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Protein

dTDP-4-dehydro-6-deoxyglucose 3-epimerase

Gene

chmJ

Organism
Streptomyces bikiniensis
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the conversion of dTDP-4-oxo-6-deoxyglucose to dTDP-4-oxo-6-deoxyallose, via a C-3 epimerization. This is a step in the biosynthesis of the mycinose moiety of the chalcomycin antibiotic.1 Publication

Catalytic activityi

dTDP-4-dehydro-6-deoxy-alpha-D-glucose = dTDP-4-dehydro-6-deoxy-alpha-D-allose.1 Publication

Kineticsi

kcat is 6.4 sec(-1).

  1. KM=04 mM for dTDP-4-dehydro-6-deoxy-alpha-D-glucose

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei21 – 211Substrate
    Binding sitei26 – 261Substrate
    Binding sitei45 – 451Substrate
    Binding sitei57 – 571Substrate
    Active sitei60 – 601Proton acceptor1 Publication
    Binding sitei70 – 701Substrate
    Binding sitei117 – 1171Substrate
    Active sitei130 – 1301Proton donor1 Publication
    Binding sitei136 – 1361Substrate
    Binding sitei141 – 1411Substrate

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Isomerase

    Keywords - Biological processi

    Antibiotic biosynthesis, Carbohydrate metabolism

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    dTDP-4-dehydro-6-deoxyglucose 3-epimerase (EC:5.1.3.27)
    Alternative name(s):
    dTDP-4-dehydro-6-deoxy-D-glucose 3-epimerase
    dTDP-4-keto-6-deoxyglucose epimerase
    dTDP-4-oxo-6-deoxy-D-glucose epimerase
    Gene namesi
    Name:chmJ
    OrganismiStreptomyces bikiniensis
    Taxonomic identifieri1896 [NCBI]
    Taxonomic lineageiBacteriaActinobacteriaStreptomycetalesStreptomycetaceaeStreptomyces

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi60 – 601H → N: No effect on substrate affinity, but 2400-fold reduction in activity. 1 Publication
    Mutagenesisi130 – 1301Y → F: Slight decrease in substrate affinity, and 1650-fold reduction in activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 196196dTDP-4-dehydro-6-deoxyglucose 3-epimerasePRO_0000425106Add
    BLAST

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Structurei

    Secondary structure

    1
    196
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi9 – 124Combined sources
    Beta strandi16 – 194Combined sources
    Beta strandi22 – 298Combined sources
    Helixi30 – 378Combined sources
    Beta strandi45 – 517Combined sources
    Beta strandi55 – 628Combined sources
    Beta strandi64 – 663Combined sources
    Beta strandi70 – 8415Combined sources
    Turni91 – 944Combined sources
    Beta strandi96 – 1027Combined sources
    Turni103 – 1053Combined sources
    Beta strandi108 – 1114Combined sources
    Beta strandi116 – 1216Combined sources
    Beta strandi126 – 1349Combined sources
    Helixi138 – 1403Combined sources
    Beta strandi141 – 1433Combined sources
    Turni149 – 1513Combined sources
    Helixi165 – 1684Combined sources
    Helixi173 – 1786Combined sources
    Helixi185 – 19612Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4HMZX-ray2.00A/B/C/D1-196[»]
    4HN0X-ray2.20A/B/C/D1-196[»]
    4HN1X-ray1.60A/B/C/D1-196[»]
    ProteinModelPortaliQ5SFD1.
    SMRiQ5SFD1. Positions 2-189.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Family and domain databases

    Gene3Di2.60.120.10. 1 hit.
    InterProiIPR000888. dTDP_sugar_isom.
    IPR014710. RmlC-like_jellyroll.
    IPR011051. RmlC_Cupin.
    [Graphical view]
    PANTHERiPTHR21047. PTHR21047. 1 hit.
    PfamiPF00908. dTDP_sugar_isom. 1 hit.
    [Graphical view]
    ProDomiPD001462. dTDP_sugar_isom. 1 hit.
    [Graphical view] [Entries sharing at least one domain]
    SUPFAMiSSF51182. SSF51182. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Q5SFD1-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MHPLSIEGAW SQEPVIHSDH RGRSHEWFRG ESFRQAFGHD FPVAQVNVAV
    60 70 80 90 100
    SHRGALRGIH YTEIPPGQAK YSVCVRGAGL DVVVDVRIGS PTFGRWEIVP
    110 120 130 140 150
    MDAERNTAVY LTAGLGRAFL SLTDDATLVY LCSSGYAPAR EHSVNPLDPD
    160 170 180 190
    LGIAWPDDIE PLLSDRDENA PTLATAERLG LLPTYQAWQE QQQAQR
    Length:196
    Mass (Da):21,683
    Last modified:December 21, 2004 - v1
    Checksum:i26C8CD880701F1CA
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AY509120 Genomic DNA. Translation: AAS79451.1.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AY509120 Genomic DNA. Translation: AAS79451.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4HMZX-ray2.00A/B/C/D1-196[»]
    4HN0X-ray2.20A/B/C/D1-196[»]
    4HN1X-ray1.60A/B/C/D1-196[»]
    ProteinModelPortaliQ5SFD1.
    SMRiQ5SFD1. Positions 2-189.
    ModBaseiSearch...
    MobiDBiSearch...

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Family and domain databases

    Gene3Di2.60.120.10. 1 hit.
    InterProiIPR000888. dTDP_sugar_isom.
    IPR014710. RmlC-like_jellyroll.
    IPR011051. RmlC_Cupin.
    [Graphical view]
    PANTHERiPTHR21047. PTHR21047. 1 hit.
    PfamiPF00908. dTDP_sugar_isom. 1 hit.
    [Graphical view]
    ProDomiPD001462. dTDP_sugar_isom. 1 hit.
    [Graphical view] [Entries sharing at least one domain]
    SUPFAMiSSF51182. SSF51182. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    1. "Chalcomycin biosynthesis gene cluster from Streptomyces bikiniensis: novel features of an unusual ketolide produced through expression of the chm polyketide synthase in Streptomyces fradiae."
      Ward S.L., Hu Z., Schirmer A., Reid R., Revill W.P., Reeves C.D., Petrakovsky O.V., Dong S.D., Katz L.
      Antimicrob. Agents Chemother. 48:4703-4712(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: NRRL 2737.
    2. "Structural and functional studies on a 3'-epimerase involved in the biosynthesis of dTDP-6-deoxy-D-allose."
      Kubiak R.L., Phillips R.K., Zmudka M.W., Ahn M.R., Maka E.M., Pyeatt G.L., Roggensack S.J., Holden H.M.
      Biochemistry 51:9375-9383(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) OF APOENZYME; COMPLEX WITH DTDP-QUINOVOSE AND MUTANT ASN-60/PHE-130 IN COMPLEX WITH DTDP, FUNCTION, CATALYTIC ACTIVITY, SUBUNIT, ACTIVE SITES, MUTAGENESIS OF HIS-60 AND TYR-130.
      Strain: NRRL 2737.

    Entry informationi

    Entry nameiCHMJ_STRBI
    AccessioniPrimary (citable) accession number: Q5SFD1
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 22, 2014
    Last sequence update: December 21, 2004
    Last modified: June 24, 2015
    This is version 32 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3

    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 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.