Cryo-EM Structure of Sulfolobus solfataricus ketol-acid reductoisomerase (Sso-KARI) in complex with Mg2+, NADPH, and CPD at pH7.5

Experimental Data Snapshot

  • Resolution: 3.35 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report

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

Chen, C.Y.Chang, Y.C.Lin, B.L.Lin, K.F.Huang, C.H.Hsieh, D.L.Ko, T.P.Tsai, M.D.

(2019) J Am Chem Soc 141: 6136-6140

  • DOI: https://doi.org/10.1021/jacs.9b01354
  • Primary Citation of Related Structures:  
    6JCV, 6JCW, 6JCZ, 6JD1, 6JD2

  • PubMed 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:2Mg 2+ . The results showed that the distances of the two catalytic Mg 2+ 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.

  • Organizational Affiliation

    Department of Life Sciences , National Central University , Taoyuan 32001 , Taiwan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ketol-acid reductoisomerase 2
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
333Saccharolobus solfataricus P2Mutation(s): 0 
Gene Names: ilvC2ilvC-2SSO1322
Find proteins for Q97YJ9 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore Q97YJ9 
Go to UniProtKB:  Q97YJ9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ97YJ9
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NDP

Download Ideal Coordinates CCD File 
AA [auth D]
BB [auth K]
DA [auth E]
HB [auth L]
IA [auth F]
AA [auth D],
BB [auth K],
DA [auth E],
HB [auth L],
IA [auth F],
LA [auth G],
O [auth A],
QA [auth H],
S [auth B],
TA [auth I],
V [auth C],
YA [auth J]
C21 H30 N7 O17 P3
Query on 9TY

Download Ideal Coordinates CCD File 
BA [auth D]
CB [auth K]
EA [auth E]
EB [auth K]
JA [auth F]
BA [auth D],
CB [auth K],
EA [auth E],
EB [auth K],
JA [auth F],
MA [auth G],
P [auth A],
RA [auth H],
T [auth B],
UA [auth I],
W [auth C],
ZA [auth J]
cyclopropane-1,1-dicarboxylic acid
C5 H6 O4
Query on MG

Download Ideal Coordinates CCD File 
AB [auth K]
CA [auth E]
DB [auth K]
FA [auth E]
FB [auth L]
AB [auth K],
CA [auth E],
DB [auth K],
FA [auth E],
FB [auth L],
GA [auth F],
GB [auth L],
HA [auth F],
KA [auth G],
M [auth A],
N [auth A],
NA [auth H],
OA [auth H],
PA [auth H],
Q [auth A],
R [auth B],
SA [auth I],
U [auth C],
VA [auth I],
WA [auth J],
X [auth C],
XA [auth J],
Y [auth D],
Z [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 3.35 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Ministry of Science and Technology (Taiwan)TaiwanAS-KPQ-105-TPP
Ministry of Science and Technology (Taiwan)TaiwanOST 106-2113-M-008-011

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-17
    Type: Initial release
  • Version 1.1: 2019-05-01
    Changes: Data collection, Database references