Structure of the LdcB LD-carboxypeptidase reveals the molecular basis of peptidoglycan recognition

Christopher N. Hoyland; Christine Aldridge; Robert M. Cleverley; Marie Clémence Duchêne; George Minasov; Olena Onopriyenko; Karzan Sidiq; Peter J. Stogios; Wayne F. Anderson; Richard A. Daniel; Alexei Savchenko; Waldemar Vollmer; Richard J. Lewis

doi:10.1016/j.str.2014.04.015

Structure of the LdcB LD-carboxypeptidase reveals the molecular basis of peptidoglycan recognition

Christopher N. Hoyland, Christine Aldridge, Robert M. Cleverley, Marie Clémence Duchêne, George Minasov, Olena Onopriyenko, Karzan Sidiq, Peter J. Stogios, Wayne F. Anderson, Richard A. Daniel, Alexei Savchenko, Waldemar Vollmer, Richard J. Lewis^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

33 Scopus citations

Abstract

Peptidoglycan surrounds the bacterial cytoplasmic membrane to protect the cell against osmolysis. The biosynthesis of peptidoglycan, made of glycan strands crosslinked by short peptides, is the target of antibiotics like β-lactams and glycopeptides. Nascent peptidoglycan contains pentapeptides that are trimmed by carboxypeptidases to tetra- and tripeptides. The well-characterized DD-carboxypeptidases hydrolyze the terminal D-alanine from the stem pentapeptide to produce a tetrapeptide. However, few LD-carboxypeptidases that produce tripeptides have been identified, and nothing is known about substrate specificity in these enzymes. We report biochemical properties and crystal structures of the LD-carboxypeptidases LdcB from Streptococcus pneumoniae, Bacillus anthracis, and Bacillus subtilis. The enzymes are active against bacterial cell wall tetrapeptides and adopt a zinc-carboxypeptidase fold characteristic of the LAS superfamily. We have also solved the structure of S. pneumoniae LdcB with a product mimic, elucidating the residues essential for peptidoglycan recognition and the conformational changes that occur on ligand binding.

Original language	English (US)
Pages (from-to)	949-960
Number of pages	12
Journal	Structure
Volume	22
Issue number	7
DOIs	https://doi.org/10.1016/j.str.2014.04.015
State	Published - Jul 8 2014

Funding

We thank the staff at the Diamond Synchrotron Light Source for access to, and help with, its beamlines for X-ray diffraction data collection. We thank Arnaud Basl\u00E9, Joseph Newman, and Vincent Rao for useful discussions; Atikah Mohd Sukor for excellent technical assistance; Z. Wawrzak, S. Shatsman, and S.N. Peterson for assistance with data collection and refinement; and T. Skarina for assistance with purification and crystallization. We also thank the authors of Meziane-Cherif et al. (2014) for sharing results and atomic coordinates prior to publication. Finally, we thank Joe Gray of the Newcastle University Pinnacle-Proteomics and Biological Mass Spectrometry facility for mass spectrometry analysis of muropeptide fractions. This project has been funded in whole or in part with federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, U.S. Department of Health and Human Services (contracts HHSN272200700058C and HHSN2722012000026C), and by the UK Biotechnology and Biological Sciences Research Council in an award to R.A.D., W.V., and R.J.L. (BB/G015902/1).

ASJC Scopus subject areas

Structural Biology
Molecular Biology

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1016/j.str.2014.04.015

Cite this

Hoyland, C. N., Aldridge, C., Cleverley, R. M., Duchêne, M. C., Minasov, G., Onopriyenko, O., Sidiq, K., Stogios, P. J., Anderson, W. F., Daniel, R. A., Savchenko, A., Vollmer, W., & Lewis, R. J. (2014). Structure of the LdcB LD-carboxypeptidase reveals the molecular basis of peptidoglycan recognition. Structure, 22(7), 949-960. https://doi.org/10.1016/j.str.2014.04.015

@article{398189a5a1ec40a8b1408db3a1efc87d,

title = "Structure of the LdcB LD-carboxypeptidase reveals the molecular basis of peptidoglycan recognition",

abstract = "Peptidoglycan surrounds the bacterial cytoplasmic membrane to protect the cell against osmolysis. The biosynthesis of peptidoglycan, made of glycan strands crosslinked by short peptides, is the target of antibiotics like β-lactams and glycopeptides. Nascent peptidoglycan contains pentapeptides that are trimmed by carboxypeptidases to tetra- and tripeptides. The well-characterized DD-carboxypeptidases hydrolyze the terminal D-alanine from the stem pentapeptide to produce a tetrapeptide. However, few LD-carboxypeptidases that produce tripeptides have been identified, and nothing is known about substrate specificity in these enzymes. We report biochemical properties and crystal structures of the LD-carboxypeptidases LdcB from Streptococcus pneumoniae, Bacillus anthracis, and Bacillus subtilis. The enzymes are active against bacterial cell wall tetrapeptides and adopt a zinc-carboxypeptidase fold characteristic of the LAS superfamily. We have also solved the structure of S. pneumoniae LdcB with a product mimic, elucidating the residues essential for peptidoglycan recognition and the conformational changes that occur on ligand binding.",

author = "Hoyland, {Christopher N.} and Christine Aldridge and Cleverley, {Robert M.} and Duch{\^e}ne, {Marie Cl{\'e}mence} and George Minasov and Olena Onopriyenko and Karzan Sidiq and Stogios, {Peter J.} and Anderson, {Wayne F.} and Daniel, {Richard A.} and Alexei Savchenko and Waldemar Vollmer and Lewis, {Richard J.}",

note = "Funding Information: We thank the staff at the Diamond Synchrotron Light Source for access to, and help with, its beamlines for X-ray diffraction data collection. We thank Arnaud Basl{\'e}, Joseph Newman, and Vincent Rao for useful discussions; Atikah Mohd Sukor for excellent technical assistance; Z. Wawrzak, S. Shatsman, and S.N. Peterson for assistance with data collection and refinement; and T. Skarina for assistance with purification and crystallization. We also thank the authors of Meziane-Cherif et al. (2014) for sharing results and atomic coordinates prior to publication. Finally, we thank Joe Gray of the Newcastle University Pinnacle-Proteomics and Biological Mass Spectrometry facility for mass spectrometry analysis of muropeptide fractions. This project has been funded in whole or in part with federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, U.S. Department of Health and Human Services (contracts HHSN272200700058C and HHSN2722012000026C), and by the UK Biotechnology and Biological Sciences Research Council in an award to R.A.D., W.V., and R.J.L. (BB/G015902/1). ",

year = "2014",

month = jul,

day = "8",

doi = "10.1016/j.str.2014.04.015",

language = "English (US)",

volume = "22",

pages = "949--960",

journal = "Structure",

issn = "0969-2126",

publisher = "Cell Press",

number = "7",

}

TY - JOUR

T1 - Structure of the LdcB LD-carboxypeptidase reveals the molecular basis of peptidoglycan recognition

AU - Hoyland, Christopher N.

AU - Aldridge, Christine

AU - Cleverley, Robert M.

AU - Duchêne, Marie Clémence

AU - Minasov, George

AU - Onopriyenko, Olena

AU - Sidiq, Karzan

AU - Stogios, Peter J.

AU - Anderson, Wayne F.

AU - Daniel, Richard A.

AU - Savchenko, Alexei

AU - Vollmer, Waldemar

AU - Lewis, Richard J.

N1 - Funding Information: We thank the staff at the Diamond Synchrotron Light Source for access to, and help with, its beamlines for X-ray diffraction data collection. We thank Arnaud Baslé, Joseph Newman, and Vincent Rao for useful discussions; Atikah Mohd Sukor for excellent technical assistance; Z. Wawrzak, S. Shatsman, and S.N. Peterson for assistance with data collection and refinement; and T. Skarina for assistance with purification and crystallization. We also thank the authors of Meziane-Cherif et al. (2014) for sharing results and atomic coordinates prior to publication. Finally, we thank Joe Gray of the Newcastle University Pinnacle-Proteomics and Biological Mass Spectrometry facility for mass spectrometry analysis of muropeptide fractions. This project has been funded in whole or in part with federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, U.S. Department of Health and Human Services (contracts HHSN272200700058C and HHSN2722012000026C), and by the UK Biotechnology and Biological Sciences Research Council in an award to R.A.D., W.V., and R.J.L. (BB/G015902/1).

PY - 2014/7/8

Y1 - 2014/7/8

N2 - Peptidoglycan surrounds the bacterial cytoplasmic membrane to protect the cell against osmolysis. The biosynthesis of peptidoglycan, made of glycan strands crosslinked by short peptides, is the target of antibiotics like β-lactams and glycopeptides. Nascent peptidoglycan contains pentapeptides that are trimmed by carboxypeptidases to tetra- and tripeptides. The well-characterized DD-carboxypeptidases hydrolyze the terminal D-alanine from the stem pentapeptide to produce a tetrapeptide. However, few LD-carboxypeptidases that produce tripeptides have been identified, and nothing is known about substrate specificity in these enzymes. We report biochemical properties and crystal structures of the LD-carboxypeptidases LdcB from Streptococcus pneumoniae, Bacillus anthracis, and Bacillus subtilis. The enzymes are active against bacterial cell wall tetrapeptides and adopt a zinc-carboxypeptidase fold characteristic of the LAS superfamily. We have also solved the structure of S. pneumoniae LdcB with a product mimic, elucidating the residues essential for peptidoglycan recognition and the conformational changes that occur on ligand binding.

AB - Peptidoglycan surrounds the bacterial cytoplasmic membrane to protect the cell against osmolysis. The biosynthesis of peptidoglycan, made of glycan strands crosslinked by short peptides, is the target of antibiotics like β-lactams and glycopeptides. Nascent peptidoglycan contains pentapeptides that are trimmed by carboxypeptidases to tetra- and tripeptides. The well-characterized DD-carboxypeptidases hydrolyze the terminal D-alanine from the stem pentapeptide to produce a tetrapeptide. However, few LD-carboxypeptidases that produce tripeptides have been identified, and nothing is known about substrate specificity in these enzymes. We report biochemical properties and crystal structures of the LD-carboxypeptidases LdcB from Streptococcus pneumoniae, Bacillus anthracis, and Bacillus subtilis. The enzymes are active against bacterial cell wall tetrapeptides and adopt a zinc-carboxypeptidase fold characteristic of the LAS superfamily. We have also solved the structure of S. pneumoniae LdcB with a product mimic, elucidating the residues essential for peptidoglycan recognition and the conformational changes that occur on ligand binding.

UR - http://www.scopus.com/inward/record.url?scp=84904103328&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84904103328&partnerID=8YFLogxK

U2 - 10.1016/j.str.2014.04.015

DO - 10.1016/j.str.2014.04.015

M3 - Article

C2 - 24909784

AN - SCOPUS:84904103328

SN - 0969-2126

VL - 22

SP - 949

EP - 960

JO - Structure

JF - Structure

IS - 7

ER -

Structure of the LdcB LD-carboxypeptidase reveals the molecular basis of peptidoglycan recognition

Abstract

Funding

ASJC Scopus subject areas

UN SDGs

Access to Document

Other files and links

Fingerprint

Crystal structure of BaLdcB / VanY-like L,D-carboxypeptidase Zinc(II)-free