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Protein

L-rhamnonate dehydratase

Gene

rhmD

Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
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 and L-mannonate, 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+1 PublicationNote: Binds 1 Mg2+ ion per subunit.1 Publication

Kineticsi

The catalytic efficiency observed with L-rhamnonate as substrate is 533- and 8-fold higher than that observed with L-lyxonate and L-mannonate, respectively.

  1. KM=0.25 mM for L-rhamnonate1 Publication
  2. KM=1.6 mM for L-lyxonate1 Publication
  3. KM=0.06 mM for L-mannonate1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei33 – 331Substrate
    Binding sitei59 – 591Substrate
    Metal bindingi226 – 2261Magnesium
    Metal bindingi252 – 2521Magnesium
    Metal bindingi280 – 2801Magnesium
    Sitei302 – 3021Increases basicity of active site His
    Active sitei329 – 3291Proton acceptor
    Binding sitei349 – 3491Substrate
    Sitei349 – 3491Transition state stabilizer

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Lyase

    Keywords - Ligandi

    Magnesium, Metal-binding

    Enzyme and pathway databases

    BioCyciSENT99287:GCTI-2306-MONOMER.
    BRENDAi4.2.1.90. 5542.

    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:STM2291
    OrganismiSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
    Taxonomic identifieri99287 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeSalmonella
    Proteomesi
    • UP000001014 Componenti: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 405405L-rhamnonate dehydratasePRO_0000351707Add
    BLAST

    Proteomic databases

    PaxDbiQ8ZNF9.
    PRIDEiQ8ZNF9.

    Interactioni

    Subunit structurei

    Homooctamer; tetramer of dimers.1 Publication

    Protein-protein interaction databases

    STRINGi99287.STM2291.

    Structurei

    Secondary structure

    1
    405
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi9 – 2012Combined sources
    Helixi40 – 423Combined sources
    Turni48 – 514Combined sources
    Helixi53 – 553Combined sources
    Helixi60 – 623Combined sources
    Turni63 – 653Combined sources
    Beta strandi69 – 768Combined sources
    Beta strandi81 – 877Combined sources
    Helixi89 – 9810Combined sources
    Helixi101 – 1044Combined sources
    Helixi112 – 12312Combined sources
    Turni124 – 1263Combined sources
    Helixi132 – 15221Combined sources
    Helixi156 – 1594Combined sources
    Beta strandi164 – 17512Combined sources
    Helixi177 – 1837Combined sources
    Beta strandi186 – 1916Combined sources
    Helixi196 – 1983Combined sources
    Helixi199 – 21719Combined sources
    Beta strandi219 – 2268Combined sources
    Helixi233 – 24311Combined sources
    Helixi244 – 2463Combined sources
    Beta strandi250 – 2523Combined sources
    Helixi260 – 26910Combined sources
    Beta strandi275 – 2784Combined sources
    Helixi285 – 2939Combined sources
    Beta strandi297 – 2993Combined sources
    Helixi303 – 3064Combined sources
    Helixi309 – 32113Combined sources
    Helixi332 – 3398Combined sources
    Beta strandi348 – 3514Combined sources
    Beta strandi357 – 3593Combined sources
    Turni363 – 3675Combined sources
    Beta strandi378 – 3803Combined sources
    Helixi381 – 3844Combined sources
    Beta strandi386 – 3883Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2GSHX-ray2.39A/B2-405[»]
    2P3ZX-ray1.80A/B2-405[»]
    3BOXX-ray1.80A/B2-405[»]
    3CXOX-ray2.00A/B2-405[»]
    3D46X-ray1.90A/B/C/D/E/F/G/H1-405[»]
    3D47X-ray1.80A/B/C/D/E/F/G/H1-405[»]
    ProteinModelPortaliQ8ZNF9.
    SMRiQ8ZNF9. Positions 1-405.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ8ZNF9.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105CXK. Bacteria.
    COG4948. LUCA.
    HOGENOMiHOG000113755.
    KOiK12661.
    OMAiINWWEEC.
    OrthoDBiEOG68Q0M0.
    PhylomeDBiQ8ZNF9.

    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.

    Q8ZNF9-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MENIMTLPKI KHVRAWFIGG ATAEKGAGGG DYHDQGGNHW IDDHIATPMS
    60 70 80 90 100
    KYRDYEQSRQ SFGINVLGTL IVEVEAENRQ TGFAVSTAGE MGCFIVEKHL
    110 120 130 140 150
    NRFIEGKCVS DIKLIHDQML GATMYYSGSG GLVMNTISCV DLALWDLFGK
    160 170 180 190 200
    VVGLPVYKLL GGAVRDEIQF YATGARPDLA KEMGFIGGKM PTHWGPHDGD
    210 220 230 240 250
    AGIRKDAAMV ADMREKCGPD FWLMLDCWMS QDVNYATKLA HACAPFNLKW
    260 270 280 290 300
    IEECLPPQQY EGYRELKRNA PAGMMVTSGE HHGTLQSFRT LAETGIDIMQ
    310 320 330 340 350
    PDVGWCGGLT TLVEIAALAK SRGQLVVPHG SSVYSHHAVI TFTNTPFSEF
    360 370 380 390 400
    LMTSPDCSTL RPQFDPILLD EPVPVNGRIH KSVLDKPGFG VELNRDCHLK

    RPYSH
    Length:405
    Mass (Da):44,706
    Last modified:March 1, 2002 - v1
    Checksum:i69787FA29E2939E5
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AE006468 Genomic DNA. Translation: AAL21192.1.
    RefSeqiNP_461233.1. NC_003197.1.
    WP_000427827.1. NC_003197.1.

    Genome annotation databases

    EnsemblBacteriaiAAL21192; AAL21192; STM2291.
    GeneIDi1253813.
    KEGGistm:STM2291.
    PATRICi32383191. VBISalEnt20916_2425.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AE006468 Genomic DNA. Translation: AAL21192.1.
    RefSeqiNP_461233.1. NC_003197.1.
    WP_000427827.1. NC_003197.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2GSHX-ray2.39A/B2-405[»]
    2P3ZX-ray1.80A/B2-405[»]
    3BOXX-ray1.80A/B2-405[»]
    3CXOX-ray2.00A/B2-405[»]
    3D46X-ray1.90A/B/C/D/E/F/G/H1-405[»]
    3D47X-ray1.80A/B/C/D/E/F/G/H1-405[»]
    ProteinModelPortaliQ8ZNF9.
    SMRiQ8ZNF9. Positions 1-405.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi99287.STM2291.

    Proteomic databases

    PaxDbiQ8ZNF9.
    PRIDEiQ8ZNF9.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAL21192; AAL21192; STM2291.
    GeneIDi1253813.
    KEGGistm:STM2291.
    PATRICi32383191. VBISalEnt20916_2425.

    Phylogenomic databases

    eggNOGiENOG4105CXK. Bacteria.
    COG4948. LUCA.
    HOGENOMiHOG000113755.
    KOiK12661.
    OMAiINWWEEC.
    OrthoDBiEOG68Q0M0.
    PhylomeDBiQ8ZNF9.

    Enzyme and pathway databases

    BioCyciSENT99287:GCTI-2306-MONOMER.
    BRENDAi4.2.1.90. 5542.

    Miscellaneous databases

    EvolutionaryTraceiQ8ZNF9.

    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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: LT2 / SGSC1412 / ATCC 700720.
    2. "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 (1.8 ANGSTROMS) IN COMPLEXES WITH MAGNESIUM AND SUBSTRATE ANALOG, FUNCTION, SUBSTRATE SPECIFICITY, COFACTOR, KINETIC PARAMETERS, SUBUNIT, CATALYTIC MECHANISM, REACTION STEREOCHEMISTRY.
      Strain: LT2 / SGSC1412 / ATCC 700720.

    Entry informationi

    Entry nameiRHMD_SALTY
    AccessioniPrimary (citable) accession number: Q8ZNF9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 14, 2008
    Last sequence update: March 1, 2002
    Last modified: January 20, 2016
    This is version 87 of the entry and version 1 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. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. 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.