Structure-Guided Functional Characterization of DUF1460 Reveals a Highly Specific NlpC/P60 Amidase Family
Abstract
GlcNAc-1,6-anhydro-MurNAc-tetrapeptide is a major peptidoglycan degradation intermediate and a cytotoxin. It is generated by lytic transglycosylases and further degraded and recycled by various enzymes. We have identified and characterized a novel, highly specific N-acetylmuramoyl-L-alanine amidase (AmiA) from Bacteroides uniformis, a member of the DUF1460 protein family, that hydrolyzes GlcNAc-1,6-anhydro-MurNAc-peptide into disaccharide and stem peptide. The high-resolution apo-structure at 1.15 Å resolution shows that AmiA is related to NlpC/P60 γ-D-Glu-meso-diaminopimelic acid amidases and shares a common catalytic core and cysteine peptidase-like active site. AmiA has evolved structural adaptations that reconfigure the substrate recognition site. The preferred substrates for AmiA were predicted in silico based on structural and bioinformatics data, and were subsequently characterized experimentally. Ultimately, further crystal structures of AmiA in complexes with GlcNAc-1,6-anhydro-MurNAc and GlcNAc have enabled us to elucidate substrate recognition and specificity. DUF1460 is highly conserved in structure and defines a new amidase family.
- Authors:
- Publication Date:
- Research Org.:
- SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES); USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1294697
- Alternate Identifier(s):
- OSTI ID: 1227566; OSTI ID: 1291095
- Grant/Contract Number:
- AC02-76SF00515; U54 GM094586; P41GM103393
- Resource Type:
- Published Article
- Journal Name:
- Structure
- Additional Journal Information:
- Journal Name: Structure Journal Volume: 22 Journal Issue: 12; Journal ID: ISSN 0969-2126
- Publisher:
- Elsevier
- Country of Publication:
- United Kingdom
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; N - acetylmuramoyl-L-alanine amidase; NlpC/P60 amidases; structure-based function prediction
Citation Formats
Xu, Qingping, Mengin-Lecreulx, Dominique, Patin, Delphine, Grant, Joanna C., Chiu, Hsiu-Ju, Jaroszewski, Lukasz, Knuth, Mark W., Godzik, Adam, Lesley, Scott A., Elsliger, Marc-André, Deacon, Ashley M., and Wilson, Ian A. Structure-Guided Functional Characterization of DUF1460 Reveals a Highly Specific NlpC/P60 Amidase Family. United Kingdom: N. p., 2014.
Web. doi:10.1016/j.str.2014.09.018.
Xu, Qingping, Mengin-Lecreulx, Dominique, Patin, Delphine, Grant, Joanna C., Chiu, Hsiu-Ju, Jaroszewski, Lukasz, Knuth, Mark W., Godzik, Adam, Lesley, Scott A., Elsliger, Marc-André, Deacon, Ashley M., & Wilson, Ian A. Structure-Guided Functional Characterization of DUF1460 Reveals a Highly Specific NlpC/P60 Amidase Family. United Kingdom. https://doi.org/10.1016/j.str.2014.09.018
Xu, Qingping, Mengin-Lecreulx, Dominique, Patin, Delphine, Grant, Joanna C., Chiu, Hsiu-Ju, Jaroszewski, Lukasz, Knuth, Mark W., Godzik, Adam, Lesley, Scott A., Elsliger, Marc-André, Deacon, Ashley M., and Wilson, Ian A. Mon .
"Structure-Guided Functional Characterization of DUF1460 Reveals a Highly Specific NlpC/P60 Amidase Family". United Kingdom. https://doi.org/10.1016/j.str.2014.09.018.
@article{osti_1294697,
title = {Structure-Guided Functional Characterization of DUF1460 Reveals a Highly Specific NlpC/P60 Amidase Family},
author = {Xu, Qingping and Mengin-Lecreulx, Dominique and Patin, Delphine and Grant, Joanna C. and Chiu, Hsiu-Ju and Jaroszewski, Lukasz and Knuth, Mark W. and Godzik, Adam and Lesley, Scott A. and Elsliger, Marc-André and Deacon, Ashley M. and Wilson, Ian A.},
abstractNote = {GlcNAc-1,6-anhydro-MurNAc-tetrapeptide is a major peptidoglycan degradation intermediate and a cytotoxin. It is generated by lytic transglycosylases and further degraded and recycled by various enzymes. We have identified and characterized a novel, highly specific N-acetylmuramoyl-L-alanine amidase (AmiA) from Bacteroides uniformis, a member of the DUF1460 protein family, that hydrolyzes GlcNAc-1,6-anhydro-MurNAc-peptide into disaccharide and stem peptide. The high-resolution apo-structure at 1.15 Å resolution shows that AmiA is related to NlpC/P60 γ-D-Glu-meso-diaminopimelic acid amidases and shares a common catalytic core and cysteine peptidase-like active site. AmiA has evolved structural adaptations that reconfigure the substrate recognition site. The preferred substrates for AmiA were predicted in silico based on structural and bioinformatics data, and were subsequently characterized experimentally. Ultimately, further crystal structures of AmiA in complexes with GlcNAc-1,6-anhydro-MurNAc and GlcNAc have enabled us to elucidate substrate recognition and specificity. DUF1460 is highly conserved in structure and defines a new amidase family.},
doi = {10.1016/j.str.2014.09.018},
journal = {Structure},
number = 12,
volume = 22,
place = {United Kingdom},
year = {Mon Dec 01 00:00:00 EST 2014},
month = {Mon Dec 01 00:00:00 EST 2014}
}
https://doi.org/10.1016/j.str.2014.09.018
Web of Science
Works referencing / citing this record:
Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2013-2014: ANALYSIS OF CARBOHYDRATES AND GLYCOCONJUGATES
journal, April 2018
- Harvey, David J.
- Mass Spectrometry Reviews, Vol. 37, Issue 4
Functional metagenomic discovery of bacterial effectors in the human microbiome and isolation of commendamide, a GPCR G2A/132 agonist
journal, August 2015
- Cohen, Louis J.; Kang, Hahk-Soo; Chu, John
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 35
Enterococcus faecium secreted antigen A generates muropeptides to enhance host immunity and limit bacterial pathogenesis
journal, April 2019
- Kim, Byungchul; Wang, Yen-Chih; Hespen, Charles W.
- eLife, Vol. 8