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

Biochemistry. 2018 Feb 6;57(5):574-584. doi: 10.1021/acs.biochem.7b01151. Epub 2018 Jan 12.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amidohydrolases / chemistry*
  • Amidohydrolases / genetics
  • Amidohydrolases / metabolism
  • Amino Acid Substitution
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Catalysis
  • Catalytic Domain
  • Crystallography, X-Ray
  • Diaminopimelic Acid / metabolism
  • Dimerization
  • Haemophilus influenzae / enzymology*
  • Haemophilus influenzae / genetics
  • Hydrogen Bonding
  • Models, Molecular
  • Mutagenesis, Site-Directed
  • Neisseria meningitidis / enzymology
  • Neisseria meningitidis / genetics
  • Protein Binding
  • Protein Conformation
  • Recombinant Proteins / chemistry
  • Rotation
  • Substrate Specificity
  • Succinic Acid / metabolism
  • Zinc / chemistry


  • Bacterial Proteins
  • Recombinant Proteins
  • Diaminopimelic Acid
  • Succinic Acid
  • Amidohydrolases
  • succinyldiaminopimelate desuccinylase
  • Zinc