The Open Protein Structure Annotation Network
PDB Keyword


    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary
    3. 3. References

    Title Crystal structure of DTDP-4-dehydrorhamnose reductase, rfbD ortholog (CAC2315) from Clostridium acetobutylicum at 2.05 A resolution. To be published
    Site JCSG
    PDB Id 1vl0 Target Id 355809
    Molecular Characteristics
    Source Clostridium acetobutylicum atcc 824
    Alias Ids TPS1350,15025322 Molecular Weight 31529.52 Da.
    Residues 280 Isoelectric Point 5.71
    Sequence mkilitgangqlgreiqkqlkgknveviptdvqdlditnvlavnkffnekkpnvvincaahtavdkcee qydlaykinaigpknlaaaaysvgaeivqistdyvfdgeakepitefdevnpqsaygktklegenfvka lnpkyyivrtawlygdgnnfvktminlgkthdelkvvhdqvgtptstvdlarvvlkvideknygtfhct ckgicswydfaveifrltgidvkvtpctteefprpakrpkysvlrnymlelttgditrewkeslkeyid llqm
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 3
    Resolution (Å) 2.05 Rfree 0.20701
    Matthews' coefficent 2.64 Rfactor 0.16921
    Waters 451 Solvent Content 53.40

    Ligand Information


    Google Scholar output for 1vl0
    1. The Buccaneer software for automated model building. 1. Tracing protein chains
    K Cowtan - Acta Crystallographica Section D: Biological , 2006 - scripts.iucr.org
    2. Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard
    TC Terwilliger, PD Adams, RJ Read - Section D: Biological , 2009 - scripts.iucr.org
    3. Fast and accurate algorithms for protein side-chain packing
    J Xu, B Berger - Journal of the ACM (JACM), 2006 - dl.acm.org
    M ADENOSYLTRANSFERASE - METHIONINE , 2011 - Wiley Online Library
    5. Modeling of folds and folding pathways for some protein families of (_+ _)-and (_/_)-classes
    AB Gordeev, AV Efimov - 2012 - Taylor & Francis

    Protein Summary

    The gene CA_C2315 from Clostridium acetobutylicum encodes an enzyme DTDP-4-dehydrorhamnose reductase PFAM:PF04321, EC: COG1091.  Alternative names: dTDP-4-keto-L-rhamnose reductase, dTDP-6-deoxy-L-mannose dehydrogenase.  The enzyme belongs to the class of alpha and beta (a+b) proteins and reveals NAD(P)-binding Rossmann-fold domains SCOP51734SUNID:51751. It belongs to the large SDR (short chain dehydrogenase/reductase) family, a branch of the RED (reductases/epimerases/dehydrogenases) superfamily. SDR family members are predominantly monomeric or dimeric, with dimers of dimers also significantly represented. 1vl0 presents a unique trimeric arrangement. The enzyme catalyzes the following reaction: dTDP-6-deoxy-L-mannose + NADP(+) <=> dTDP-4-dehydro-6-deoxy-L-mannose + NADPH.  The enzyme participates in 3 metabolic pathways: nucleotide sugars metabolism, streptomycin biosynthesis, and polyketide sugar unit biosynthesis.

    Ligand Summary





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