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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)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

    • 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 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

    Protein-protein interaction databases

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

    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

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

    Protein-protein interaction databases

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

    Proteomic databases

    PaxDbiP77215.
    PRIDEiP77215.

    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.
    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. 1 hit.
    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...

    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: November 2, 2016
    This is version 129 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.