4Q5K

Crystal structure of a N-acetylmuramoyl-L-alanine amidase (BACUNI_02947) from Bacteroides uniformis ATCC 8492 at 1.30 A resolution

Summary for 4Q5K

• Entry DOI: 10.2210/pdb4q5k/pdb
• Descriptor: Uncharacterized protein, (2R)-2-[[(1R,2S,3R,4R,5R)-4-acetamido-2-[(2S,3R,4R,5S,6R)-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]oxy-6,8-dioxabicyclo[3.2.1]octan-3-yl]oxy]propanoic acid, SODIUM ION, ... (4 entities in total)
• Functional Keywords: pf07313 family protein, duf 1460, structural genomics, joint center for structural genomics, jcsg, protein structure initiative, psi-biology, unknown function
• Biological source: Bacteroides uniformis
• Total number of polymer chains: 1
• Total formula weight: 27400.06

Authors

Joint Center for Structural Genomics (JCSG) (deposition date: 2014-04-17, release date: 2014-05-21, Last modification date: 2024-10-16)

Primary citation

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.
Structure-guided functional characterization of DUF1460 reveals a highly specific NlpC/P60 amidase family.
Structure, 22:1799-1809, 2014

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.

PubMed: 25465128
DOI: 10.1016/j.str.2014.09.018

Experimental method

X-RAY DIFFRACTION (1.3 Å)