RRAAH_YEAST
ID RRAAH_YEAST Reviewed; 234 AA.
AC P40011; D3DLQ7;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1995, sequence version 1.
DT 03-AUG-2022, entry version 140.
DE RecName: Full=4-hydroxy-4-methyl-2-oxoglutarate aldolase;
DE Short=HMG aldolase;
DE EC=4.1.3.17;
DE AltName: Full=Oxaloacetate decarboxylase;
DE Short=OAA decarboxylase;
DE EC=4.1.1.112;
DE AltName: Full=Regulator of ribonuclease activity homolog;
DE AltName: Full=RraA-like protein;
GN OrderedLocusNames=YER010C;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169868;
RA Dietrich F.S., Mulligan J.T., Hennessy K.M., Yelton M.A., Allen E.,
RA Araujo R., Aviles E., Berno A., Brennan T., Carpenter J., Chen E.,
RA Cherry J.M., Chung E., Duncan M., Guzman E., Hartzell G., Hunicke-Smith S.,
RA Hyman R.W., Kayser A., Komp C., Lashkari D., Lew H., Lin D., Mosedale D.,
RA Nakahara K., Namath A., Norgren R., Oefner P., Oh C., Petel F.X.,
RA Roberts D., Sehl P., Schramm S., Shogren T., Smith V., Taylor P., Wei Y.,
RA Botstein D., Davis R.W.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome V.";
RL Nature 387:78-81(1997).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [3]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [4]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, CLEAVAGE OF INITIATOR
RP METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS SPECTROMETRY
RP [LARGE SCALE ANALYSIS].
RX PubMed=22814378; DOI=10.1073/pnas.1210303109;
RA Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
RA Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E.,
RA Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.;
RT "N-terminal acetylome analyses and functional insights of the N-terminal
RT acetyltransferase NatB.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, ACTIVITY
RP REGULATION, AND COFACTOR.
RX PubMed=24359411; DOI=10.1021/bi401486g;
RA Mazurkewich S., Wang W., Seah S.Y.;
RT "Biochemical and structural analysis of RraA proteins to decipher their
RT relationships with 4-hydroxy-4-methyl-2-oxoglutarate/4-carboxy-4-hydroxy-2-
RT oxoadipate aldolases.";
RL Biochemistry 53:542-553(2014).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) OF 1-234, AND SUBUNIT.
RX PubMed=16195557; DOI=10.1110/ps.051684005;
RA Leulliot N., Quevillon-Cheruel S., Graille M., Schiltz M., Blondeau K.,
RA Janin J., Van Tilbeurgh H.;
RT "Crystal structure of yeast YER010Cp, a knotable member of the RraA protein
RT family.";
RL Protein Sci. 14:2751-2758(2005).
CC -!- FUNCTION: Catalyzes the aldol cleavage of 4-hydroxy-4-methyl-2-
CC oxoglutarate (HMG) into 2 molecules of pyruvate. Also contains a
CC secondary oxaloacetate (OAA) decarboxylase activity due to the common
CC pyruvate enolate transition state formed following C-C bond cleavage in
CC the retro-aldol and decarboxylation reactions.
CC {ECO:0000269|PubMed:24359411}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=4-hydroxy-4-methyl-2-oxoglutarate = 2 pyruvate;
CC Xref=Rhea:RHEA:22748, ChEBI:CHEBI:15361, ChEBI:CHEBI:58276;
CC EC=4.1.3.17; Evidence={ECO:0000269|PubMed:24359411};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H(+) + oxaloacetate = CO2 + pyruvate; Xref=Rhea:RHEA:15641,
CC ChEBI:CHEBI:15361, ChEBI:CHEBI:15378, ChEBI:CHEBI:16452,
CC ChEBI:CHEBI:16526; EC=4.1.1.112;
CC Evidence={ECO:0000269|PubMed:24359411};
CC -!- COFACTOR:
CC Name=Ni(2+); Xref=ChEBI:CHEBI:49786;
CC Evidence={ECO:0000269|PubMed:24359411};
CC Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC Evidence={ECO:0000269|PubMed:24359411};
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:24359411};
CC Note=Divalent metal cation. Has preference for nickel ions for the HMG
CC aldolase activity. Has preference for cobalt and zinc ions for the OAA
CC decarboxylase activity. {ECO:0000269|PubMed:24359411};
CC -!- ACTIVITY REGULATION: Competitively inhibited by oxalate, a pyruvate
CC enolate analog. {ECO:0000269|PubMed:24359411}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=126.5 uM for 4-hydroxy-4-methyl-2-oxoglutarate
CC {ECO:0000269|PubMed:24359411};
CC KM=132.5 uM for oxaloacetate {ECO:0000269|PubMed:24359411};
CC Note=kcat is 0.0276 sec(-1) with 4-hydroxy-4-methyl-2-oxoglutarate as
CC substrate and 3.91 sec(-1) with oxaloacetate as substrate.;
CC -!- SUBUNIT: Homotrimer. Forms a ring-like structure with a central cavity.
CC {ECO:0000269|PubMed:16195557}.
CC -!- MISCELLANEOUS: Present with 846 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the class II aldolase/RraA-like family.
CC {ECO:0000305}.
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DR EMBL; U18778; AAB64543.1; -; Genomic_DNA.
DR EMBL; BK006939; DAA07661.1; -; Genomic_DNA.
DR PIR; S50468; S50468.
DR RefSeq; NP_010926.3; NM_001178901.3.
DR PDB; 2C5Q; X-ray; 1.70 A; A/B/C/D/E/F=1-234.
DR PDBsum; 2C5Q; -.
DR AlphaFoldDB; P40011; -.
DR SMR; P40011; -.
DR BioGRID; 36741; 65.
DR DIP; DIP-4095N; -.
DR IntAct; P40011; 1.
DR STRING; 4932.YER010C; -.
DR iPTMnet; P40011; -.
DR MaxQB; P40011; -.
DR PaxDb; P40011; -.
DR PRIDE; P40011; -.
DR TopDownProteomics; P40011; -.
DR EnsemblFungi; YER010C_mRNA; YER010C; YER010C.
DR GeneID; 856728; -.
DR KEGG; sce:YER010C; -.
DR SGD; S000000812; YER010C.
DR VEuPathDB; FungiDB:YER010C; -.
DR eggNOG; ENOG502RZ5Y; Eukaryota.
DR HOGENOM; CLU_072626_0_1_1; -.
DR InParanoid; P40011; -.
DR OMA; FTPCDVS; -.
DR BioCyc; YEAST:G3O-30197-MON; -.
DR ChiTaRS; YER010C; yeast.
DR EvolutionaryTrace; P40011; -.
DR PRO; PR:P40011; -.
DR Proteomes; UP000002311; Chromosome V.
DR RNAct; P40011; protein.
DR GO; GO:0047443; F:4-hydroxy-4-methyl-2-oxoglutarate aldolase activity; IDA:SGD.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0008948; F:oxaloacetate decarboxylase activity; IDA:SGD.
DR GO; GO:0019619; P:3,4-dihydroxybenzoate catabolic process; IDA:SGD.
DR CDD; cd16841; RraA_family; 1.
DR InterPro; IPR005493; RraA/RraA-like.
DR InterPro; IPR036704; RraA/RraA-like_sf.
DR Pfam; PF03737; RraA-like; 1.
DR SUPFAM; SSF89562; SSF89562; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Lyase; Metal-binding; Reference proteome.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0007744|PubMed:22814378"
FT CHAIN 2..234
FT /note="4-hydroxy-4-methyl-2-oxoglutarate aldolase"
FT /id="PRO_0000202621"
FT BINDING 100..103
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 122
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 123
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250"
FT MOD_RES 2
FT /note="N-acetylserine"
FT /evidence="ECO:0007744|PubMed:22814378"
FT HELIX 3..7
FT /evidence="ECO:0007829|PDB:2C5Q"
FT HELIX 12..23
FT /evidence="ECO:0007829|PDB:2C5Q"
FT TURN 26..29
FT /evidence="ECO:0007829|PDB:2C5Q"
FT STRAND 35..38
FT /evidence="ECO:0007829|PDB:2C5Q"
FT STRAND 41..43
FT /evidence="ECO:0007829|PDB:2C5Q"
FT STRAND 45..56
FT /evidence="ECO:0007829|PDB:2C5Q"
FT STRAND 59..61
FT /evidence="ECO:0007829|PDB:2C5Q"
FT HELIX 67..69
FT /evidence="ECO:0007829|PDB:2C5Q"
FT STRAND 74..80
FT /evidence="ECO:0007829|PDB:2C5Q"
FT HELIX 82..84
FT /evidence="ECO:0007829|PDB:2C5Q"
FT HELIX 101..109
FT /evidence="ECO:0007829|PDB:2C5Q"
FT STRAND 114..121
FT /evidence="ECO:0007829|PDB:2C5Q"
FT HELIX 124..130
FT /evidence="ECO:0007829|PDB:2C5Q"
FT STRAND 134..139
FT /evidence="ECO:0007829|PDB:2C5Q"
FT TURN 145..147
FT /evidence="ECO:0007829|PDB:2C5Q"
FT STRAND 148..154
FT /evidence="ECO:0007829|PDB:2C5Q"
FT STRAND 157..160
FT /evidence="ECO:0007829|PDB:2C5Q"
FT STRAND 166..169
FT /evidence="ECO:0007829|PDB:2C5Q"
FT STRAND 174..178
FT /evidence="ECO:0007829|PDB:2C5Q"
FT STRAND 181..185
FT /evidence="ECO:0007829|PDB:2C5Q"
FT TURN 187..189
FT /evidence="ECO:0007829|PDB:2C5Q"
FT HELIX 192..214
FT /evidence="ECO:0007829|PDB:2C5Q"
FT HELIX 219..227
FT /evidence="ECO:0007829|PDB:2C5Q"
FT HELIX 228..230
FT /evidence="ECO:0007829|PDB:2C5Q"
SQ SEQUENCE 234 AA; 25563 MW; EC109F224240F980 CRC64;
MSDLQKLQRF STCDISDGLL NVYNIPTGGY FPNLTAISPP QNSSIVGTAY TVLFAPIDDP
RPAVNYIDSV PPNSILVLAL EPHLQSQFHP FIKITQAMYG GLMSTRAQYL KSNGTVVFGR
IRDVDEHRTL NHPVFAYGVG SCAPKAVVKA VGTNVQLKIL TSDGVTQTIC PGDYIAGDNN
GIVRIPVQET DISKLVTYIE KSIEVDLLVS EDIKNGIPAK QAQNDRRSVL KKYI
