Structural Evidence of a Major Conformational Change Triggered by Substrate Binding in DapE Enzymes: Impact on the Catalytic Mechanism

Authors

Boguslaw P. Nocek, Argonne National LaboratoryFollow
Cory Reidl, Loyola University Chicago
Anna Starus, Loyola University Chicago
Tahirah Heath, Loyola University Chicago
David L. Bienvenue, Loyola University ChicagoFollow
Jerzy Osipiuk, Argonne National Laboratory
Robert Jedrzejczak, Argonne National Laboratory
Andzrej Joachimiak, Argonne National Laboratory
Daniel P. Becker, Loyola University ChicagoFollow
Richard C. Holz, Marquette UniversityFollow

Document Type

Article

Language

Eng

Publication Date

2018

Publisher

American Chemical Society

Source Publication

Biochemistry

Source ISSN

0006-2960

Abstract

The 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 Å. Surprisingly, the structure bound to the products revealed that HiDapE undergoes a significant conformational change in which the catalytic domain rotates ∼50° and shifts ∼10.1 Å (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 μ-1,3 fashion forming a bis(μ-carboxylato)dizinc(II) core with a Zn–Zn distance of 3.8 Å. Surprisingly, His194.B, which is located on the dimerization domain of the opposing chain ∼10.1 Å from the dinuclear Zn(II) active site, forms a hydrogen bond (2.9 Å) 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 ∼10 Å 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.

Comments

Accepted version. Biochemistry, Vol. 57, No. 5 (2018): 574-584. DOI. © 2017 American Chemical Society. Used with permission.

Recommended Citation

Nocek, Boguslaw P.; Reidl, Cory; Starus, Anna; Heath, Tahirah; Bienvenue, David L.; Osipiuk, Jerzy; Jedrzejczak, Robert; Joachimiak, Andzrej; Becker, Daniel P.; and Holz, Richard C., "Structural Evidence of a Major Conformational Change Triggered by Substrate Binding in DapE Enzymes: Impact on the Catalytic Mechanism" (2018). Chemistry Faculty Research and Publications. 892.
https://epublications.marquette.edu/chem_fac/892