skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

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

Abstract

In this paper, 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 carbonmore » 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. Finally, these data provide insight into the catalytic reaction mechanism and also the future design of new, potent inhibitors of DapE enzymes.« less

Authors:
 [1];  [2];  [2];  [2];  [3];  [1];  [1];  [1];  [2]; ORCiD logo [3]
  1. Argonne National Lab. (ANL), Argonne, IL (United States). Midwest Center for Structural Genomics. Structural Biology Center. Biosciences Division
  2. Loyola Univ. Chicago, IL (United States). Dept. of Chemistry and Biochemistry
  3. Marquette Univ., Milwaukee, WI (United States). Dept. of Chemistry
Publication Date:
Research Org.:
Argonne National Laboratory (ANL), Argonne, IL (United States); Loyola Univ. Chicago, IL (United States); Marquette Univ., Milwaukee, WI (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER); National Inst. of Health (NIH) (United States); National Science Foundation (NSF); Todd Wehr Foundation (United States)
OSTI Identifier:
1427504
Grant/Contract Number:  
AC02-06CH11357; HHSN272200700058C; HHSN272201200026C; CHE-1412443
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Biochemistry
Additional Journal Information:
Journal Volume: 57; Journal Issue: 5; Journal ID: ISSN 0006-2960
Publisher:
American Chemical Society (ACS)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats

Nocek, Boguslaw, Reidl, Cory, Starus, Anna, Heath, Tahirah, Bienvenue, David, Osipiuk, Jerzy, Jedrzejczak, Robert, Joachimiak, Andrzej, 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. United States: N. p., 2017. Web. doi:10.1021/acs.biochem.7b01151.
Nocek, Boguslaw, Reidl, Cory, Starus, Anna, Heath, Tahirah, Bienvenue, David, Osipiuk, Jerzy, Jedrzejczak, Robert, Joachimiak, Andrzej, Becker, Daniel P., & Holz, Richard C. Structural Evidence of a Major Conformational Change Triggered by Substrate Binding in DapE Enzymes: Impact on the Catalytic Mechanism. United States. https://doi.org/10.1021/acs.biochem.7b01151
Nocek, Boguslaw, Reidl, Cory, Starus, Anna, Heath, Tahirah, Bienvenue, David, Osipiuk, Jerzy, Jedrzejczak, Robert, Joachimiak, Andrzej, Becker, Daniel P., and Holz, Richard C. 2017. "Structural Evidence of a Major Conformational Change Triggered by Substrate Binding in DapE Enzymes: Impact on the Catalytic Mechanism". United States. https://doi.org/10.1021/acs.biochem.7b01151. https://www.osti.gov/servlets/purl/1427504.
@article{osti_1427504,
title = {Structural Evidence of a Major Conformational Change Triggered by Substrate Binding in DapE Enzymes: Impact on the Catalytic Mechanism},
author = {Nocek, Boguslaw and Reidl, Cory and Starus, Anna and Heath, Tahirah and Bienvenue, David and Osipiuk, Jerzy and Jedrzejczak, Robert and Joachimiak, Andrzej and Becker, Daniel P. and Holz, Richard C.},
abstractNote = {In this paper, 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. Finally, these data provide insight into the catalytic reaction mechanism and also the future design of new, potent inhibitors of DapE enzymes.},
doi = {10.1021/acs.biochem.7b01151},
url = {https://www.osti.gov/biblio/1427504}, journal = {Biochemistry},
issn = {0006-2960},
number = 5,
volume = 57,
place = {United States},
year = {Fri Dec 22 00:00:00 EST 2017},
month = {Fri Dec 22 00:00:00 EST 2017}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 12 works
Citation information provided by
Web of Science

Figures / Tables:

Figure 1 Figure 1: Enzymatic cleavage of L,L-SDAP (1) by DapE yielding succinate (2) and L,L-DAP (3).

Save / Share:

Works referenced in this record:

Antimicrobial resistance: action to combat the rising microbial challenges
journal, June 2013


Antibiotics and Bacterial Resistance in the 21st Century
journal, January 2014


Lysine biosynthesis in bacteria: a metallodesuccinylase as a potential antimicrobial target
journal, December 2012


Inhibition of lysine biosynthesis: an evolving antibiotic strategy
journal, January 2007


The dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase from Haemophilus influenzae contains two active-site histidine residues
journal, August 2008


Structural Basis for Catalysis by the Mono- and Dimetalated Forms of the dapE-Encoded N-succinyl-l,l-Diaminopimelic Acid Desuccinylase
journal, April 2010


The Dimerization Domain in DapE Enzymes Is required for Catalysis
journal, May 2014


[20] Processing of X-ray diffraction data collected in oscillation mode
book, January 1997


Molecular replacement with MOLREP
journal, December 2009


REFMAC 5 for the refinement of macromolecular crystal structures
journal, March 2011


PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010


MolProbity: all-atom contacts and structure validation for proteins and nucleic acids
journal, May 2007


Structural and mechanistic insight into substrate binding from the conformational dynamics in apo and substrate-bound DapE enzyme
journal, January 2016


Small revisions to predicted distances around metal sites in proteins
journal, May 2006


Structural Analysis of a Ternary Complex of Allantoate Amidohydrolase from Escherichia coli Reveals its Mechanics
journal, April 2007


Structural and Functional Analyses Reveal That Staphylococcus aureus Antibiotic Resistance Factor HmrA Is a Zinc-dependent Endopeptidase
journal, July 2011


Crystallization and preliminary X-ray analysis of β-alanine synthase from the yeast Saccharomyces kluyveri
journal, June 2003


Enzyme Catalysis by Hydrogen Bonds: The Balance between Transition State Binding and Substrate Binding in Oxyanion Holes
journal, March 2010


Solid-State 17 O NMR of Unstable Acyl-Enzyme Intermediates: A Direct Probe of Hydrogen Bonding Interactions in the Oxyanion Hole of Serine Proteases
journal, October 2016


The d apE -encoded N -Succinyl- l , l -Diaminopimelic Acid Desuccinylase from Haemophilus i nfluenzae Is a Dinuclear Metallohydrolase
journal, December 2003


Kinetic and spectroscopic characterization of the E134A- and E134D-altered dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase from Haemophilus influenzae
journal, January 2006


Structural basis of catalysis by monometalated methionine aminopeptidase
journal, June 2006


Kinetic and Spectroscopic Characterization of the H178A Methionyl Aminopeptidase from Escherichia coli
journal, May 2003


Works referencing / citing this record: