Use of Cryo-EM To Uncover Structural Bases of pH Effect and Cofactor Bispecificity of Ketol-Acid Reductoisomerase

J Am Chem Soc. 2019 Apr 17;141(15):6136-6140. doi: 10.1021/jacs.9b01354. Epub 2019 Apr 2.

Abstract

While cryo-EM is revolutionizing structural biology, its impact on enzymology is yet to be fully demonstrated. The ketol-acid reductoisomerase (KARI) catalyzes conversion of (2 S)-acetolactate or (2 S)-aceto-2-hydroxybutyrate to 2,3-dihydroxy-3-alkylbutyrate. We found that KARI from archaea Sulfolobus solfataricus (Sso-KARI) is unusual in being a dodecamer, bispecific to NADH and NADPH, and losing activity above pH 7.8. While crystals were obtainable only at pH 8.5, cryo-EM structures were solved at pH 7.5 and 8.5 for Sso-KARI:2Mg2+. The results showed that the distances of the two catalytic Mg2+ ions are lengthened in both structures at pH 8.5. We next solved cryo-EM structures of two Sso-KARI complexes, with NADH+inhibitor and NADPH+inhibitor at pH 7.5, which indicate that the bispecificity can be attributed to a unique asparagine at the cofactor binding loop. Unexpectedly, Sso-KARI also differs from other KARI enzymes in lacking "induced-fit", reflecting structural rigidity. Thus, cryo-EM is powerful for structural and mechanistic enzymology.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alcohols / chemistry
  • Alcohols / metabolism*
  • Archaea / enzymology*
  • Crystallography, X-Ray
  • Hydrogen-Ion Concentration
  • Ketol-Acid Reductoisomerase / chemistry*
  • Ketol-Acid Reductoisomerase / metabolism
  • Ketones / chemistry
  • Ketones / metabolism*
  • Models, Molecular
  • Molecular Conformation

Substances

  • Alcohols
  • Ketones
  • Ketol-Acid Reductoisomerase