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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)DescriptionActionsGraphical viewLength
    Active sitei49Proton acceptor1
    Sitei74Transition state stabilizer1
    Sitei88Increases basicity of active site His1
    Binding sitei151Substrate1
    Metal bindingi153Magnesium1 Publication1
    Binding sitei178Substrate; via amide nitrogen1
    Metal bindingi179Magnesium1 Publication1
    Binding sitei179Substrate1

    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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    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)DescriptionActionsGraphical viewLength
    Mutagenesisi49H → A: Loss of activity. 1 Publication1
    Mutagenesisi74R → A: Loss of activity. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00002070941 – 2672-keto-3-deoxy-L-rhamnonate aldolaseAdd BLAST267

    Proteomic databases

    PaxDbiP76469.
    PRIDEiP76469.

    Interactioni

    Subunit structurei

    Homohexamer.1 Publication

    Protein-protein interaction databases

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

    Structurei

    Secondary structure

    1267
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi8 – 14Combined sources7
    Beta strandi19 – 24Combined sources6
    Helixi29 – 36Combined sources8
    Beta strandi41 – 46Combined sources6
    Turni47 – 49Combined sources3
    Helixi54 – 64Combined sources11
    Beta strandi67 – 74Combined sources8
    Helixi80 – 88Combined sources9
    Beta strandi93 – 96Combined sources4
    Helixi102 – 111Combined sources10
    Turni115 – 117Combined sources3
    Helixi124 – 126Combined sources3
    Helixi128 – 133Combined sources6
    Helixi138 – 145Combined sources8
    Beta strandi147 – 151Combined sources5
    Helixi155 – 159Combined sources5
    Helixi161 – 165Combined sources5
    Beta strandi172 – 175Combined sources4
    Helixi177 – 183Combined sources7
    Beta strandi187 – 189Combined sources3
    Helixi193 – 208Combined sources16
    Beta strandi212 – 216Combined sources5
    Helixi220 – 228Combined sources9
    Beta strandi233 – 238Combined sources6
    Helixi239 – 252Combined sources14

    3D structure databases

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

    Miscellaneous databases

    EvolutionaryTraceiP76469.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105CNV. Bacteria.
    COG3836. LUCA.
    HOGENOMiHOG000179750.
    InParanoidiP76469.
    KOiK12660.
    OMAiIARASQW.
    PhylomeDBiP76469.

    Family and domain databases

    Gene3Di3.20.20.60. 1 hit.
    HAMAPiMF_01290. KDR_aldolase. 1 hit.
    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
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2VWSX-ray1.39A/B/C1-267[»]
    2VWTX-ray1.93A/B/C1-267[»]
    ProteinModelPortaliP76469.
    SMRiP76469.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

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

    Proteomic databases

    PaxDbiP76469.
    PRIDEiP76469.

    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.
    OMAiIARASQW.
    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. 1 hit.
    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...

    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: November 2, 2016
    This is version 113 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.