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1vrd

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

    Title Crystal structure of Inosine-5'-monophosphate dehydrogenase (TM1347) from THERMOTOGA MARITIMA at 2.18 A resolution. To be published
    Site JCSG
    PDB Id 1vrd Target Id 283208
    Molecular Characteristics
    Source Thermotoga maritima msb8
    Alias Ids TPS1278,TM1347, 282192 Molecular Weight 52011.54 Da.
    Residues 482 Isoelectric Point 6.37
    Sequence mkealtfddvllvpqysevlpkdvkidtrltrqiriniplvsaamdtvteaalakalareggigiihkn ltpdeqarqvsivkktengiiydpitvtpdmtvkeaidlmaeykigglpvvdeegrlvglltnrdvrfe knlskkikdlmtpreklivappdislekakeilhqhrieklplvskdnklvglitikdimsviehpnaa rdekgrllvgaavgtspetmerveklvkagvdvividtahghsrrvietlemikadypdlpvvagnvat pegtealikagadavkvgvgpgsicttrvvagvgvpqltavmecsevarkydvpiiadggirysgdivk alaagaesvmvgsifagteeapgetilyqgrkykayrgmgslgamrsgsadrygqegenkfvpegiegm vpykgtvkdvvhqlvgglrsgmgyigartikelqekavfvkitpagvkeshphdiiitkespnywvqa
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.18 Rfree 0.25759
    Matthews' coefficent 3.80 Rfactor 0.21653
    Waters 206 Solvent Content 67.42

    Pathway

    Reactions found in Metabolic Reconstruction for TM1347

    Name: IMP dehydrogenase
    Metabolic Subsystem: Purine Metabolism
    Reaction: : h2o + imp + nad --> h + nadh + xmp
    Classification: EC:1.1.1.205
     

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 1vrd
    1. Inosine monophosphate dehydrogenase (IMPDH) as a target in drug discovery
    Q Shu, V Nair - Medicinal research reviews, 2008 - Wiley Online Library
     
    2. SPINE workshop on automated X-ray analysis: a progress report
    M Bahar, C Ballard, SX Cohen, KD Cowtan - Section D: Biological , 2006 - scripts.iucr.org
     
    3. Autoindexing with outlier rejection and identification of superimposed lattices
    NK Sauter, BK Poon - Journal of Applied Crystallography, 2010 - scripts.iucr.org
     
    4. Crystal structure of human guanosine monophosphate reductase 2 (GMPR2) in complex with GMP
    J Li, Z Wei, M Zheng, X Gu, Y Deng, R Qiu - Journal of molecular , 2006 - Elsevier
     
    5. Bacillus anthracis IMP Dehydrogenase in Action: The First Bacterial Series of Structures of Phosphate Ion-, Substrate-and Product-bound Complexes
    M Makowska-Grzyska, Y Kim, R Wu, R Wilton - Biochemistry, 2012 - ACS Publications
     

    Protein Summary

    The gene TM1347 from Thermotoga maritima encodes the catalytic domain of inosine-5'-monophosphate dehydrogenase PF00478 (IMPDH).  IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of the guanine nucleotides. There is often a CBS domain PF00571 inserted in the middle of this domain, which is proposed to play a regulatory role.  Members of this family contain a TIM barrel structure.   IMPDH is a key enzyme in the regulation of cell proliferation and differentiation.  The mammalian form of the enzyme is a possible target for cancer chemotherapy.

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    Inosine monophosphate dehydrogenase activity of TM1347 (1VRD)

     

    The Thermotoga maritima TM1347 ORF (1VRD) was annotated as a putative inosine 5’-monophosphate dehydrogenase (IMPDH; 1.1.1.205) based on structure and sequence comparisons. TM1347 sequence is similar to IMPDH from Streptococcus pyogenes (1ZFJ; 58% identity, 74% similarity) and Borrelia burgdorferi (1EEP; 58% identity, 76% similarity), both of which have been functionally characterized1-5.TM1347 also contains the TIM barrel catalytic domain and CBS subdomain commonly found in conjunction with the IMPDH domain of IMPDH proteins3. The catalytic domain contains an active site loop with a trio of catalytic residues essential to enzymatic activity: C301, D334 and E409.

     

    Michaelis-Menten kinetics data demonstrate TM1347 has IMPDH activity. TM1347 catalyzes the conversion of inosine 5’-monophosphate (IMP) to xanthosine 5’-monophosphate (KM = 31 µM and kcat= 0.028 s-1at 37 °C) (Figure 1). Because TM1347 may exhibit positive cooperativity with inosine 5’-monophosphate (n=1.8) (Figure 1B; different from the positive cooperativity observed with monovalent cations4,6), kinetic parameters are based on curve-fitting to the data using the Hill equation. TM1347 showed an increased kcat (0.10 s-1) and KM (71 µM) when tested at 70 °C (T. maritima optimal growth temperature). The KM for TM1347 is comparable to that of IMPDH from B. burgdorferi (29 ± 8 µM) and similar to that of IMPDH from S. pyogenes (62 ± 19 µM), though the activity (kcat) is much lower compared to both (S. pyogenes, 24.3 ± 3 s-1; B. burgdorferi, 2.6 ±0.3 s-1)2,3.

     

    The dependence on and specificity of TM1347 for monocovalent cations was determined at 70 °C, pH 8.0, by substitution of K+ in the standard assay (50 mMTris [pH 8.5], 1 mM β-mercaptoethanol, 3 mM EDTA, and 1 mM NAD+) with either Li+, Na+, or no cation. There was an approximately 50% decrease in reaction rate when K+ was substituted or removed (Figure 2). These data support the observation that IMPDHs are activated ~100 fold by K+ and similar monovalent cations4.TM1347 activity decreased as the size of the monovalent cation decreases in size (K+>Na+>Li+) and was lowest in the absence of monovalent cation.

     

    BioLEd Contributors: Jacqueline Stevens, Evans Wralstad, Alice Yeh, Vernon Forrester, Bridget Bailey, Ahmed Ragab, Tomasz Kabzinski, Kaitlin Bailey, Cameron Mura, Carol Price, Linda Columbus. Funded by NSF DUE 1044858.

     

    References

    1.      Shu, Q., and Nair, V. 2008. Inosine Monophosphate Dehydrogenase (IMPDH) as a Target in Drug Discovery. Med. Res. Rev. 28:219-232.

    2.      Zhang, R. G., Evans, GRotella, F. J., Westbrook, E. M., Beno, D., Huberman, E., Joachimiak, A., and Collart, F. R. 1999 Characteristics and Crystal Structure of Bacterial inosine-5'-monophosphate dehydrogenase. Biochemistry. 38(15):4691-4700.

    3.      Zhou, X., Cahoon, M., Rosa, P., and Hedstrom, L. 1997. Expression, Purification, and Characterization of Inosine 5'-Monophosphate Dehydrogenase from Borreliaburgdorferi. J. Biol. Chem. 272(35):21977-21981.

    4.      Hedstrom, L. 2009. IMP Dehydrogenase: Structure, Mechanism, and Inhibition. Chem. Rev. 109:2903-2928.

    5.      Pimkin, M., and Markham, G. D. 2008. The CBS Subdomain of Inosine 5'-Monophosphate Dehydrogenase Regulates Purine Nucleotide Turnover. Mol. Microbiol. 68:342-359.

    6.      Riera, T. V., Zheng, L., Josephine, H. R., Min, D., Yang, W., and Hedstrom, L. 2011. Allosteric Activation via Kinetic Control: Potassium Accelerates a Conformational Change in IMP Dehydrogenase. Biochemistry. 50:8508-8518.

    Ligand Summary



    References

    Reviews

    References

     

    No references found.

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    Files (2)

    FileSizeDateAttached by 
     TM1347 Figure 1.png
    Kinetic data
    56.64 kB19:14, 13 May 2015cawpriceActions
     TM1347 Figure 2.png
    Dependence on monovalent cations
    42.44 kB19:14, 13 May 2015cawpriceActions
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