Crystal Structures of the Putative Isocitrate Dehydrogenase from Strain 7 in the Apo and NADP-Bound Forms

Overview

Journal Archaea

Specialty Microbiology

Date 2019 Jan 22

PMID 30662370

Citations 1

Authors

Hisanori Kondo

Midori Murakami

Affiliations

Soon will be listed here.

Abstract

Isocitrate dehydrogenase is a catabolic enzyme that acts during the third step of the tricarboxylic acid cycle. The hypothetical protein ST2166 from the archaeon was isolated and crystallized. It shares high primary structure homology with prokaryotic NADP-dependent IDHs, suggesting that these enzymes share a common enzymatic mechanism. The crystal structure of ST2166 was determined at 2.0 Å resolution in the apo form, and then the structure of the crystal soaked with NADP was also determined at 2.4 Å resolution, which contained NADP bound at the putative active site. Comparisons between the structures of apo and NADP-bound forms and NADP-IDHs from other prokaryotes suggest that prokaryotic NADP-IDHs recognize their cofactors using conserved Lys335, Tyr336, and Arg386 in ST2166 at the opening cleft before the domain closure.

Citing Articles

Biochemical Characterization of Recombinant Isocitrate Dehydrogenase and Its Putative Role in the Physiology of an Acidophilic Micrarchaeon.

Winkler D, Gfrerer S, Gescher J Microorganisms. 2021; 9(11).

PMID: 34835444 PMC: 8623467. DOI: 10.3390/microorganisms9112318.

References

. The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr. 1994; 50(Pt 5):760-3. DOI: 10.1107/S0907444994003112. View

Murakami M, Kouyama T . Crystal Structures of Two Isozymes of Citrate Synthase from Sulfolobus tokodaii Strain 7. Biochem Res Int. 2016; 2016:7560919. PMC: 5021468. DOI: 10.1155/2016/7560919. View

Cupp J, McAlister-Henn L . NAD(+)-dependent isocitrate dehydrogenase. Cloning, nucleotide sequence, and disruption of the IDH2 gene from Saccharomyces cerevisiae. J Biol Chem. 1991; 266(33):22199-205. View

Brunger A, Adams P, Clore G, DeLano W, Gros P, Grosse-Kunstleve R . Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr. 1998; 54(Pt 5):905-21. DOI: 10.1107/s0907444998003254. View

Bolduc J, Dyer D, Scott W, Singer P, Sweet R, Koshland Jr D . Mutagenesis and Laue structures of enzyme intermediates: isocitrate dehydrogenase. Science. 1995; 268(5215):1312-8. DOI: 10.1126/science.7761851. View

Doyle S, Beernink P, Koshland Jr D . Structural basis for a change in substrate specificity: crystal structure of S113E isocitrate dehydrogenase in a complex with isopropylmalate, Mg2+, and NADP. Biochemistry. 2001; 40(14):4234-41. DOI: 10.1021/bi002533q. View

Jeong J, Sonoda T, Fushinobu S, Shoun H, Wakagi T . Crystal structure of isocitrate dehydrogenase from Aeropyrum pernix. Proteins. 2004; 55(4):1087-9. DOI: 10.1002/prot.20121. View

Hurley J, Thorsness P, Ramalingam V, Helmers N, Koshland Jr D, Stroud R . Structure of a bacterial enzyme regulated by phosphorylation, isocitrate dehydrogenase. Proc Natl Acad Sci U S A. 1989; 86(22):8635-9. PMC: 298342. DOI: 10.1073/pnas.86.22.8635. View

Kawarabayasi Y, Hino Y, Horikawa H, Takahashi M, Sekine M, Baba S . Complete genome sequence of an aerobic thermoacidophilic crenarchaeon, Sulfolobus tokodaii strain7. DNA Res. 2001; 8(4):123-40. DOI: 10.1093/dnares/8.4.123. View

10.

Karlstrom M, Stokke R, Steen I, Birkeland N, Ladenstein R . Isocitrate dehydrogenase from the hyperthermophile Aeropyrum pernix: X-ray structure analysis of a ternary enzyme-substrate complex and thermal stability. J Mol Biol. 2004; 345(3):559-77. DOI: 10.1016/j.jmb.2004.10.025. View

11.

Cherbavaz D, Lee M, Stroud R, Koshland Jr D . Active site water molecules revealed in the 2.1 A resolution structure of a site-directed mutant of isocitrate dehydrogenase. J Mol Biol. 2000; 295(3):377-85. DOI: 10.1006/jmbi.1999.3195. View

12.

Steen I, Madern D, Karlstrom M, Lien T, Ladenstein R, Birkeland N . Comparison of isocitrate dehydrogenase from three hyperthermophiles reveals differences in thermostability, cofactor specificity, oligomeric state, and phylogenetic affiliation. J Biol Chem. 2001; 276(47):43924-31. DOI: 10.1074/jbc.M105999200. View

13.

Robert X, Gouet P . Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Res. 2014; 42(Web Server issue):W320-4. PMC: 4086106. DOI: 10.1093/nar/gku316. View

14.

Stoddard B, Dean A, Koshland Jr D . Structure of isocitrate dehydrogenase with isocitrate, nicotinamide adenine dinucleotide phosphate, and calcium at 2.5-A resolution: a pseudo-Michaelis ternary complex. Biochemistry. 1993; 32(36):9310-6. DOI: 10.1021/bi00087a008. View

15.

Yates S, Edwards T, Bryan C, Stein A, Van Voorhis W, Myler P . Structural basis of the substrate specificity of bifunctional isocitrate dehydrogenase kinase/phosphatase. Biochemistry. 2011; 50(38):8103-6. PMC: 3354702. DOI: 10.1021/bi200809p. View

16.

McRee D . XtalView/Xfit--A versatile program for manipulating atomic coordinates and electron density. J Struct Biol. 1999; 125(2-3):156-65. DOI: 10.1006/jsbi.1999.4094. View

17.

LARKIN M, Blackshields G, Brown N, Chenna R, McGettigan P, McWilliam H . Clustal W and Clustal X version 2.0. Bioinformatics. 2007; 23(21):2947-8. DOI: 10.1093/bioinformatics/btm404. View

18.

Wang S, Shen Q, Chen G, Zheng J, Tan H, Jia Z . The phosphatase mechanism of bifunctional kinase/phosphatase AceK. Chem Commun (Camb). 2014; 50(91):14117-20. DOI: 10.1039/c4cc05375c. View

19.

Finer-Moore J, Tsutakawa S, Cherbavaz D, LaPorte D, Koshland Jr D, Stroud R . Access to phosphorylation in isocitrate dehydrogenase may occur by domain shifting. Biochemistry. 1997; 36(45):13890-6. DOI: 10.1021/bi9711691. View

20.

Venkat S, Chen H, Stahman A, Hudson D, McGuire P, Gan Q . Characterizing Lysine Acetylation of Isocitrate Dehydrogenase in Escherichia coli. J Mol Biol. 2018; 430(13):1901-1911. PMC: 5988991. DOI: 10.1016/j.jmb.2018.04.031. View