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Title: 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 Lab., Menlo Park, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22); USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1294697
Alternate Identifier(s):
OSTI ID: 1227566; OSTI ID: 1291095
Grant/Contract Number:  
AC02-76SF00515; U54 GM094586; P41GM103393
Resource Type:
Journal Article: 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. 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., and Wilson, Ian A. Mon . "Structure-Guided Functional Characterization of DUF1460 Reveals a Highly Specific NlpC/P60 Amidase Family". United Kingdom. doi: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},
issn = {0969-2126},
number = 12,
volume = 22,
place = {United Kingdom},
year = {2014},
month = {12}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record at 10.1016/j.str.2014.09.018

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Cited by: 3 works
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