The Open Protein Structure Annotation Network
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    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary
    3. 3. References

    Title Crystal structure of glycerol dehydrogenase (NP_348253.1) from Clostridium acetobutylicum at 2.37 A resolution. To be published
    Site JCSG
    PDB Id 3ce9 Target Id 379134
    Molecular Characteristics
    Source Clostridium acetobutylicum atcc 824
    Alias Ids TPS1732,NP_348253.1, _0066.000283_, RER070207002353, 335497 Molecular Weight 39126.04 Da.
    Residues 353 Isoelectric Point 7.14
    Sequence mkgishriaiplilevgnnkiynigqiikkgnfkrvslyfgegiyelfgetieksikssnieieavetv knidfdeigtnafkipaevdaligigggkaidavkymaflrklpfisvptstsndgfsspvasllingk rtsvpaktpdgivvdidvikgspekfiysgigdlvsnitalydwkfeeenhksiiddfavmiskksvns fvrtdfksikdevflkelvdsltmngiameiagnsspasgaehlishaldkflpnpqlhgiqvgvatyi mskvhkhreerikkilsdtgffnyvkglnmkksdfkraiseahlikparytylhvekncetakeivdtd eilrnilv
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 4
    Resolution (Å) 2.37 Rfree 0.214
    Matthews' coefficent 2.66 Rfactor 0.188
    Waters 199 Solvent Content 53.71

    Ligand Information


    Google Scholar output for 3ce9
    1. Characterization of the interaction of interleukin-8 with hyaluronan, chondroitin sulfate, dermatan sulfate and their sulfated derivatives by spectroscopy and molecular
    A Pichert, SA Samsonov, S Theisgen, L Thomas - , 2012 - Soc Glycobiology
    2. Docking glycosaminoglycans to proteins: analysis of solvent inclusion
    SA Samsonov, J Teyra, MT Pisabarro - Journal of computer-aided , 2011 - Springer

    Protein Summary

    The crystal structure contains four protein monomers per asymmetric unit of the crystal lattice. Crystal packing suggests that a tetramer should be the biologically relevant oligomeric form. Analytical SEC indicates the possibility of a dimer, but with low confidence.

    PSI-BLAST (1 round) returns hits with 3-dehydroquinate synthase, gylcerol dehydrogenases and conserved hypothetical proteins with sequence identities ranging from 69% (exp=2e-139) to 27% id (exp=7e-05). There are several PDB structures of proteins in this range: 
    1KQ3 (Crystal Structure Of Glycerol Dehydrogenase (Tm0423) From Thermotoga Maritima, 1TA9 (Crystal Structure Of Glycerol Dehydrogenase From Schizosaccharomyces Pombe) and 1JPU (Bacillus Stearothermophilus Glycerol Dehydrogenase Complex With Glycerol) .
    According to JCSG/TVPC, low similarity (30% id over ~43% coverage to 24%id over ~78% coverage) to PDB ids 1KQ3, 1TA9, 1JPU, 1JQ5, 1JQA. The top DALI hits are 1JQA, 1OJ7, 1O2D, 1DQS, and 2D2X.

    This protein could belong to one of two possible Pfams: PF01761:DHQ_synthase; PF00465: Fe-ADH.

    The figure below depicts the superimposition of this protein (red) on the 1JQA (Bacillus stearothermophilus glycerol dehydrogenase complex with glycerol) structure.

    There is a zinc ion bound (verified by fluorescence scan and anomalous difference Fourier maps) to the putative active site that can be defined based on the structural similarity to 1JQA (which also has a bound zinc):

    Detail of the putative active site comprised of Asp171, H250 and H266. Identically conserved in 1JQA as Asp173, His256 and His274:

    Ligand Summary





    No references found.

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