3.17)
    Short name:
    HMG aldolase
    Alternative name(s):
    Oxaloacetate decarboxylase (EC:4.1.1.3)
    Short name:
    OAA decarboxylase
    Regulator of ribonuclease activity homolog
    RraA-like protein
    Gene namesi
    Ordered Locus Names:YER010C
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311 Componenti: Chromosome V

    Organism-specific databases

    CYGDiYER010c.
    EuPathDBiFungiDB:YER010C.
    SGDiS000000812. YER010C.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 2342334-hydroxy-4-methyl-2-oxoglutarate aldolasePRO_0000202621Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei2 – 21N-acetylserine1 Publication

    Keywords - PTMi

    Acetylation

    Proteomic databases

    MaxQBiP40011.
    PaxDbiP40011.
    PeptideAtlasiP40011.

    Interactioni

    Subunit structurei

    Homotrimer. Forms a ring-like structure with a central cavity.1 Publication

    Protein-protein interaction databases

    BioGridi36741. 8 interactions.
    DIPiDIP-4095N.
    IntActiP40011. 1 interaction.
    MINTiMINT-536635.
    STRINGi4932.YER010C.

    Structurei

    Secondary structure

    1
    234
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi3 – 75Combined sources
    Helixi12 – 2312Combined sources
    Turni26 – 294Combined sources
    Beta strandi35 – 384Combined sources
    Beta strandi41 – 433Combined sources
    Beta strandi45 – 5612Combined sources
    Beta strandi59 – 613Combined sources
    Helixi67 – 693Combined sources
    Beta strandi74 – 807Combined sources
    Helixi82 – 843Combined sources
    Helixi101 – 1099Combined sources
    Beta strandi114 – 1218Combined sources
    Helixi124 – 1307Combined sources
    Beta strandi134 – 1396Combined sources
    Turni145 – 1473Combined sources
    Beta strandi148 – 1547Combined sources
    Beta strandi157 – 1604Combined sources
    Beta strandi166 – 1694Combined sources
    Beta strandi174 – 1785Combined sources
    Beta strandi181 – 1855Combined sources
    Turni187 – 1893Combined sources
    Helixi192 – 21423Combined sources
    Helixi219 – 2279Combined sources
    Helixi228 – 2303Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2C5QX-ray1.70A/B/C/D/E/F1-234[»]
    ProteinModelPortaliP40011.
    SMRiP40011. Positions 2-234.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP40011.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni100 – 1034Substrate bindingBy similarity

    Sequence similaritiesi

    Belongs to the class II aldolase/RraA-like family.Curated

    Phylogenomic databases

    eggNOGiCOG0684.
    HOGENOMiHOG000107599.
    InParanoidiP40011.
    OMAiRDLDEHN.
    OrthoDBiEOG7DJSZ4.

    Family and domain databases

    Gene3Di3.50.30.40. 1 hit.
    InterProiIPR005493. RNase_E_inh/diMeMenaQ_MeTrfase.
    [Graphical view]
    PfamiPF03737. Methyltransf_6. 1 hit.
    [Graphical view]
    SUPFAMiSSF89562. SSF89562. 1 hit.

    Sequencei

    Sequence statusi: Complete.

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

    P40011-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSDLQKLQRF STCDISDGLL NVYNIPTGGY FPNLTAISPP QNSSIVGTAY
    60 70 80 90 100
    TVLFAPIDDP RPAVNYIDSV PPNSILVLAL EPHLQSQFHP FIKITQAMYG
    110 120 130 140 150
    GLMSTRAQYL KSNGTVVFGR IRDVDEHRTL NHPVFAYGVG SCAPKAVVKA
    160 170 180 190 200
    VGTNVQLKIL TSDGVTQTIC PGDYIAGDNN GIVRIPVQET DISKLVTYIE
    210 220 230
    KSIEVDLLVS EDIKNGIPAK QAQNDRRSVL KKYI
    Length:234
    Mass (Da):25,563
    Last modified:February 1, 1995 - v1
    Checksum:iEC109F224240F980
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U18778 Genomic DNA. Translation: AAB64543.1.
    BK006939 Genomic DNA. Translation: DAA07661.1.
    PIRiS50468.
    RefSeqiNP_010926.3. NM_001178901.3.

    Genome annotation databases

    EnsemblFungiiYER010C; YER010C; YER010C.
    GeneIDi856728.
    KEGGisce:YER010C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U18778 Genomic DNA. Translation: AAB64543.1.
    BK006939 Genomic DNA. Translation: DAA07661.1.
    PIRiS50468.
    RefSeqiNP_010926.3. NM_001178901.3.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2C5QX-ray1.70A/B/C/D/E/F1-234[»]
    ProteinModelPortaliP40011.
    SMRiP40011. Positions 2-234.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi36741. 8 interactions.
    DIPiDIP-4095N.
    IntActiP40011. 1 interaction.
    MINTiMINT-536635.
    STRINGi4932.YER010C.

    Proteomic databases

    MaxQBiP40011.
    PaxDbiP40011.
    PeptideAtlasiP40011.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblFungiiYER010C; YER010C; YER010C.
    GeneIDi856728.
    KEGGisce:YER010C.

    Organism-specific databases

    CYGDiYER010c.
    EuPathDBiFungiDB:YER010C.
    SGDiS000000812. YER010C.

    Phylogenomic databases

    eggNOGiCOG0684.
    HOGENOMiHOG000107599.
    InParanoidiP40011.
    OMAiRDLDEHN.
    OrthoDBiEOG7DJSZ4.

    Enzyme and pathway databases

    BioCyciYEAST:G3O-30197-MONOMER.

    Miscellaneous databases

    EvolutionaryTraceiP40011.
    NextBioi982835.
    PROiP40011.

    Family and domain databases

    Gene3Di3.50.30.40. 1 hit.
    InterProiIPR005493. RNase_E_inh/diMeMenaQ_MeTrfase.
    [Graphical view]
    PfamiPF03737. Methyltransf_6. 1 hit.
    [Graphical view]
    SUPFAMiSSF89562. SSF89562. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    2. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    3. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    4. Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS], CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS].
    5. "Biochemical and structural analysis of RraA proteins to decipher their relationships with 4-hydroxy-4-methyl-2-oxoglutarate/4-carboxy-4-hydroxy-2-oxoadipate aldolases."
      Mazurkewich S., Wang W., Seah S.Y.
      Biochemistry 53:542-553(2014) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION, COFACTOR.
    6. "Crystal structure of yeast YER010Cp, a knotable member of the RraA protein family."
      Leulliot N., Quevillon-Cheruel S., Graille M., Schiltz M., Blondeau K., Janin J., Van Tilbeurgh H.
      Protein Sci. 14:2751-2758(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) OF 1-234, SUBUNIT.

    Entry informationi

    Entry nameiRRAAH_YEAST
    AccessioniPrimary (citable) accession number: P40011
    Secondary accession number(s): D3DLQ7
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1995
    Last sequence update: February 1, 1995
    Last modified: June 24, 2015
    This is version 97 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 846 molecules/cell in log phase SD medium.1 Publication

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families
    3. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    4. Yeast chromosome V
      Yeast (Saccharomyces cerevisiae) chromosome V: entries and gene names

    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.