4Q68

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.07 Å
  • R-Value Free: 0.138 
  • R-Value Work: 0.110 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

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: 10.1016/j.str.2014.09.018
  • Primary Citation of Related Structures:  

  • 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 s ...

    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); Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA.,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.,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.,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.,Joint Center for Structural Genomics (JCSG); Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.,Joint Center for Structural Genomics (JCSG); Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.,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.,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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein
A
240Bacteroides uniformis (strain ATCC 8492 / DSM 6597 / CIP 103695 / JCM 5828 / NCTC 13054 / VPI 0061)Mutation(s): 0 
Find proteins for A7V5T8 (Bacteroides uniformis (strain ATCC 8492 / DSM 6597 / CIP 103695 / JCM 5828 / NCTC 13054 / VPI 0061))
Go to UniProtKB:  A7V5T8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 46.473α = 90.00
b = 63.552β = 90.00
c = 73.997γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
MolProbitymodel building
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-07
    Type: Initial release
  • Version 1.1: 2014-12-24
    Type: Structure summary
  • Version 1.2: 2017-11-22
    Type: Refinement description
  • Version 1.3: 2018-01-24
    Type: Database references
  • Version 1.4: 2019-09-18
    Type: Data collection, Database references, Derived calculations