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P40011

- RRAAH_YEAST

UniProt

P40011 - RRAAH_YEAST

Protein

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

Gene

YER010C

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 92 (01 Oct 2014)
      Sequence version 1 (01 Feb 1995)
      Previous versions | rss
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    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

    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

    1. 4-hydroxy-4-methyl-2-oxoglutarate aldolase activity Source: SGD
    2. oxaloacetate decarboxylase activity Source: SGD

    GO - Biological processi

    1. protocatechuate catabolic process Source: SGD

    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: Chromosome V

    Organism-specific databases

    CYGDiYER010c.
    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.

    Expressioni

    Gene expression databases

    GenevestigatoriP40011.

    Interactioni

    Subunit structurei

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

    Protein-protein interaction databases

    BioGridi36741. 7 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 – 75
    Helixi12 – 2312
    Turni26 – 294
    Beta strandi35 – 384
    Beta strandi41 – 433
    Beta strandi45 – 5612
    Beta strandi59 – 613
    Helixi67 – 693
    Beta strandi74 – 807
    Helixi82 – 843
    Helixi101 – 1099
    Beta strandi114 – 1218
    Helixi124 – 1307
    Beta strandi134 – 1396
    Turni145 – 1473
    Beta strandi148 – 1547
    Beta strandi157 – 1604
    Beta strandi166 – 1694
    Beta strandi174 – 1785
    Beta strandi181 – 1855
    Turni187 – 1893
    Helixi192 – 21423
    Helixi219 – 2279
    Helixi228 – 2303

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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.
    OMAiYIPKRVE.
    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

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    MSDLQKLQRF STCDISDGLL NVYNIPTGGY FPNLTAISPP QNSSIVGTAY    50
    TVLFAPIDDP RPAVNYIDSV PPNSILVLAL EPHLQSQFHP FIKITQAMYG 100
    GLMSTRAQYL KSNGTVVFGR IRDVDEHRTL NHPVFAYGVG SCAPKAVVKA 150
    VGTNVQLKIL TSDGVTQTIC PGDYIAGDNN GIVRIPVQET DISKLVTYIE 200
    KSIEVDLLVS EDIKNGIPAK QAQNDRRSVL KKYI 234
    Length:234
    Mass (Da):25,563
    Last modified:February 1, 1995 - v1
    Checksum:iEC109F224240F980
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U18778 Genomic DNA. Translation: AAB64543.1 .
    BK006939 Genomic DNA. Translation: DAA07661.1 .
    PIRi S50468.
    RefSeqi NP_010926.3. NM_001178901.3.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2C5Q X-ray 1.70 A/B/C/D/E/F 1-234 [» ]
    ProteinModelPortali P40011.
    SMRi P40011. Positions 2-234.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 36741. 7 interactions.
    DIPi DIP-4095N.
    IntActi P40011. 1 interaction.
    MINTi MINT-536635.
    STRINGi 4932.YER010C.

    Proteomic databases

    MaxQBi P40011.
    PaxDbi P40011.
    PeptideAtlasi P40011.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YER010C ; YER010C ; YER010C .
    GeneIDi 856728.
    KEGGi sce:YER010C.

    Organism-specific databases

    CYGDi YER010c.
    SGDi S000000812. YER010C.

    Phylogenomic databases

    eggNOGi COG0684.
    HOGENOMi HOG000107599.
    OMAi YIPKRVE.
    OrthoDBi EOG7DJSZ4.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-30197-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P40011.
    NextBioi 982835.

    Gene expression databases

    Genevestigatori P40011.

    Family and domain databases

    Gene3Di 3.50.30.40. 1 hit.
    InterProi IPR005493. RNase_E_inh/diMeMenaQ_MeTrfase.
    [Graphical view ]
    Pfami PF03737. Methyltransf_6. 1 hit.
    [Graphical view ]
    SUPFAMi SSF89562. SSF89562. 1 hit.
    ProtoNeti Search...

    Publicationsi

    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: October 1, 2014
    This is version 92 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