Crystal structure of a N-acetylmuramoyl-L-alanine amidase (BACUNI_02947) from Bacteroides uniformis ATCC 8492 at 1.07 A resolution

Experimental Data Snapshot

  • Resolution: 1.07 Å
  • R-Value Free: 0.138 
  • R-Value Work: 0.110 
  • R-Value Observed: 0.112 

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This is version 1.8 of the entry. See complete history


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

Xu, Q.Mengin-Lecreulx, D.Patin, D.Grant, J.C.Chiu, H.J.Jaroszewski, L.Knuth, M.W.Godzik, A.Lesley, S.A.Elsliger, M.A.Deacon, A.M.Wilson, I.A.

(2014) Structure 22: 1799-1809

  • DOI: https://doi.org/10.1016/j.str.2014.09.018
  • Primary Citation of Related Structures:  
    4H4J, 4Q5K, 4Q68

  • PubMed 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.

  • Organizational Affiliation

    Joint Center for Structural Genomics (JCSG); Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein240Bacteroides uniformis ATCC 8492Mutation(s): 0 
Gene Names: BACUNI_02947
Find proteins for A7V5T8 (Bacteroides uniformis (strain ATCC 8492 / DSM 6597 / CCUG 4942 / CIP 103695 / JCM 5828 / KCTC 5204 / NCTC 13054 / VPI 0061))
Explore A7V5T8 
Go to UniProtKB:  A7V5T8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7V5T8
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.473α = 90
b = 63.552β = 90
c = 73.997γ = 90
Software Package:
Software NamePurpose
MolProbitymodel building
PDB_EXTRACTdata extraction
XSCALEdata scaling
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-07
    Type: Initial release
  • Version 1.1: 2014-12-24
    Changes: Structure summary
  • Version 1.2: 2017-11-22
    Changes: Refinement description
  • Version 1.3: 2018-01-24
    Changes: Database references
  • Version 1.4: 2019-09-18
    Changes: Data collection, Database references, Derived calculations
  • Version 1.5: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.6: 2023-02-01
    Changes: Database references, Structure summary
  • Version 1.7: 2023-09-20
    Changes: Data collection, Refinement description
  • Version 1.8: 2023-12-06
    Changes: Data collection