6JCZ

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

PDB DOI: https://doi.org/10.2210/pdb6JCZ/pdb
EM Map EMD-9800: EMDB EMDataResource

Classification: ISOMERASE
Organism(s): Saccharolobus solfataricus P2
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-01-30 Released: 2019-04-17
Deposition Author(s): Chen, C.Y., Chang, Y.C., Lin, K.F., Huang, C.H., Lin, B.L., Ko, T.P., Hsieh, D.L., Tsai, M.D.
Funding Organization(s): Ministry of Science and Technology (Taiwan)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.35 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

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

PubMed: 30921515 Search on PubMed
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.

Macromolecule Content

Total Structure Weight: 457.85 kDa
Atom Count: 31,951
Modelled Residue Count: 3,959
Deposited Residue Count: 3,996
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative ketol-acid reductoisomerase 2	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	333	Saccharolobus solfataricus P2	Mutation(s): 0 Gene Names: ilvC2, ilvC-2, SSO1322 EC: 1.1.1.86
UniProt
Find proteins for Q97YJ9 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q97YJ9 Go to UniProtKB: Q97YJ9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q97YJ9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP Query on NDP Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BB [auth K] SDF format, chain DA [auth E] SDF format, chain HB [auth L] SDF format, chain IA [auth F] SDF format, chain LA [auth G] SDF format, chain O [auth A] SDF format, chain QA [auth H] SDF format, chain S [auth B] SDF format, chain TA [auth I] SDF format, chain V [auth C] SDF format, chain YA [auth J] MOL2 format, chain AA [auth D] MOL2 format, chain BB [auth K] MOL2 format, chain DA [auth E] MOL2 format, chain HB [auth L] MOL2 format, chain IA [auth F] MOL2 format, chain LA [auth G] MOL2 format, chain O [auth A] MOL2 format, chain QA [auth H] MOL2 format, chain S [auth B] MOL2 format, chain TA [auth I] MOL2 format, chain V [auth C] MOL2 format, chain YA [auth J]	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]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain AA [auth D] Focus chain BB [auth K] Focus chain DA [auth E] Focus chain HB [auth L] Focus chain IA [auth F] Focus chain LA [auth G] Focus chain O [auth A] Focus chain QA [auth H] Focus chain S [auth B] Focus chain TA [auth I] Focus chain V [auth C] Focus chain YA [auth J] Interactions & Density Focus chain AA [auth D] Focus chain BB [auth K] Focus chain DA [auth E] Focus chain HB [auth L] Focus chain IA [auth F] Focus chain LA [auth G] Focus chain O [auth A] Focus chain QA [auth H] Focus chain S [auth B] Focus chain TA [auth I] Focus chain V [auth C] Focus chain YA [auth J]
9TY Query on 9TY Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CB [auth K] SDF format, chain EA [auth E] SDF format, chain EB [auth K] SDF format, chain JA [auth F] SDF format, chain MA [auth G] SDF format, chain P [auth A] SDF format, chain RA [auth H] SDF format, chain T [auth B] SDF format, chain UA [auth I] SDF format, chain W [auth C] SDF format, chain ZA [auth J] MOL2 format, chain BA [auth D] MOL2 format, chain CB [auth K] MOL2 format, chain EA [auth E] MOL2 format, chain EB [auth K] MOL2 format, chain JA [auth F] MOL2 format, chain MA [auth G] MOL2 format, chain P [auth A] MOL2 format, chain RA [auth H] MOL2 format, chain T [auth B] MOL2 format, chain UA [auth I] MOL2 format, chain W [auth C] MOL2 format, chain ZA [auth J]	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 FDKLLWKMYAMLIF-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain CB [auth K] Focus chain EA [auth E] Focus chain EB [auth K] Focus chain JA [auth F] Focus chain MA [auth G] Focus chain P [auth A] Focus chain RA [auth H] Focus chain T [auth B] Focus chain UA [auth I] Focus chain W [auth C] Focus chain ZA [auth J] Interactions & Density Focus chain BA [auth D] Focus chain CB [auth K] Focus chain EA [auth E] Focus chain EB [auth K] Focus chain JA [auth F] Focus chain MA [auth G] Focus chain P [auth A] Focus chain RA [auth H] Focus chain T [auth B] Focus chain UA [auth I] Focus chain W [auth C] Focus chain ZA [auth J]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AB [auth K] SDF format, chain CA [auth E] SDF format, chain DB [auth K] SDF format, chain FA [auth E] SDF format, chain FB [auth L] SDF format, chain GA [auth F] SDF format, chain GB [auth L] SDF format, chain HA [auth F] SDF format, chain KA [auth G] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth H] SDF format, chain OA [auth H] SDF format, chain PA [auth H] SDF format, chain Q [auth A] SDF format, chain R [auth B] SDF format, chain SA [auth I] SDF format, chain U [auth C] SDF format, chain VA [auth I] SDF format, chain WA [auth J] SDF format, chain X [auth C] SDF format, chain XA [auth J] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain AB [auth K] MOL2 format, chain CA [auth E] MOL2 format, chain DB [auth K] MOL2 format, chain FA [auth E] MOL2 format, chain FB [auth L] MOL2 format, chain GA [auth F] MOL2 format, chain GB [auth L] MOL2 format, chain HA [auth F] MOL2 format, chain KA [auth G] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth H] MOL2 format, chain OA [auth H] MOL2 format, chain PA [auth H] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth B] MOL2 format, chain SA [auth I] MOL2 format, chain U [auth C] MOL2 format, chain VA [auth I] MOL2 format, chain WA [auth J] MOL2 format, chain X [auth C] MOL2 format, chain XA [auth J] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D]	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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AB [auth K] Focus chain CA [auth E] Focus chain DB [auth K] Focus chain FA [auth E] Focus chain FB [auth L] Focus chain GA [auth F] Focus chain GB [auth L] Focus chain HA [auth F] Focus chain KA [auth G] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth H] Focus chain OA [auth H] Focus chain PA [auth H] Focus chain Q [auth A] Focus chain R [auth B] Focus chain SA [auth I] Focus chain U [auth C] Focus chain VA [auth I] Focus chain WA [auth J] Focus chain X [auth C] Focus chain XA [auth J] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AB [auth K] Focus chain CA [auth E] Focus chain DB [auth K] Focus chain FA [auth E] Focus chain FB [auth L] Focus chain GA [auth F] Focus chain GB [auth L] Focus chain HA [auth F] Focus chain KA [auth G] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth H] Focus chain OA [auth H] Focus chain PA [auth H] Focus chain Q [auth A] Focus chain R [auth B] Focus chain SA [auth I] Focus chain U [auth C] Focus chain VA [auth I] Focus chain WA [auth J] Focus chain X [auth C] Focus chain XA [auth J] Focus chain Y [auth D] Focus chain Z [auth D]