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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
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

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

Ligand Information


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
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: (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.



KM (mM)

kcat (s-1)

kcat/KM (s-1 M-1)

T. maritima (NAD+)




T. maritima (NADP+)




G. oxydans*




G. suboxydans




X. campestris





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





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