5vo3
Crystal structure of DapE in complex with the products (succinic acid and diaminopimelic acid)Crystal structure of DapE in complex with the products (succinic acid and diaminopimelic acid)
Structural highlights
FunctionDAPE_HAEIN Catalyzes the hydrolysis of N-succinyl-L,L-diaminopimelic acid (SDAP), forming succinate and LL-2,6-diaminoheptanedioate (DAP), an intermediate involved in the bacterial biosynthesis of lysine and meso-diaminopimelic acid, an essential component of bacterial cell walls. It can only hydrolyze L,L-N-succinyl-diaminopimelic acid (L,L-SDAP) and is inactive toward D,L-, L,D-, and D,D-SDAP.[1] [2] [3] Publication Abstract from PubMedThe X-ray crystal structure of the dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase from Haemophilus influenzae (HiDapE) bound by the products of hydrolysis, succinic acid and l,l-DAP, was determined at 1.95 A. Surprisingly, the structure bound to the products revealed that HiDapE undergoes a significant conformational change in which the catalytic domain rotates approximately 50 degrees and shifts approximately 10.1 A (as measured at the position of the Zn atoms) relative to the dimerization domain. This heretofore unobserved closed conformation revealed significant movements within the catalytic domain compared to that of wild-type HiDapE, which results in effectively closing off access to the dinuclear Zn(II) active site with the succinate carboxylate moiety bridging the dinculear Zn(II) cluster in a mu-1,3 fashion forming a bis(mu-carboxylato)dizinc(II) core with a Zn-Zn distance of 3.8 A. Surprisingly, His194.B, which is located on the dimerization domain of the opposing chain approximately 10.1 A from the dinuclear Zn(II) active site, forms a hydrogen bond (2.9 A) with the oxygen atom of succinic acid bound to Zn2, forming an oxyanion hole. As the closed structure forms upon substrate binding, the movement of His194.B by more than approximately 10 A is critical, based on site-directed mutagenesis data, for activation of the scissile carbonyl carbon of the substrate for nucleophilic attack by a hydroxide nucleophile. Employing the HiDapE product-bound structure as the starting point, a reverse engineering approach called product-based transition-state modeling provided structural models for each major catalytic step. These data provide insight into the catalytic reaction mechanism and also the future design of new, potent inhibitors of DapE enzymes. Structural Evidence of a Major Conformational Change Triggered by Substrate Binding in DapE Enzymes: Impact on the Catalytic Mechanism.,Nocek B, Reidl C, Starus A, Heath T, Bienvenue D, Osipiuk J, Jedrzejczak R, Joachimiak A, Becker DP, Holz RC Biochemistry. 2018 Feb 6;57(5):574-584. doi: 10.1021/acs.biochem.7b01151. Epub, 2018 Jan 12. PMID:29272107[4] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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