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Lysine Biosynthesis in Bacteria: A Metallodesuccinylase as a Lysine Biosynthesis in Bacteria: A Metallodesuccinylase as a
Potential Antimicrobial Target Potential Antimicrobial Target
Danuta M. Gillner
Silesian University of Technology
Daniel P. Becker Ph.D.
Loyola University Chicago
, dbecke3@luc.edu
Richard C. Holz
Loyola University Chicago
, rholz1@luc.edu
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Recommended Citation Recommended Citation
Gillner, Danuta M.; Becker, Daniel P. Ph.D.; and Holz, Richard C.. Lysine Biosynthesis in Bacteria: A
Metallodesuccinylase as a Potential Antimicrobial Target. JBIC Journal of Biological Inorganic Chemistry,
18, 2: 155-163, 2013. Retrieved from Loyola eCommons, Chemistry: Faculty Publications and Other Works,
http://dx.doi.org/10.1007/s00775-012-0965-1
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Lysine Biosynthesis in Bacteria:
A Metallodesuccinylase as a Potential Antimicrobial Target
Danuta M. Gillner
1,2
*, Daniel Becker
1
, and Richard C. Holz
1
*
Contribution from the Department of Chemistry and Biochemistry, Loyola University-
Chicago, 1068 W. Sheridan Rd., Chicago, IL 60626 and the Department of Chemistry,
Silesian University of Technology, ul. Krzywoustego 4, 44-100 Gliwice, Poland
Running Title: dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase
1
Loyola University Chicago,
2
Silesian University of Technology
†
This work was supported by the National Institutes of Health (R15 AI085559-01A1, RCH).
*
Address correspondence to: Richard C. Holz, Department of Chemistry, Loyola University-
Chicago, 1068 W. Sheridan Rd., Chicago, IL 60626, Phone (773) 508-3092, Fax: (773) 508-
3086, Internet:
rholz1@luc.edu or Danuta M. Gillner, Department of Chemistry, Silesian
University of Technology, ul. Krzywoustego 4, 44-100 Gliwice, Poland, Phone +48 32 237 27
91, Fax: +48 32 237 10 32, Internet:
Danuta.Gilner@polsl.pl.
Antibiotic Resistance
2
Abstract
In this review, we summarize the recent literature on the dapE-encoded N-succinyl-
L,L-diaminopimelic acid desuccinylase (DapE) enzymes with an emphasis on structure-
function studies, which have provided insight into the catalytic mechanism of DapE enzymes.
Crystallographic data has also provided insight into residues that might be involved in
substrate, and hence inhibitor recognition and binding. These data have led to the design and
synthesis of several new DapE inhibitors, which are described along with what is known
about how inhibitors interact with the active site of DapE enzymes including the efficacy of a
moderately strong DapE inhibitor.
Key Words: DapE, Metallohydrolase, Antibiotics, Zinc, X-ray Crystallography, Inhibitor
Design, Catalytic Mechanism.
3
The emergence of antibiotic-resistant bacterial infections has created a significant and
growing medical problem in the United States and throughout the world [1-5]. Antibiotic
resistance has been recognized since the introduction of penicillin more than 50 years ago
when penicillin-resistant infections caused by Staphylococcus aureus rapidly appeared [3, 6].
Because bacteria have been exposed to many of the currently available antibiotics such as β–
lactams, fluoroquinolones, macrolides, tetracyclines, aminoglycosides, glycopeptides, or
trimethoprim combinations for years, they have evolved resistance to these drugs due to
mutation or the acquisition of genes that impart resistance from other organisms [3, 7-10]. In
fact, several pathogenic bacteria, some of which were thought to have been eradicated, have
made a significant resurgence due to bacterial resistance to antibiotics [3, 6]. For example,
tuberculosis is currently the leading cause of death in adults by an infectious disease
worldwide, which is significant given that death rates due to tuberculosis had declined to near
imperceptible levels in industrial nations [11-13]. According to the CDC, several bacterial
strains currently exhibit multidrug resistance with more than 60% hospital acquired infections
in the United States caused by the so-called ESKAPE pathogens (E
nterococcus faecium,
S
taphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas
aeruginosa, and E
nterobacter species).
Antibiotics work by interfering with a vital bacterial cell function at a specific cellular
target by either killing the bacteria or arresting their multiplication [5]. This allows the
patient's immune system to clear the bacteria from the body. Inhibitors of cell wall
biosynthesis (vancomycin and β-lactams, to name a few) have proven to be very potent
antibiotics, evidence that interfering with cell-wall synthesis has deleterious effects on
bacterial cell survival. Enzymes that are targeted by these antibiotics tend to be present in all
bacteria and are highly similar in structure and function, such that certain antibiotics kill or
inhibit the growth of a broad range of bacterial species (i.e., broad-spectrum antibiotics) [3, 7-
4
10]. Unfortunately, only two new classes of anti-bacterial drugs have emerged since 1962.
According to the Infectious Diseases Society of America at least ten new systemic
antibacterial drugs should enter the market by the year 2020; however, most of these are
derivatives of existing classes of antibiotics. Since every antibiotic has a finite lifetime, as
resistance will ultimately occur particularly if the same enzymes are repeatedly targeted,
development of new classes of inhibitors that target previously untargeted cellular enzymes is
essential to retain control of infectious disease [14, 15].
Lysine Biosynthetic Pathway
Based on bacterial genetic information, the meso-diaminopimelate (mDAP)/lysine
biosynthetic pathway offers several potential antibacterial enzyme targets that have yet to be
explored (Figure 1) [16-18]. One of the products of this pathway, lysine, is required in
protein synthesis and is also used in the peptidoglycan layer of Gram-positive bacterial cell
walls. A second product of this pathway, mDAP is an essential component of the
peptidoglycan cell wall for Gram-negative bacteria, providing a link between polysaccharide
strands. Since lysine is an essential amino acid and is not synthesized by humans, it must be
ingested. However, most bacteria, plants and algae synthesize lysine and mDAP from
aspartic acid through three related pathways that diverge after the production of L-
tetrahydrodipicolinate [16, 17, 19]. The presence of multiple biosynthetic pathways in
bacteria for the synthesis of mDAP/lysine highlights the importance of mDAP/lysine for
bacterial cell survival.
The succinylase pathway is the primary biosynthetic pathway for mDAP/lysine and is
utilized by all Gram-negative and most Gram-positive bacteria [16]. The dehydrogenase
pathway forms mDAP directly from L-tetrahydrodipicolinate but this is a high-energy
transformation and is limited to only a few Bacillus species [16]. The acetylase pathway is