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TitleUse of Cryo-EM To Uncover Structural Bases of pH Effect and Cofactor Bispecificity of Ketol-Acid Reductoisomerase.
Journal, issue, pagesJ Am Chem Soc, Vol. 141, Issue 15, Page 6136-6140, Year 2019
Publish dateApr 17, 2019
AuthorsChin-Yu Chen / Yuan-Chih Chang / Bo-Lin Lin / Kuan-Fu Lin / Chun-Hsiang Huang / Dong-Lin Hsieh / Tzu-Ping Ko / Ming-Daw Tsai /
PubMed AbstractWhile 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 ...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:2Mg. The results showed that the distances of the two catalytic Mg 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.
External linksJ Am Chem Soc / PubMed:30921515
MethodsEM (single particle) / X-ray diffraction
Resolution2.53 - 3.38 Å
Structure data

9798

6jcv

EMDB-9798, PDB-6jcv:
Cryo-EM structure of Sulfolobus solfataricus ketol-acid reductoisomerase (Sso-KARI) with Mg2+ at pH7.5
Method: EM (single particle) / Resolution: 2.92 Å

9799

6jcw

EMDB-9799, PDB-6jcw:
Cryo-EM Structure of Sulfolobus solfataricus ketol-acid reductoisomerase (Sso-KARI) with Mg2+ at pH8.5
Method: EM (single particle) / Resolution: 3.04 Å

9800

6jcz

EMDB-9800, PDB-6jcz:
Cryo-EM Structure of Sulfolobus solfataricus ketol-acid reductoisomerase (Sso-KARI) in complex with Mg2+, NADPH, and CPD at pH7.5
Method: EM (single particle) / Resolution: 3.35 Å

9801

6jd1

EMDB-9801, PDB-6jd1:
Cryo-EM Structure of Sulfolobus solfataricus ketol-acid reductoisomerase (Sso-KARI) in complex with Mg2+, NADH, and CPD at pH7.5
Method: EM (single particle) / Resolution: 3.38 Å

PDB-6jd2:
Crystal structure of Sulfolobus solfataricus ketol-acid reductoisomerase (Sso-KARI) in complex with Mg2+ at pH8.5
Method: X-RAY DIFFRACTION / Resolution: 2.53 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-HOH:
WATER / Water

ChemComp-NDP:
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate

ChemComp-9TY:
cyclopropane-1,1-dicarboxylic acid

ChemComp-NAI:
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Nicotinamide adenine dinucleotide

ChemComp-BME:
BETA-MERCAPTOETHANOL / 2-Mercaptoethanol

Source
  • Sulfolobus solfataricus P2 (archaea)
  • saccharolobus solfataricus (strain atcc 35092 / dsm 1617 / jcm 11322 / p2) (archaea)
KeywordsISOMERASE / Bi-specific / Thermostable / Reductoisomerase / Magnesium-dependent / Dodecamer / Knot-structure / Knotted protein

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