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Protein

L-rhamnonate dehydratase

Gene

rhmD

Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
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 and L-mannonate, 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+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)DescriptionActionsGraphical viewLength
    Binding sitei33Substrate1
    Binding sitei59Substrate1
    Metal bindingi226Magnesium1
    Metal bindingi252Magnesium1
    Metal bindingi280Magnesium1
    Sitei302Increases basicity of active site His1
    Active sitei329Proton acceptor1
    Binding sitei349Substrate1
    Sitei349Transition state stabilizer1

    GO - Molecular functioni

    GO - Biological processi

    Keywordsi

    Molecular functionLyase
    LigandMagnesium, Metal-binding

    Enzyme and pathway databases

    BioCyciSENT99287:G1FZD-2312-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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeSalmonella
    Proteomesi
    • UP000001014 Componenti: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00003517071 – 405L-rhamnonate dehydrataseAdd BLAST405

    Proteomic databases

    PaxDbiQ8ZNF9
    PRIDEiQ8ZNF9

    Interactioni

    Subunit structurei

    Homooctamer; tetramer of dimers.1 Publication

    Protein-protein interaction databases

    STRINGi99287.STM2291

    Structurei

    Secondary structure

    1405
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi9 – 20Combined sources12
    Helixi40 – 42Combined sources3
    Turni48 – 51Combined sources4
    Helixi53 – 55Combined sources3
    Helixi60 – 62Combined sources3
    Turni63 – 65Combined sources3
    Beta strandi69 – 76Combined sources8
    Beta strandi81 – 87Combined sources7
    Helixi89 – 98Combined sources10
    Helixi101 – 104Combined sources4
    Helixi112 – 123Combined sources12
    Turni124 – 126Combined sources3
    Helixi132 – 152Combined sources21
    Helixi156 – 159Combined sources4
    Beta strandi164 – 175Combined sources12
    Helixi177 – 183Combined sources7
    Beta strandi186 – 191Combined sources6
    Helixi196 – 198Combined sources3
    Helixi199 – 217Combined sources19
    Beta strandi219 – 226Combined sources8
    Helixi233 – 243Combined sources11
    Helixi244 – 246Combined sources3
    Beta strandi250 – 252Combined sources3
    Helixi260 – 269Combined sources10
    Beta strandi275 – 278Combined sources4
    Helixi285 – 293Combined sources9
    Beta strandi297 – 299Combined sources3
    Helixi303 – 306Combined sources4
    Helixi309 – 321Combined sources13
    Helixi332 – 339Combined sources8
    Beta strandi348 – 351Combined sources4
    Beta strandi357 – 359Combined sources3
    Turni363 – 367Combined sources5
    Beta strandi378 – 380Combined sources3
    Helixi381 – 384Combined sources4
    Beta strandi386 – 388Combined sources3

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB 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
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ8ZNF9

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105CXK Bacteria
    COG4948 LUCA
    HOGENOMiHOG000113755
    KOiK12661
    OMAiNINWWEE
    PhylomeDBiQ8ZNF9

    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.

    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_003197.2
    WP_000427827.1, NC_003197.2

    Genome annotation databases

    EnsemblBacteriaiAAL21192; AAL21192; STM2291
    GeneIDi1253813
    KEGGistm:STM2291
    PATRICifig|99287.12.peg.2425

    Similar proteinsi

    Entry informationi

    Entry nameiRHMD_SALTY
    AccessioniPrimary (citable) accession number: Q8ZNF9
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 14, 2008
    Last sequence update: March 1, 2002
    Last modified: March 28, 2018
    This is version 98 of the entry and version 1 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
    UniProt is an ELIXIR core data resource
    Main funding by: National Institutes of Health