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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)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

    Complete GO annotation...

    Keywords - Molecular functioni

    Lyase

    Keywords - Ligandi

    Magnesium, Metal-binding

    Enzyme and pathway databases

    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.
    OMAiINWWEEC.
    PhylomeDBiQ8ZNF9.

    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.

    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
    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...

    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.
    PhylomeDBiQ8ZNF9.

    Enzyme and pathway databases

    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. 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_SALTY
    AccessioniPrimary (citable) accession number: Q8ZNF9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 14, 2008
    Last sequence update: March 1, 2002
    Last modified: November 2, 2016
    This is version 90 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.