2EV9

Crystal Structure of Shikimate 5-Dehydrogenase (AroE) from Thermus Thermophilus HB8 in complex with NADP(H) and shikimate

Summary for 2EV9

• Entry DOI: 10.2210/pdb2ev9/pdb
• Related: 1WXD 2CY0 2D5C
• Descriptor: shikimate 5-dehydrogenase, SULFATE ION, (3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC ACID, ... (5 entities in total)
• Functional Keywords: substrate, shikimate, cofactor, dimer, structural genomics, nppsfa, national project on protein structural and functional analyses, riken structural genomics/proteomics initiative, rsgi, oxidoreductase
• Biological source: Thermus thermophilus
• Total number of polymer chains: 2
• Total formula weight: 57917.42

Authors

Bagautdinov, B.,Kunishima, N.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2005-10-31, release date: 2006-05-01, Last modification date: 2023-10-25)

Primary citation

Bagautdinov, B.,Kunishima, N.
Crystal Structures of Shikimate Dehydrogenase AroE from Thermus thermophilus HB8 and its Cofactor and Substrate Complexes: Insights into the Enzymatic Mechanism
J.Mol.Biol., 373:424-438, 2007

PubMed Abstract: Shikimate dehydrogenase (EC 1.1.1.25) catalyses the fourth step of the shikimate pathway which is required for the synthesis of the aromatic amino acids and other aromatic compounds in bacteria, microbial eukaryotes, and plants. The crystal structures of the shikimate dehydrogenase AroE from Thermus thermophilus HB8 in its ligand-free form, binary complexes with cofactor NADP+ or substrate shikimate, and the ternary complex with both NADP(H) and shikimate were determined by X-ray diffraction method at atomic resolutions. The crystals are nearly isomorphous with the asymmetric unit containing a dimer, each subunit of which has a bi-domain structure of compact alpha/beta sandwich folds. The two subunits of the enzyme display asymmetry in the crystals due to different relative orientations between the N- and C-terminal domains resulting in a slightly different closure of the interdomain clefts. NADP(H) is bound to the more closed form only. This closed conformation with apparent higher affinity to the cofactor is also observed in the unliganded crystal form, indicating that the NADP(H) binding to TtAroE may follow the selection mode where the cofactor binds to the subunit that happens to be in the closed conformation in solution. Crystal structures of the closed subunits with and without NADP(H) show no significant structural difference, suggesting that the cofactor binding to the closed subunit corresponds to the lock-and-key model in TtAroE. On the other hand, shikimate binds to both open and closed subunit conformers of both apo and NADP(H)-liganded holo enzyme forms. The ternary complex TtAroE:NADP(H):shikimate allows unambiguous visualization of the SDH permitting elucidation of the roles of conserved residues Lys64 and Asp100 in the hydride ion transfer between NADP(H) and shikimate.

PubMed: 17825835
DOI: 10.1016/j.jmb.2007.08.017

Experimental method

X-RAY DIFFRACTION (1.9 Å)