.
The Open Protein Structure Annotation Network
PDB Keyword
.

1vl8

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

    Title Crystal structure of Gluconate 5-dehydrogenase (TM0441) from Thermotoga maritima at 2.07 A resolution. To be published
    Site JCSG
    PDB Id 1vl8 Target Id 359776
    Molecular Characteristics
    Source Thermotoga maritima msb8
    Alias Ids TPS1434,TM0441, MCSG_3.40.50.300_ID_1367, 429688 Molecular Weight 27915.45 Da.
    Residues 255 Isoelectric Point 5.52
    Sequence mkevfdlrgrvalvtggsrglgfgiaqglaeagcsvvvasrnleeaseaaqkltekygvetmafrcdvs nyeevkklleavkekfgkldtvvnaaginrrhpaeefpldefrqvievnlfgtyyvcreafsllresdn psiinigsltveevtmpnisayaaskggvasltkalakewgrygirvnviapgwyrtkmteavfsdpek ldymlkriplgrtgvpedlkgvavflaseeakyvtgqiifvdggwtan
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.07 Rfree 0.17955
    Matthews' coefficent 3.89 Rfactor 0.14999
    Waters 331 Solvent Content 68.14

    Access denied for user 'root'@'localhost' (using password: YES) (click for details)

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 1vl8
    1. Structural insight into the catalytic mechanism of gluconate 5_dehydrogenase from Streptococcus suis: Crystal structures of the substrate_free and quaternary complex
    Q Zhang, H Peng, F Gao, Y Liu, H Cheng - Protein , 2009 - Wiley Online Library
     
    2. Variation in potential effector genes distinguishing Australian and non_Australian isolates of the cotton wilt pathogen Fusarium oxysporum f. sp. vasinfectum
    A Chakrabarti, M Rep, B Wang, A Ashton - Plant , 2011 - Wiley Online Library
     
    3. Crystal Structures of Enoyl-ACP Reductases I (FabI) and III (FabL) from B. subtilis
    KH Kim, BH Ha, SJ Kim, SK Hong, KY Hwang - Journal of molecular , 2011 - Elsevier
     
    4. Structural insight into substrate differentiation of the sugar-metabolizing enzyme galactitol dehydrogenase from Rhodobacter sphaeroides D
    Y Carius, H Christian, A Faust, U Zander - Journal of Biological , 2010 - ASBMB
     
    5. Crystallization and preliminary X-ray analysis of the NADPH-dependent 3-quinuclidinone reductase from Rhodotorula rubra
    D Takeshita, M Kataoka, T Miyakawa - Section F: Structural , 2009 - scripts.iucr.org
     
    6. Crystallization and preliminary X-ray analysis of 5-keto-D-gluconate reductase from Gluconobacter suboxydans IFO12528 complexed with 5-keto-D-gluconate and
    K Kubota, K Miyazono, K Nagata, H Toyama - Section F: Structural , 2010 - scripts.iucr.org
     
    7. Partial Geometric Hashing for Retrieving Similar Interaction Protein Using Profile
    Y Kiuchi, T Ozaki, T Ohkawa - Information Technology, 2007. , 2007 - ieeexplore.ieee.org
     
    8. Sequence fingerprint and structural analysis of the SCOR enzyme A3DFK9 from Clostridium thermocellum
    R Huether, ZJ Liu, H Xu, BC Wang - Proteins: Structure, , 2010 - Wiley Online Library
     
    9. In silico docking of herbal based 'epigallocatechin'onto homology modeled ketoacyl-ACP reductase domain of FAS protein from Mycobacterium tuberculosis H37Rv
    KV Ramesh, S Chandy, D Pai - Indian Journal of , 2012 - nopr.niscair.res.in
     
    10. Structural insight into the molecular basis of polyextremophilicity of short-chain alcohol dehydrogenase from the hyperthermophilic archaeon Thermococcus
    EY Bezsudnova, KM Boyko, KM Polyakov - Biochimie, 2012 - Elsevier
     
    11. Structure of a short-chain dehydrogenase/reductase from Bacillus anthracis
    J Hou, K Wojciechowska, H Zheng - Section F: Structural , 2012 - scripts.iucr.org
     
    12. METHOD FOR DESIGNING HEAT-RESISTANT TYROSINE-DEPENDENT SHORT-CHAIN DEHYDROGENASE/REDUCTASE AND HEAT-RESISTANT TYROSINE-
    D Yamaguchi, S Yamada, Y Goto - US Patent App. 13/ , 2011 - Google Patents
     
    13. Ajocin (Allicin+ Ajoene) can inhibit the enzymatic activity of aflatoxin biosynthesis in peanuts and prevent human carcinogenic exposure
    A Prabahar, S Vellingiri, S Natarajan, K Raja - 2011 - urpjournals.com
     

    Protein Summary

    The gene TM0441 from Thermotoga maritima encodes the enzyme gluconate 5-dehydrogenase EC:1.1.1.69 (alternative names: 5-keto-D-gluconate 5-reductase, 5-ketogluconate reductase).  The enzyme belongs to the large family of short-chain dehydrogenases/reductases (SDR) PF00106, specifically those acting on the CH-OH group of donor with NAD+ or NADP+ as acceptor.  The enzyme catalyzes the following reaction: D-gluconate + NAD(P)+  --> 5-dehydro-D-gluconate + NAD(P)H + H+.  The enzyme belongs to the class of alpha and beta proteins and contains NAD(P)-binding Rossmann-fold domain SCOP51734.

    ************************************************************************************************************************************************

    TM0441: A Confirmed Gluconate 5-Dehydrogenase from Thermotoga maritima

     

    The Thermotoga maritima enzyme TM0441 (PDB ID 1VL8) is annotated as a putative gluconate 5-dehydrogenase (Ga5DH) based on sequence and structural comparisons.  TM0441 is similar to homologs such as Ga5DH from Streptococcus suis (PDB ID 3CXR)[1] and is in the family of short-chain dehydrogenases[2].  Specifically, TM0441 contains a conserved Ga5DH catalytic triad, S-Y-K[3] (residues 146, 160, and 164, respectively; Figure 1).

    Both the forward oxidation reaction of D-gluconate to 5-keto-D-gluconate and the reverse reduction were experimentally investigated.  In the limit of rapid Michaelis-Menten  pre-equilibrium between the reactants (E+S) and the Michaelis complex (ES) states, the rate of ESàE + P is much slower, and thus KM = KD. A lower affinity for D-gluconate was observed for TM0441 compared to homologs from Gluconobacter Oxydans,Gluconobacter Suboxydans, andXanthomonas Campestris (Table 1). 

     

    Substrate Specificity:

                TM0441 demonstrated higher activity with D-gluconate than with D-sorbitol, D-glucose, and D-galactose. D-glucose was found to competitively inhibited D-gluconate turnover (Figure 2).

    Co-factor Specificity:

                The co-factor specificity of NADP+, along with NAD+,  was investigated for the forward reaction (Table 1).  Though the reaction proceeded with both NADP+ and NAD+, the overall catalytic efficiency was three-fold less with NAD+ (Figure 3). 

    pH Dependence:

                TM0441 acts via general acid/base catalysis (eg. the catalytic triad S146-Y160-K164) and so pH greatly affects the activity of the enzyme.  For the forward reaction, literature reviews[4] and experimental studies showed that a pH of 10.0 was optimal.  At this pH the acid/base catalysis through the triad is greatly facilitated; the physical basis of this is that the pKa of Y160 (normally ~10.07) is lowered by NADP+ and so at pH 10 Y160 can be deprotonated and thus facilitate the oxidation of D-gluconate.

     

    Through bioinformatic and enzymatic (spectrophotometric) characterization, the findings reported here support the annotation of TM0441 as a gluconate 5-dehydrogenase.

     

    Organism

    KM (mM)

    kcat (s-1)

    kcat/KM (s-1 M-1)

    T. maritima (NAD+)

    206

    0.0609

    0.299

    T. maritima (NADP+)

    956

    0.241

    0.252

    G. oxydans*

    20

    (N/A)

    (N/A)

    G. suboxydans

    161

    (N/A)

    (N/A)

    X. campestris

    109

    (N/A)

    (N/A)

     

    Table 1. Michaelis-Menten kinetic parameters of Ga5DHs from various organisms in the forward direction with cofactor NADP+.  (Values for kcat/Km were not available in the literature.) Experimental conditions: * 0.5 mM NADP and 300 mM sodium gluconic acid in a 100 mM sodium carbonate buffer, pH 10; † 30°C in 100 mM sodium acetate, pH 5.5, with 1 mM magnesium chloride, 1 mM calcium chloride, 6 µg/mL pyrroloquinoline quinone, 0.6 mM 2,6-dichloroindophenol, and 31 mM sorbitol; ‡at 30°C in 100 mM sodium acetate, pH 5.5, with 1 mM magnesium chloride, 1 mM calcium chloride, 6 µg/mL pyrroloquinoline quinone, 0.6 mM 2,6-dichloroindophenol, and 31 mM sorbitol.

    BioLEd Contributors: Kanishk Jain, Ryan Oliver, Brandon Wade, Dado Kim, Erik Haley, Joseph Muldoon, Morgan Savoia, Tiffany Chu, Cameron Mura, Carol Price, Linda Columbus.

    Funded by NSF DUE 1044858.


    1 Filling C, Berndt K, Benach J, Knapp S Prozorovski T, Nordling E, Ladenstein R, Jornvall H, and Udo Oppermann. Critical Residues for Structure and Catalysis in Short-chain Dehydrogenases/Reductases. The Journal of Biological Chemistry. 2007 277(28): 25677-25684.

    2 Salusjarvi T, Povelainen M, Hvorselv N, Eneyskaya E, Kulminshkay A, Shabalin K, Neutrosev K, Kalkkinen N, and A N Miasnikov. Cloning of a gluconate/polyol dehydrogenase gene from Gluconobacter suboxydans IFO 12528, characterization of the enzyme and its use for the production of 5-ketogluconate in a recombinant Escherichia coli strain. Applied Genetics and Molecular Biotechnology. 2004 65: 306-314.

    3 Marchler-Bauer A, et al. (2011), “CDD: a Conserved Domian Database for the functional annotation of proteins.”,Nucleic Acids Res.39(D)225-9.

    4 Zhang Q, Peng H, Feng G, Liu Y, Cheng H, Thompson J, and George F. Gao. Structural insight into the catalytic mechanism of gluconate 5-dehydrogenase from Streptococcus suis: Crystal structures of the substrate-free and quaternary complex enzymes. Protein Science. 2009 18:294-303

    Ligand Summary



    References

    Reviews

    References

     

    No references found.

    Tag page
    You must login to post a comment.
    All content on this site is licensed under a Creative Commons Attribution 3.0 License
    Powered by MindTouch