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Protein

2-keto-3-deoxy-L-rhamnonate aldolase

Gene

rhmA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the reversible retro-aldol cleavage of 2-keto-3-deoxy-L-rhamnonate (KDR) to pyruvate and lactaldehyde. 2-keto-3-deoxy-L-mannonate, 2-keto-3-deoxy-L-lyxonate and 4-hydroxy-2-ketoheptane-1,7-dioate (HKHD) are also reasonably good substrates, although 2-keto-3-deoxy-L-rhamnonate is likely to be the physiological substrate.2 Publications

Catalytic activityi

2-dehydro-3-deoxy-L-rhamnonate = pyruvate + (S)-lactaldehyde.

Cofactori

Mg2+1 Publication, Ni2+1 PublicationNote: Binds 1 Mg2+ ion per subunit. Is more efficient when using Ni2+ ion, although it is not likely to be the physiologically relevant active site metal.1 Publication

Kineticsi

The catalytic efficiency observed with HKHD as substrate is 750-fold higher with Ni2+ as cofactor than that with Mg2+ as cofactor. 4-hydroxy-2-keto-5-phenyl-pentanoate and 4-hydroxy-2-keto-6-phenylhexanoate are not substrates, suggesting a requirement for an aliphatic or less bulky distal end of the substrate.

  1. KM=0.078 mM for 2-keto-3-deoxy-L-rhamnonate (in the presence of magnesium)1 Publication
  2. KM=0.14 mM for 2-keto-3-deoxy-L-mannonate (in the presence of magnesium)1 Publication
  3. KM=0.8 mM for 2-keto-3-deoxy-L-lyxonate (in the presence of magnesium)1 Publication
  4. KM=0.15 mM for 4-hydroxy-2-ketoheptane-1,7-dioate (in the presence of magnesium)1 Publication
  5. KM=0.1 mM for 4-hydroxy-2-ketoheptane-1,7-dioate (in the presence of nickel)1 Publication
  6. KM=0.1 mM for 4-hydroxy-2-ketopentanoate (in the presence of nickel)1 Publication
  7. KM=0.05 mM for 4-hydroxy-2-ketohexanoate (in the presence of nickel)1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei49 – 491Proton acceptor
    Sitei74 – 741Transition state stabilizer
    Sitei88 – 881Increases basicity of active site His
    Binding sitei151 – 1511Substrate
    Metal bindingi153 – 1531Magnesium1 Publication
    Binding sitei178 – 1781Substrate; via amide nitrogen
    Metal bindingi179 – 1791Magnesium1 Publication
    Binding sitei179 – 1791Substrate

    GO - Molecular functioni

    • aldehyde-lyase activity Source: EcoCyc
    • magnesium ion binding Source: UniProtKB-HAMAP
    • nickel cation binding Source: EcoliWiki

    GO - Biological processi

    • carbohydrate metabolic process Source: GO_Central
    • cellular aromatic compound metabolic process Source: EcoliWiki
    Complete GO annotation...

    Keywords - Molecular functioni

    Lyase

    Keywords - Ligandi

    Magnesium, Metal-binding, Nickel

    Enzyme and pathway databases

    BioCyciEcoCyc:G7158-MONOMER.
    ECOL316407:JW2239-MONOMER.
    MetaCyc:G7158-MONOMER.
    BRENDAi4.1.2.53. 2026.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    2-keto-3-deoxy-L-rhamnonate aldolase (EC:4.1.2.53)
    Short name:
    KDR aldolase
    Alternative name(s):
    2-dehydro-3-deoxyrhamnonate aldolase
    2-keto-3-deoxy acid sugar aldolase
    Gene namesi
    Name:rhmA
    Synonyms:yfaU
    Ordered Locus Names:b2245, JW2239
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG14083. rhmA.

    Subcellular locationi

    GO - Cellular componenti

    • cytoplasm Source: EcoliWiki
    Complete GO annotation...

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi49 – 491H → A: Loss of activity. 1 Publication
    Mutagenesisi74 – 741R → A: Loss of activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 2672672-keto-3-deoxy-L-rhamnonate aldolasePRO_0000207094Add
    BLAST

    Proteomic databases

    PaxDbiP76469.

    Interactioni

    Subunit structurei

    Homohexamer.1 Publication

    Protein-protein interaction databases

    BioGridi4261484. 18 interactions.
    DIPiDIP-11953N.
    STRINGi511145.b2245.

    Structurei

    Secondary structure

    1
    267
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi8 – 147Combined sources
    Beta strandi19 – 246Combined sources
    Helixi29 – 368Combined sources
    Beta strandi41 – 466Combined sources
    Turni47 – 493Combined sources
    Helixi54 – 6411Combined sources
    Beta strandi67 – 748Combined sources
    Helixi80 – 889Combined sources
    Beta strandi93 – 964Combined sources
    Helixi102 – 11110Combined sources
    Turni115 – 1173Combined sources
    Helixi124 – 1263Combined sources
    Helixi128 – 1336Combined sources
    Helixi138 – 1458Combined sources
    Beta strandi147 – 1515Combined sources
    Helixi155 – 1595Combined sources
    Helixi161 – 1655Combined sources
    Beta strandi172 – 1754Combined sources
    Helixi177 – 1837Combined sources
    Beta strandi187 – 1893Combined sources
    Helixi193 – 20816Combined sources
    Beta strandi212 – 2165Combined sources
    Helixi220 – 2289Combined sources
    Beta strandi233 – 2386Combined sources
    Helixi239 – 25214Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2VWSX-ray1.39A/B/C1-267[»]
    2VWTX-ray1.93A/B/C1-267[»]
    ProteinModelPortaliP76469.
    SMRiP76469. Positions 1-256.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP76469.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105CNV. Bacteria.
    COG3836. LUCA.
    HOGENOMiHOG000179750.
    InParanoidiP76469.
    KOiK12660.
    OMAiFANGARK.
    OrthoDBiEOG6NPM5P.
    PhylomeDBiP76469.

    Family and domain databases

    Gene3Di3.20.20.60. 1 hit.
    HAMAPiMF_01290. KDR_aldolase.
    InterProiIPR005000. Aldolase/citrate-lyase_domain.
    IPR023593. KDR_aldolase.
    IPR015813. Pyrv/PenolPyrv_Kinase-like_dom.
    [Graphical view]
    PfamiPF03328. HpcH_HpaI. 1 hit.
    [Graphical view]
    SUPFAMiSSF51621. SSF51621. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P76469-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MNALLSNPFK ERLRKGEVQI GLWLSSTTAY MAEIAATSGY DWLLIDGEHA
    60 70 80 90 100
    PNTIQDLYHQ LQAVAPYASQ PVIRPVEGSK PLIKQVLDIG AQTLLIPMVD
    110 120 130 140 150
    TAEQARQVVS ATRYPPYGER GVGASVARAA RWGRIENYMA QVNDSLCLLV
    160 170 180 190 200
    QVESKTALDN LDEILDVEGI DGVFIGPADL SASLGYPDNA GHPEVQRIIE
    210 220 230 240 250
    TSIRRIRAAG KAAGFLAVAP DMAQQCLAWG ANFVAVGVDT MLYSDALDQR
    260
    LAMFKSGKNG PRIKGSY
    Length:267
    Mass (Da):28,916
    Last modified:February 1, 1997 - v1
    Checksum:iF68506D8A11D23FE
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U00096 Genomic DNA. Translation: AAC75305.1.
    AP009048 Genomic DNA. Translation: BAA16064.2.
    PIRiC64995.
    RefSeqiNP_416748.1. NC_000913.3.
    WP_000992954.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC75305; AAC75305; b2245.
    BAA16064; BAA16064; BAA16064.
    GeneIDi948054.
    KEGGiecj:JW2239.
    eco:b2245.
    PATRICi32119853. VBIEscCol129921_2336.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U00096 Genomic DNA. Translation: AAC75305.1.
    AP009048 Genomic DNA. Translation: BAA16064.2.
    PIRiC64995.
    RefSeqiNP_416748.1. NC_000913.3.
    WP_000992954.1. NZ_LN832404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2VWSX-ray1.39A/B/C1-267[»]
    2VWTX-ray1.93A/B/C1-267[»]
    ProteinModelPortaliP76469.
    SMRiP76469. Positions 1-256.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4261484. 18 interactions.
    DIPiDIP-11953N.
    STRINGi511145.b2245.

    Proteomic databases

    PaxDbiP76469.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC75305; AAC75305; b2245.
    BAA16064; BAA16064; BAA16064.
    GeneIDi948054.
    KEGGiecj:JW2239.
    eco:b2245.
    PATRICi32119853. VBIEscCol129921_2336.

    Organism-specific databases

    EchoBASEiEB3836.
    EcoGeneiEG14083. rhmA.

    Phylogenomic databases

    eggNOGiENOG4105CNV. Bacteria.
    COG3836. LUCA.
    HOGENOMiHOG000179750.
    InParanoidiP76469.
    KOiK12660.
    OMAiFANGARK.
    OrthoDBiEOG6NPM5P.
    PhylomeDBiP76469.

    Enzyme and pathway databases

    BioCyciEcoCyc:G7158-MONOMER.
    ECOL316407:JW2239-MONOMER.
    MetaCyc:G7158-MONOMER.
    BRENDAi4.1.2.53. 2026.

    Miscellaneous databases

    EvolutionaryTraceiP76469.
    PROiP76469.

    Family and domain databases

    Gene3Di3.20.20.60. 1 hit.
    HAMAPiMF_01290. KDR_aldolase.
    InterProiIPR005000. Aldolase/citrate-lyase_domain.
    IPR023593. KDR_aldolase.
    IPR015813. Pyrv/PenolPyrv_Kinase-like_dom.
    [Graphical view]
    PfamiPF03328. HpcH_HpaI. 1 hit.
    [Graphical view]
    SUPFAMiSSF51621. SSF51621. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features."
      Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T.
      , Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.
      DNA Res. 4:91-113(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    3. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    4. "Expression, purification, crystallization and preliminary characterization of an HHED aldolase homologue from Escherichia coli K12."
      Wright A., Blewett A., Fueloep V., Cooper R., Burrows S., Jones C., Roper D.
      Acta Crystallogr. D 58:2191-2193(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: CRYSTALLIZATION.
      Strain: K12 / MG1655 / ATCC 47076.
    5. "Evolution of enzymatic activities in the enolase superfamily: L-rhamnonate dehydratase."
      Rakus J.F., Fedorov A.A., Fedorov E.V., Glasner M.E., Hubbard B.K., Delli J.D., Babbitt P.C., Almo S.C., Gerlt J.A.
      Biochemistry 47:9944-9954(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
      Strain: K12 / MG1655 / ATCC 47076.
    6. "Crystal structure and functional assignment of YfaU, a metal ion dependent class II aldolase from Escherichia coli K12."
      Rea D., Hovington R., Rakus J.F., Gerlt J.A., Fueloep V., Bugg T.D.H., Roper D.I.
      Biochemistry 47:9955-9965(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.39 ANGSTROMS) OF APOENZYME AND IN COMPLEX WITH MAGNESIUM AND PYRUVATE, FUNCTION, SUBSTRATE SPECIFICITY, COFACTOR, KINETIC PARAMETERS, SUBUNIT, CATALYTIC MECHANISM, MUTAGENESIS OF HIS-49 AND ARG-74.
      Strain: K12 / MG1655 / ATCC 47076.

    Entry informationi

    Entry nameiRHMA_ECOLI
    AccessioniPrimary (citable) accession number: P76469
    Secondary accession number(s): P76925
    , P76926, P76928, P76929
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 1, 2000
    Last sequence update: February 1, 1997
    Last modified: January 20, 2016
    This is version 110 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. 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.