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Protein

L-rhamnonate dehydratase

Gene

rhmD

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

Functioni

Catalyzes the dehydration of L-rhamnonate to 2-keto-3-deoxy-L-rhamnonate (KDR). Can also dehydrate L-lyxonate, L-mannonate and D-gulonate, although less efficiently, but not 2-keto-4-hydroxyheptane-1,7-dioate.1 Publication

Catalytic activityi

L-rhamnonate = 2-dehydro-3-deoxy-L-rhamnonate + H2O.

Cofactori

Mg2+By similarityNote: Binds 1 Mg2+ ion per subunit.By similarity

Kineticsi

The catalytic efficiency observed with L-rhamnonate as substrate is 70- and 16-fold higher than that observed with L-lyxonate and L-mannonate, respectively.

  1. KM=0.15 mM for L-rhamnonate1 Publication
  2. KM=2.0 mM for L-lyxonate1 Publication
  3. KM=0.15 mM for L-mannonate1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei29 – 291Substrate
    Binding sitei55 – 551SubstrateBy similarity
    Metal bindingi222 – 2221MagnesiumBy similarity
    Metal bindingi248 – 2481MagnesiumBy similarity
    Metal bindingi276 – 2761MagnesiumBy similarity
    Sitei298 – 2981Increases basicity of active site HisBy similarity
    Active sitei325 – 3251Proton acceptor
    Binding sitei345 – 3451SubstrateBy similarity
    Sitei345 – 3451Transition state stabilizerBy similarity

    GO - Molecular functioni

    • L-rhamnonate dehydratase activity Source: EcoCyc
    • magnesium ion binding Source: UniProtKB-HAMAP

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Lyase

    Keywords - Ligandi

    Magnesium, Metal-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:G7160-MONOMER.
    ECOL316407:JW2241-MONOMER.
    MetaCyc:G7160-MONOMER.
    BRENDAi4.2.1.90. 2165.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    L-rhamnonate dehydratase (EC:4.2.1.90)
    Short name:
    RhamD
    Gene namesi
    Name:rhmD
    Synonyms:yfaW
    Ordered Locus Names:b2247, JW2241
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG14085. rhmD.

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi29 – 291H → N: Loss of activity due to absence of substrate binding. 1 Publication
    Mutagenesisi277 – 2771H → N: 35-fold decrease in activity. 59-fold decrease in substrate affinity. 1 Publication
    Mutagenesisi325 – 3251H → N: Loss of activity. 2-fold decrease in substrate affinity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 401401L-rhamnonate dehydratasePRO_0000171262Add
    BLAST

    Proteomic databases

    PaxDbiP77215.

    Interactioni

    Subunit structurei

    Homooctamer; tetramer of dimers.1 Publication

    Protein-protein interaction databases

    BioGridi4261221. 139 interactions.
    DIPiDIP-11955N.
    IntActiP77215. 11 interactions.
    STRINGi511145.b2247.

    Structurei

    Secondary structure

    1
    401
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi5 – 1612Combined sources
    Turni44 – 474Combined sources
    Turni49 – 513Combined sources
    Beta strandi65 – 728Combined sources
    Beta strandi77 – 837Combined sources
    Helixi85 – 9410Combined sources
    Helixi97 – 1004Combined sources
    Helixi108 – 11811Combined sources
    Helixi120 – 1234Combined sources
    Helixi127 – 14822Combined sources
    Helixi152 – 1554Combined sources
    Beta strandi160 – 17112Combined sources
    Helixi173 – 1786Combined sources
    Beta strandi182 – 1876Combined sources
    Helixi192 – 1943Combined sources
    Helixi195 – 21319Combined sources
    Beta strandi215 – 2228Combined sources
    Helixi229 – 23911Combined sources
    Helixi240 – 2423Combined sources
    Beta strandi246 – 2483Combined sources
    Helixi256 – 26510Combined sources
    Beta strandi271 – 2744Combined sources
    Helixi281 – 2888Combined sources
    Turni289 – 2913Combined sources
    Beta strandi293 – 2953Combined sources
    Turni299 – 3035Combined sources
    Helixi305 – 31713Combined sources
    Helixi329 – 3357Combined sources
    Beta strandi344 – 3474Combined sources
    Beta strandi350 – 3534Combined sources
    Turni359 – 3635Combined sources
    Beta strandi364 – 3663Combined sources
    Beta strandi374 – 3763Combined sources
    Helixi377 – 3804Combined sources
    Beta strandi382 – 3843Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2I5QX-ray2.10A/B1-401[»]
    ProteinModelPortaliP77215.
    SMRiP77215. Positions 1-401.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP77215.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105CXK. Bacteria.
    COG4948. LUCA.
    HOGENOMiHOG000113755.
    InParanoidiP77215.
    KOiK12661.
    OrthoDBiEOG68Q0M0.
    PhylomeDBiP77215.

    Family and domain databases

    Gene3Di3.20.20.120. 1 hit.
    3.30.390.10. 1 hit.
    HAMAPiMF_01288. Rhamnon_dehydrat.
    InterProiIPR029065. Enolase_C-like.
    IPR029017. Enolase_N-like.
    IPR023444. L-Rhamnon_dehydrat.
    IPR018110. Mandel_Rmase/mucon_lact_enz_CS.
    IPR013342. Mandelate_racemase_C.
    IPR013341. Mandelate_racemase_N_dom.
    IPR001354. MR/MLE/MAL.
    [Graphical view]
    PANTHERiPTHR13794. PTHR13794. 1 hit.
    PfamiPF13378. MR_MLE_C. 1 hit.
    PF02746. MR_MLE_N. 1 hit.
    [Graphical view]
    SMARTiSM00922. MR_MLE. 1 hit.
    [Graphical view]
    SUPFAMiSSF51604. SSF51604. 1 hit.
    SSF54826. SSF54826. 1 hit.
    PROSITEiPS00908. MR_MLE_1. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P77215-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MTLPKIKQVR AWFTGGATAE KGAGGGDYHD QGANHWIDDH IATPMSKYRD
    60 70 80 90 100
    YEQSRQSFGI NVLGTLVVEV EAENGQTGFA VSTAGEMGCF IVEKHLNRFI
    110 120 130 140 150
    EGKCVSDIKL IHDQMLSATL YYSGSGGLVM NTISCVDLAL WDLFGKVVGL
    160 170 180 190 200
    PVYKLLGGAV RDEIQFYATG ARPDLAKEMG FIGGKMPTHW GPHDGDAGIR
    210 220 230 240 250
    KDAAMVADMR EKCGEDFWLM LDCWMSQDVN YATKLAHACA PYNLKWIEEC
    260 270 280 290 300
    LPPQQYESYR ELKRNAPVGM MVTSGEHHGT LQSFRTLSET GIDIMQPDVG
    310 320 330 340 350
    WCGGLTTLVE IAAIAKSRGQ LVVPHGSSVY SHHAVITFTN TPFSEFLMTS
    360 370 380 390 400
    PDCSTMRPQF DPILLNEPVP VNGRIHKSVL DKPGFGVELN RDCNLKRPYS

    H
    Length:401
    Mass (Da):44,226
    Last modified:November 24, 2009 - v2
    Checksum:i4622CE539229AD58
    GO

    Sequence cautioni

    The sequence BAA16071.1 differs from that shown. Reason: Erroneous initiation. Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U00096 Genomic DNA. Translation: AAC75307.2.
    AP009048 Genomic DNA. Translation: BAA16071.1. Different initiation.
    PIRiE64995.
    RefSeqiNP_416750.2. NC_000913.3.
    WP_001319848.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC75307; AAC75307; b2247.
    BAA16071; BAA16071; BAA16071.
    GeneIDi945881.
    KEGGiecj:JW2241.
    eco:b2247.
    PATRICi32119857. VBIEscCol129921_2338.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U00096 Genomic DNA. Translation: AAC75307.2.
    AP009048 Genomic DNA. Translation: BAA16071.1. Different initiation.
    PIRiE64995.
    RefSeqiNP_416750.2. NC_000913.3.
    WP_001319848.1. NZ_LN832404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2I5QX-ray2.10A/B1-401[»]
    ProteinModelPortaliP77215.
    SMRiP77215. Positions 1-401.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4261221. 139 interactions.
    DIPiDIP-11955N.
    IntActiP77215. 11 interactions.
    STRINGi511145.b2247.

    Proteomic databases

    PaxDbiP77215.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC75307; AAC75307; b2247.
    BAA16071; BAA16071; BAA16071.
    GeneIDi945881.
    KEGGiecj:JW2241.
    eco:b2247.
    PATRICi32119857. VBIEscCol129921_2338.

    Organism-specific databases

    EchoBASEiEB3838.
    EcoGeneiEG14085. rhmD.

    Phylogenomic databases

    eggNOGiENOG4105CXK. Bacteria.
    COG4948. LUCA.
    HOGENOMiHOG000113755.
    InParanoidiP77215.
    KOiK12661.
    OrthoDBiEOG68Q0M0.
    PhylomeDBiP77215.

    Enzyme and pathway databases

    BioCyciEcoCyc:G7160-MONOMER.
    ECOL316407:JW2241-MONOMER.
    MetaCyc:G7160-MONOMER.
    BRENDAi4.2.1.90. 2165.

    Miscellaneous databases

    EvolutionaryTraceiP77215.
    PROiP77215.

    Family and domain databases

    Gene3Di3.20.20.120. 1 hit.
    3.30.390.10. 1 hit.
    HAMAPiMF_01288. Rhamnon_dehydrat.
    InterProiIPR029065. Enolase_C-like.
    IPR029017. Enolase_N-like.
    IPR023444. L-Rhamnon_dehydrat.
    IPR018110. Mandel_Rmase/mucon_lact_enz_CS.
    IPR013342. Mandelate_racemase_C.
    IPR013341. Mandelate_racemase_N_dom.
    IPR001354. MR/MLE/MAL.
    [Graphical view]
    PANTHERiPTHR13794. PTHR13794. 1 hit.
    PfamiPF13378. MR_MLE_C. 1 hit.
    PF02746. MR_MLE_N. 1 hit.
    [Graphical view]
    SMARTiSM00922. MR_MLE. 1 hit.
    [Graphical view]
    SUPFAMiSSF51604. SSF51604. 1 hit.
    SSF54826. SSF54826. 1 hit.
    PROSITEiPS00908. MR_MLE_1. 1 hit.
    [Graphical view]
    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. "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: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS), FUNCTION, SUBSTRATE SPECIFICITY, KINETIC PARAMETERS, SUBUNIT, CATALYTIC MECHANISM, REACTION STEREOCHEMISTRY, MUTAGENESIS OF HIS-29; HIS-277 AND HIS-325.
      Strain: K12 / MG1655 / ATCC 47076.

    Entry informationi

    Entry nameiRHMD_ECOLI
    AccessioniPrimary (citable) accession number: P77215
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 30, 2000
    Last sequence update: November 24, 2009
    Last modified: January 20, 2016
    This is version 126 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Reaction proceeds via a syn dehydration.

    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.