skip to main content
DOE PAGES 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 Lab. (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:
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. 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., & 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.. Fri . "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},
journal = {Biochemistry},
number = 5,
volume = 57,
place = {United States},
year = {2017},
month = {12}
}

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

Citation Metrics:
Cited by: 1 work
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

  • Fair, Richard J.; Tor, Yitzhak
  • Perspectives in Medicinal Chemistry, Vol. 6
  • DOI: 10.4137/PMC.S14459

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

  • Gillner, Danuta M.; Becker, Daniel P.; Holz, Richard C.
  • JBIC Journal of Biological Inorganic Chemistry, Vol. 18, Issue 2
  • DOI: 10.1007/s00775-012-0965-1

Characterization of Helicobacter pylori dapE and construction of a conditionally lethal dapE mutant.
journal, January 1997


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

  • Hutton, Craig A.; Perugini, Matthew A.; Gerrard, Juliet A.
  • Molecular BioSystems, Vol. 3, Issue 7
  • DOI: 10.1039/b705624a

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

  • Gillner, Danuta M.; Bienvenue, David L.; Nocek, Boguslaw P.
  • JBIC Journal of Biological Inorganic Chemistry, Vol. 14, Issue 1
  • DOI: 10.1007/s00775-008-0418-z

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

  • Nocek, Boguslaw P.; Gillner, Danuta M.; Fan, Yao
  • Journal of Molecular Biology, Vol. 397, Issue 3
  • DOI: 10.1016/j.jmb.2010.01.062

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


Inhibition of the dapE -Encoded N -Succinyl- l , l -diaminopimelic Acid Desuccinylase from Neisseria meningitidis by l -Captopril
journal, July 2015


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


Molecular replacement with MOLREP
journal, December 2009

  • Vagin, Alexei; Teplyakov, Alexei
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1
  • DOI: 10.1107/S0907444909042589

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

  • Murshudov, Garib N.; Skubák, Pavol; Lebedev, Andrey A.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
  • DOI: 10.1107/S0907444911001314

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

  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
  • DOI: 10.1107/S0907444909052925

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

  • Davis, I. W.; Leaver-Fay, A.; Chen, V. B.
  • Nucleic Acids Research, Vol. 35, Issue Web Server
  • DOI: 10.1093/nar/gkm216

Coot model-building tools for molecular graphics
journal, November 2004

  • Emsley, Paul; Cowtan, Kevin
  • Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132
  • DOI: 10.1107/S0907444904019158

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

  • Dutta, Debodyuti; Mishra, Sabyashachi
  • Physical Chemistry Chemical Physics, Vol. 18, Issue 3
  • DOI: 10.1039/C5CP06024A

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

  • Harding, Marjorie M.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 6
  • DOI: 10.1107/S0907444906014594

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

  • Agarwal, Rakhi; Burley, Stephen K.; Swaminathan, Subramanyam
  • Journal of Molecular Biology, Vol. 368, Issue 2
  • DOI: 10.1016/j.jmb.2007.02.028

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

  • Botelho, Tiago O.; Guevara, Tibisay; Marrero, Aniebrys
  • Journal of Biological Chemistry, Vol. 286, Issue 29
  • DOI: 10.1074/jbc.M111.247437

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

  • Dobritzsch, Doreen; Gojković, Zoran; Andersen, Birgit
  • Acta Crystallographica Section D Biological Crystallography, Vol. 59, Issue 7
  • DOI: 10.1107/S0907444903009120

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

  • Simón, Luis; Goodman, Jonathan M.
  • The Journal of Organic Chemistry, Vol. 75, Issue 6
  • DOI: 10.1021/jo901503d

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

  • Tang, Aaron W.; Kong, Xianqi; Terskikh, Victor
  • The Journal of Physical Chemistry B, Vol. 120, Issue 43
  • DOI: 10.1021/acs.jpcb.6b08798

MAB, a generally applicable molecular force field for structure modelling in medicinal chemistry
journal, June 1995

  • Gerber, Paul R.; M�ller, Klaus
  • Journal of Computer-Aided Molecular Design, Vol. 9, Issue 3
  • DOI: 10.1007/BF00124456

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

  • Cosper, Nathaniel J.; Bienvenue, David L.; Shokes, Jacob E.
  • Journal of the American Chemical Society, Vol. 125, Issue 48
  • DOI: 10.1021/ja036650v

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

  • Davis, Ryan; Bienvenue, David; Swierczek, Sabina I.
  • JBIC Journal of Biological Inorganic Chemistry, Vol. 11, Issue 2
  • DOI: 10.1007/s00775-005-0071-8

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

  • Ye, Q. -Z.; Xie, S. -X.; Ma, Z. -Q.
  • Proceedings of the National Academy of Sciences, Vol. 103, Issue 25
  • DOI: 10.1073/pnas.0602433103

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

  • Copik, Alicja J.; Swierczek, Sabina I.; Lowther, W. Todd
  • Biochemistry, Vol. 42, Issue 20
  • DOI: 10.1021/bi027327s

    Works referencing / citing this record: