8XZ2

The structural model of a homodimeric D-Ala-D-Ala metallopeptidase, VanX, from vancomycin-resistant bacteria

Summary for 8XZ2

• Entry DOI: 10.2210/pdb8xz2/pdb
• Related: 1r44
• Descriptor: D-alanyl-D-alanine dipeptidase (1 entity in total)
• Functional Keywords: acid-selective unlabeling, antimicrobial resistance, homodimer, residual dipolar coupling (rdc), transfer cross saturation (tcs), vancomycin-resistant enterococci, vanx, metal binding protein
• Biological source: Enterococcus faecium
• Total number of polymer chains: 2
• Total formula weight: 46816.34

Authors

Konuma, T.,Takai, T.,Tsuchiya, C.,Nishida, M.,Hashiba, M.,Yamada, Y.,Shirai, H.,Motoda, Y.,Nagadoi, A.,Chikaishi, E.,Akagi, K.,Akashi, S.,Yamazaki, T.,Akutsu, H.,Oe, A.,Ikegami, T. (deposition date: 2024-01-20, release date: 2024-05-22)

Primary citation

Konuma, T.,Takai, T.,Tsuchiya, C.,Nishida, M.,Hashiba, M.,Yamada, Y.,Shirai, H.,Motoda, Y.,Nagadoi, A.,Chikaishi, E.,Akagi, K.I.,Akashi, S.,Yamazaki, T.,Akutsu, H.,Ikegami, T.
Analysis of the homodimeric structure of a D-Ala-D-Ala metallopeptidase, VanX, from vancomycin-resistant bacteria.
Protein Sci., 33:e5002-e5002, 2024

PubMed Abstract: Bacteria that have acquired resistance to most antibiotics, particularly those causing nosocomial infections, create serious problems. Among these, the emergence of vancomycin-resistant enterococci was a tremendous shock, considering that vancomycin is the last resort for controlling methicillin-resistant Staphylococcus aureus. Therefore, there is an urgent need to develop an inhibitor of VanX, a protein involved in vancomycin resistance. Although the crystal structure of VanX has been resolved, its asymmetric unit contains six molecules aligned in a row. We have developed a structural model of VanX as a stable dimer in solution, primarily utilizing nuclear magnetic resonance (NMR) residual dipolar coupling. Despite the 46 kDa molecular mass of the dimer, the analyses, which are typically not as straightforward as those of small proteins around 10 kDa, were successfully conducted. We assigned the main chain using an amino acid-selective unlabeling method. Because we found that the zinc ion-coordinating active sites in the dimer structure were situated in the opposite direction to the dimer interface, we generated an active monomer by replacing an amino acid at the dimer interface. The monomer consists of only 202 amino acids and is expected to be used in future studies to screen and improve inhibitors using NMR.

PubMed: 38723146
DOI: 10.1002/pro.5002

Experimental method

SOLUTION NMR