skip to main content

DOE PAGESDOE PAGES

Title: Structure-Guided Functional Characterization of DUF1460 Reveals a Highly Specific NlpC/P60 Amidase Family

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:
 [1] ;  [2] ;  [3] ;  [4] ;  [1] ;  [5] ;  [4] ;  [5] ;  [6] ;  [7] ;  [1] ;  [7]
  1. Joint Center for Structural Genomics (United States); SLAC National Accelerator Lab., Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource (SSRL)
  2. Univ. Paris-Sud, Orsay (France). Lab. of Bacterial Envelopes and Antibiotics; Centre National de la Recherche Scientifique (CNRS), Orsay (France)
  3. Univ. Paris-Sud, Orsay (France). Lab. of Bacterial Envelopes and Antibiotics; Centre National de la Recherche Scientifique (CNRS), Orsay (France)
  4. Joint Center for Structural Genomics (United States); Genomics Inst. of the Novartis Research Foundation, San Diego, CA (United States). Protein Sciences Dept.
  5. Joint Center for Structural Genomics (United States); Univ. of California, San Diego, CA (United States). Center for Research in Biological Systems; Sanford-Burnham Inst. for Medical Research, La Jolla, CA (United States). Program on Bioinformatics and Systems Biology
  6. Joint Center for Structural Genomics (United States); Genomics Inst. of the Novartis Research Foundation, San Diego, CA (United States). Protein Sciences Dept.; Scripps Research Inst., La Jolla, CA (United States). Dept of Integrative Structural and Computational Biology
  7. Joint Center for Structural Genomics (United States); Scripps Research Inst., La Jolla, CA (United States). Dept of Integrative Structural and Computational Biology
Publication Date:
Grant/Contract Number:
U54 GM094586; P41GM103393; AC02-76SF00515
Type:
Published Article
Journal Name:
Structure
Additional Journal Information:
Journal Volume: 22; Journal Issue: 12; Journal ID: ISSN 0969-2126
Publisher:
Elsevier
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)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; N - acetylmuramoyl-L-alanine amidase; NlpC/P60 amidases; structure-based function prediction
OSTI Identifier:
1294697
Alternate Identifier(s):
OSTI ID: 1227566; OSTI ID: 1291095