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P40011

- RRAAH_YEAST

UniProt

P40011 - RRAAH_YEAST

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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: 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.

Catalytic activityi

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

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.

Enzyme regulationi

Competitively inhibited by oxalate, a pyruvate enolate analog.

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-oxoglutarate
  2. KM=132.5 µM for oxaloacetate

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei122 – 1221Substrate By similarity
Metal bindingi123 – 1231Divalent metal cation By 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
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: 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.

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.

Miscellaneous databases

EvolutionaryTraceiP40011.

Family & Domainsi

Region

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

Sequence similaritiesi

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

« Hide

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

« 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: September 3, 2014
This is version 91 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.

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

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