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Protein

L-rhamnonate dehydratase

Gene

rhmD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -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

Miscellaneous

Reaction proceeds via a syn dehydration.

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)DescriptionActionsGraphical viewLength
    Binding sitei29Substrate1
    Binding sitei55SubstrateBy similarity1
    Metal bindingi222MagnesiumBy similarity1
    Metal bindingi248MagnesiumBy similarity1
    Metal bindingi276MagnesiumBy similarity1
    Sitei298Increases basicity of active site HisBy similarity1
    Active sitei325Proton acceptor1
    Binding sitei345SubstrateBy similarity1
    Sitei345Transition state stabilizerBy similarity1

    GO - Molecular functioni

    • identical protein binding Source: EcoCyc
    • L-rhamnonate dehydratase activity Source: EcoCyc
    • metal ion binding Source: UniProtKB-KW

    GO - Biological processi

    Keywordsi

    Molecular functionLyase
    LigandMagnesium, Metal-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:G7160-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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG14085 rhmD

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi29H → N: Loss of activity due to absence of substrate binding. 1 Publication1
    Mutagenesisi277H → N: 35-fold decrease in activity. 59-fold decrease in substrate affinity. 1 Publication1
    Mutagenesisi325H → N: Loss of activity. 2-fold decrease in substrate affinity. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001712621 – 401L-rhamnonate dehydrataseAdd BLAST401

    Proteomic databases

    PaxDbiP77215
    PRIDEiP77215

    Interactioni

    Subunit structurei

    Homooctamer; tetramer of dimers.1 Publication

    GO - Molecular functioni

    • identical protein binding Source: EcoCyc

    Protein-protein interaction databases

    BioGridi4261221, 144 interactors
    DIPiDIP-11955N
    IntActiP77215, 11 interactors
    STRINGi316385.ECDH10B_2407

    Structurei

    Secondary structure

    1401
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi5 – 16Combined sources12
    Turni44 – 47Combined sources4
    Turni49 – 51Combined sources3
    Beta strandi65 – 72Combined sources8
    Beta strandi77 – 83Combined sources7
    Helixi85 – 94Combined sources10
    Helixi97 – 100Combined sources4
    Helixi108 – 118Combined sources11
    Helixi120 – 123Combined sources4
    Helixi127 – 148Combined sources22
    Helixi152 – 155Combined sources4
    Beta strandi160 – 171Combined sources12
    Helixi173 – 178Combined sources6
    Beta strandi182 – 187Combined sources6
    Helixi192 – 194Combined sources3
    Helixi195 – 213Combined sources19
    Beta strandi215 – 222Combined sources8
    Helixi229 – 239Combined sources11
    Helixi240 – 242Combined sources3
    Beta strandi246 – 248Combined sources3
    Helixi256 – 265Combined sources10
    Beta strandi271 – 274Combined sources4
    Helixi281 – 288Combined sources8
    Turni289 – 291Combined sources3
    Beta strandi293 – 295Combined sources3
    Turni299 – 303Combined sources5
    Helixi305 – 317Combined sources13
    Helixi329 – 335Combined sources7
    Beta strandi344 – 347Combined sources4
    Beta strandi350 – 353Combined sources4
    Turni359 – 363Combined sources5
    Beta strandi364 – 366Combined sources3
    Beta strandi374 – 376Combined sources3
    Helixi377 – 380Combined sources4
    Beta strandi382 – 384Combined sources3

    3D structure databases

    ProteinModelPortaliP77215
    SMRiP77215
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP77215

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105CXK Bacteria
    COG4948 LUCA
    HOGENOMiHOG000113755
    InParanoidiP77215
    KOiK12661
    PhylomeDBiP77215

    Family and domain databases

    Gene3Di3.20.20.120, 1 hit
    3.30.390.10, 1 hit
    HAMAPiMF_01288 Rhamnon_dehydrat, 1 hit
    InterProiView protein in InterPro
    IPR036849 Enolase-like_C_sf
    IPR029017 Enolase-like_N
    IPR034390 Enolase-like_superfamily
    IPR029065 Enolase_C-like
    IPR023444 L-Rhamnon_dehydrat
    IPR018110 Mandel_Rmase/mucon_lact_enz_CS
    IPR034593 Mandelate_racemase-like
    IPR013342 Mandelate_racemase_C
    IPR013341 Mandelate_racemase_N_dom
    PANTHERiPTHR13794:SF59 PTHR13794:SF59, 1 hit
    PfamiView protein in Pfam
    PF13378 MR_MLE_C, 1 hit
    PF02746 MR_MLE_N, 1 hit
    SFLDiSFLDF00006 rhamnonate_dehydratase, 1 hit
    SFLDG00179 mandelate_racemase, 1 hit
    SFLDS00001 Enolase, 1 hit
    SMARTiView protein in SMART
    SM00922 MR_MLE, 1 hit
    SUPFAMiSSF51604 SSF51604, 1 hit
    PROSITEiView protein in PROSITE
    PS00908 MR_MLE_1, 1 hit

    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 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
    PATRICifig|511145.12.peg.2338

    Similar proteinsi

    Entry informationi

    Entry nameiRHMD_ECOLI
    AccessioniPrimary (citable) accession number: P77215
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 30, 2000
    Last sequence update: November 24, 2009
    Last modified: February 28, 2018
    This is version 138 of the entry and version 2 of the sequence. See 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

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