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Protein

4-hydroxy-2-oxovalerate aldolase 4

Gene

bphI

Organism
Burkholderia xenovorans (strain LB400)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the retro-aldol cleavage of both 4-hydroxy-2-oxopentanoate (HOPA) and 4-hydroxy-2-oxohexanoate (HOHA) to pyruvate and acetaldehyde or propanaldehyde, respectively. The aldehydes produced by this reaction are directly channeled from BphI to the dehydrogenase BphJ, ensuring that these toxic aldehydes are sequestered from cellular components. Is involved in the meta-cleavage pathway for the degradation of polychlorinated biphenyls (PCBs). Appears to be stereospecific since it can cleave (4S)-4-hydroxy-2-oxopentanoate but not the (4R) isomer. Also exhibits a secondary oxaloacetate decarboxylase activity. Finally, is also able to catalyze the reverse reaction, albeit much less efficiently, i.e. the condensation of aldehyde acceptors of two to three carbons in length with pyruvate. This aldol addition reaction is stereospecific; the condensation of acetaldehyde and pyruvate with BphI produces only the (4S)-4-hydroxy-2-oxopentanoate isomer. Aldehyde channeling in the BphI-BphJ complex can occur in reverse, from the dehydrogenase to the aldolase active sites, and the BphJ reductive deacylation reaction increases 4-fold when BphI is catalyzing the aldol addition reaction. Therefore, the BphI-BphJ enzyme complex exhibits unique bidirectionality in substrate channeling and allosteric activation.2 Publications

Catalytic activityi

(S)-4-hydroxy-2-oxopentanoate = acetaldehyde + pyruvate.1 Publication
(S)-4-hydroxy-2-oxohexanoate = propanal + pyruvate.1 Publication

Cofactori

Mn2+1 Publication, Cd2+1 Publication, Co2+1 PublicationNote: Divalent metal cation. Has the highest activity with Mn2+ as cofactor. Can also use Cd2+ at low concentrations (0.01-0.1 mM) or Co2+, although with less efficiency. Mg2+ and Ni2+ are very poor metal cofactors.1 Publication

Enzyme regulationi

Competitively inhibited by oxalate. Also inhibited by high concentrations of Cd2+ (1 mM) in vitro. Appears to be allosterically activated by aldehyde turnover occurring in BphJ, partly via NADH.

Kineticsi

The catalytic efficiency is similar when using 4-hydroxy-2-oxopentanoate or 4-hydroxy-2-oxohexanoate as substrate, but is 10-fold lower with 4-hydroxy-2-oxoheptanoate. It is also 25-fold higher when NADH is present than the value obtained without nucleotides. Moreover, the catalytic efficiency is similar when using acetaldehyde or propanaldehyde as substrate in the aldol addition reaction.

  1. KM=89 µM for (4S)-4-hydroxy-2-oxopentanoate (in the presence of NADH at pH 8 and 25 degrees Celsius)3 Publications
  2. KM=0.22 mM for racemic 4-hydroxy-2-oxopentanoate (in the presence of NADH at pH 8 and 25 degrees Celsius)3 Publications
  3. KM=1.12 mM for racemic 4-hydroxy-2-oxopentanoate (in the absence of NADH at pH 8 and 25 degrees Celsius)3 Publications
  4. KM=0.18 mM for racemic 4-hydroxy-2-oxohexanoate (in the presence of NADH at pH 8 and 25 degrees Celsius)3 Publications
  5. KM=0.35 mM for racemic 4-hydroxy-2-oxoheptanoate (in the presence of NADH at pH 8 and 25 degrees Celsius)3 Publications
  6. KM=64.28 mM for acetaldehyde (in the absence of NADH at pH 8 and 25 degrees Celsius)3 Publications
  7. KM=135.9 mM for propanaldehyde (in the absence of NADH at pH 8 and 25 degrees Celsius)3 Publications
  8. KM=13.0 mM for pyruvate (at pH 8 and 25 degrees Celsius)3 Publications

    pH dependencei

    Activity increases from pH 6.5 to 9.1 Publication

    Pathwayi: polychlorinated biphenyl degradation

    This protein is involved in the pathway polychlorinated biphenyl degradation, which is part of Xenobiotic degradation.
    View all proteins of this organism that are known to be involved in the pathway polychlorinated biphenyl degradation and in Xenobiotic degradation.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sitei16Transition state stabilizer1
    Metal bindingi17ManganeseBy similarity1
    Active sitei20Proton acceptorSequence analysis1
    Sitei87Important for aldehyde specificity, and governs stereochemical control1
    Sitei89Important for aldehyde specificity; governs substrate alkyl chain length1
    Binding sitei170SubstrateBy similarity1
    Metal bindingi199Manganese; via tele nitrogenBy similarity1
    Binding sitei199SubstrateBy similarity1
    Metal bindingi201Manganese; via tele nitrogenBy similarity1
    Binding sitei290SubstrateBy similarity1
    Sitei290Governs stereochemical control1

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Lyase

    Keywords - Biological processi

    Aromatic hydrocarbons catabolism

    Keywords - Ligandi

    Cadmium, Cobalt, Manganese, Metal-binding

    Enzyme and pathway databases

    BRENDAi4.1.3.39. 9987.
    4.1.3.43. 7691.
    SABIO-RKP51015.
    UniPathwayiUPA01002.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    4-hydroxy-2-oxovalerate aldolase 4 (EC:4.1.3.39)
    Short name:
    HOA 4
    Alternative name(s):
    4-hydroxy-2-keto-pentanoic acid aldolase 4
    4-hydroxy-2-oxohexanoate aldolase (EC:4.1.3.43)
    4-hydroxy-2-oxopentanoate aldolase 4
    Gene namesi
    Name:bphI
    Ordered Locus Names:Bxeno_C1121
    ORF Names:Bxe_C1187
    OrganismiBurkholderia xenovorans (strain LB400)
    Taxonomic identifieri266265 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesBurkholderiaceaeParaburkholderia
    Proteomesi
    • UP000001817 Componenti: Chromosome 3

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi16R → A: Loss of aldol cleavage activity. 1 Publication1
    Mutagenesisi16R → K: 4000-fold decrease in the catalytic efficiency of the aldol cleavage reaction. 1 Publication1
    Mutagenesisi20H → A or S: 100-fold decrease in the catalytic efficiency of the aldol cleavage reaction. Dramatic reduction in acetaldehyde and propanaldehyde channeling efficiency by more than 70%. 2 Publications1
    Mutagenesisi87L → A: 32-fold reduction in the catalytic efficiency with acetaldehyde as substrate of the aldol addition reaction, but no change in the catalytic efficiency using propanaldehyde; thus, exhibits a 40-fold preference for propanaldehyde over acetaldehyde. 2 Publications1
    Mutagenesisi87L → N or W: Loss of aldolase activity (with either enantiomer of HOPA), but retains some decarboxylase activity for the smaller oxaloacetate substrate. In the retro-aldol cleavage reaction, is inactive toward 4(S)-HOPA but is active toward 4(R)-HOPA, albeit with a great reduction in catalytic efficiency, and in the aldol addition reaction, produces also exclusively the 4(R)-enantiomer; when associated with F-290. 2 Publications1
    Mutagenesisi89L → A: As the wild-type enzyme, exhibits similar catalytic efficiency with acetaldehyde or propanaldehyde as substrate in the aldol addition reaction but displays higher catalytic efficiency with longer aldehydes (50-fold increase using pentaldehyde). Shows a reduction in aldehyde channeling efficiency by 30%. 2 Publications1
    Mutagenesisi290Y → F: Loss of stereochemical control as the mutant is able to catalyze the aldol cleavage of substrates with both R and S configurations at C4 with similar kinetic parameters. 3.5-fold decrease in the catalytic efficiency of the aldol cleavage reaction. Reduction in aldehyde channeling efficiency by more than 30%. In the retro-aldol cleavage reaction, is inactive toward 4(S)-HOPA but is active toward 4(R)-HOPA, albeit with a great reduction in catalytic efficiency, and in the aldol addition reaction, produces also exclusively the 4(R)-enantiomer; when associated with N-87 or W-87. 3 Publications1
    Mutagenesisi290Y → S: Loss of stereochemical control as the mutant is able to catalyze the aldol cleavage of substrates with both R and S configurations at C4 with similar kinetic parameters. 3.5-fold decrease in the catalytic efficiency of the aldol cleavage reaction. 3 Publications1
    Mutagenesisi322G → A: Displays a reduction in aldehyde channeling efficiency of about 20%. 1 Publication1
    Mutagenesisi322G → F or L: Unable to channel either acetaldehyde or propanaldehyde. 1 Publication1
    Mutagenesisi323G → A: Able to channel butyraldehyde (with less efficiency than wild-type) but not its isomer isobutyraldehyde. 1 Publication1
    Mutagenesisi323G → F: Unable to channel either acetaldehyde or propanaldehyde. 1 Publication1
    Mutagenesisi323G → L: Able to channel acetaldehyde but not the larger propanaldehyde. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00000649781 – 3464-hydroxy-2-oxovalerate aldolase 4Add BLAST346

    Interactioni

    Subunit structurei

    Heterotetramer composed of two BphI (aldolase) and two BphJ (dehydrogenase).1 Publication

    Protein-protein interaction databases

    STRINGi266265.Bxe_C1187.

    Structurei

    3D structure databases

    ProteinModelPortaliP51015.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini8 – 260Pyruvate carboxyltransferasePROSITE-ProRule annotationAdd BLAST253

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni16 – 17Substrate bindingBy similarity2

    Sequence similaritiesi

    Contains 1 pyruvate carboxyltransferase domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiENOG4105DF3. Bacteria.
    COG0119. LUCA.
    HOGENOMiHOG000048047.
    KOiK18365.
    OMAiIDLYKIM.
    OrthoDBiPOG091H086P.

    Family and domain databases

    Gene3Di3.20.20.70. 1 hit.
    HAMAPiMF_01656. HOA. 1 hit.
    InterProiIPR017629. 4OH_2_O-val_aldolase.
    IPR013785. Aldolase_TIM.
    IPR012425. DmpG_comm.
    IPR000891. PYR_CT.
    [Graphical view]
    PANTHERiPTHR10277:SF3. PTHR10277:SF3. 1 hit.
    PfamiPF07836. DmpG_comm. 1 hit.
    PF00682. HMGL-like. 1 hit.
    [Graphical view]
    ProDomiPD005364. DmpG_comm. 1 hit.
    [Graphical view] [Entries sharing at least one domain]
    TIGRFAMsiTIGR03217. 4OH_2_O_val_ald. 1 hit.
    PROSITEiPS50991. PYR_CT. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P51015-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MKLEGKKVTV HDMTLRDGMH PKRHQMTLEQ MKSIACGLDA AGIPLIEVTH
    60 70 80 90 100
    GDGLGGSSVN YGFPAHSDEE YLGAVIPLMK QAKVSALLLP GIGTVEHLKM
    110 120 130 140 150
    AKDLGVNTIR VATHCTEADV SEQHITQSRK LGLDTVGFLM MAHMASPEKL
    160 170 180 190 200
    VSQALLMQGY GANCIYVTDS AGYMLPDDVK ARLSAVRAAL KPETELGFHG
    210 220 230 240 250
    HHNLAMGVAN SIAAIEAGAT RIDAAAAGLG AGAGNTPMEV FIAVCARMGI
    260 270 280 290 300
    ETGVDVFKIQ DVAEDLVVPI MDHVIRIDRD SLTLGYAGVY SSFLLFAKRA
    310 320 330 340
    SAKYGVPARD ILVELGRRGM VGGQEDMIED TAMTMARERG LTLTAA
    Length:346
    Mass (Da):36,798
    Last modified:September 19, 2006 - v2
    Checksum:iBD4A951D513C97CE
    GO

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti263A → S in CAA54036 (PubMed:8026764).Curated1
    Sequence conflicti302A → E in CAA54036 (PubMed:8026764).Curated1

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X76500 Genomic DNA. Translation: CAA54036.1.
    CP000272 Genomic DNA. Translation: ABE37049.1.
    RefSeqiWP_003450974.1. NZ_CP008761.1.

    Genome annotation databases

    EnsemblBacteriaiABE37049; ABE37049; Bxe_C1187.
    GeneIDi4010699.
    KEGGibxb:DR64_8618.
    bxe:Bxe_C1187.
    PATRICi19343359. VBIBurXen52548_8937.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X76500 Genomic DNA. Translation: CAA54036.1.
    CP000272 Genomic DNA. Translation: ABE37049.1.
    RefSeqiWP_003450974.1. NZ_CP008761.1.

    3D structure databases

    ProteinModelPortaliP51015.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi266265.Bxe_C1187.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiABE37049; ABE37049; Bxe_C1187.
    GeneIDi4010699.
    KEGGibxb:DR64_8618.
    bxe:Bxe_C1187.
    PATRICi19343359. VBIBurXen52548_8937.

    Phylogenomic databases

    eggNOGiENOG4105DF3. Bacteria.
    COG0119. LUCA.
    HOGENOMiHOG000048047.
    KOiK18365.
    OMAiIDLYKIM.
    OrthoDBiPOG091H086P.

    Enzyme and pathway databases

    UniPathwayiUPA01002.
    BRENDAi4.1.3.39. 9987.
    4.1.3.43. 7691.
    SABIO-RKP51015.

    Family and domain databases

    Gene3Di3.20.20.70. 1 hit.
    HAMAPiMF_01656. HOA. 1 hit.
    InterProiIPR017629. 4OH_2_O-val_aldolase.
    IPR013785. Aldolase_TIM.
    IPR012425. DmpG_comm.
    IPR000891. PYR_CT.
    [Graphical view]
    PANTHERiPTHR10277:SF3. PTHR10277:SF3. 1 hit.
    PfamiPF07836. DmpG_comm. 1 hit.
    PF00682. HMGL-like. 1 hit.
    [Graphical view]
    ProDomiPD005364. DmpG_comm. 1 hit.
    [Graphical view] [Entries sharing at least one domain]
    TIGRFAMsiTIGR03217. 4OH_2_O_val_ald. 1 hit.
    PROSITEiPS50991. PYR_CT. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiHOA4_BURXL
    AccessioniPrimary (citable) accession number: P51015
    Secondary accession number(s): Q13FU0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1996
    Last sequence update: September 19, 2006
    Last modified: November 2, 2016
    This is version 90 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    The aldol addition reaction proceeds via a compulsory order mechanism, with pyruvate binding first.

    Keywords - Technical termi

    Allosteric enzyme, Complete proteome, Reference proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. SIMILARITY comments
      Index of protein domains and families

    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 one 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.