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Structure. 2014 Dec 2;22(12):1799-1809. doi: 10.1016/j.str.2014.09.018. Epub 2014 Nov 20.

Structure-guided functional characterization of DUF1460 reveals a highly specific NlpC/P60 amidase family.

Author information

1
Joint Center for Structural Genomics (JCSG); Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
2
Laboratoire des Enveloppes Bactériennes et Antibiotiques, Université Paris-Sud, IBBMC, UMR 8619, Orsay F-91405, France; Centre National de la Recherche Scientifique (CNRS), Orsay F-91405, France. Electronic address: dominique.mengin-lecreulx@u-psud.fr.
3
Laboratoire des Enveloppes Bactériennes et Antibiotiques, Université Paris-Sud, IBBMC, UMR 8619, Orsay F-91405, France; Centre National de la Recherche Scientifique (CNRS), Orsay F-91405, France.
4
Joint Center for Structural Genomics (JCSG); Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA.
5
Joint Center for Structural Genomics (JCSG); Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA 92093, USA; Program on Bioinformatics and Systems Biology, Sanford-Burnham Institute for Medical Research, La Jolla, CA 92037, USA.
6
Joint Center for Structural Genomics (JCSG); Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
7
Joint Center for Structural Genomics (JCSG); Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
8
Joint Center for Structural Genomics (JCSG); Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address: wilson@scripps.edu.

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 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 subsequently were characterized experimentally. 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 another amidase family.

PMID:
25465128
PMCID:
PMC4255150
DOI:
10.1016/j.str.2014.09.018
[Indexed for MEDLINE]
Free PMC Article

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