7VXR

Crystal structure of BPSL1038 from Burkholderia pseudomallei

Summary for 7VXR

• Entry DOI: 10.2210/pdb7vxr/pdb
• Descriptor: BPSL1038, SODIUM ION (3 entities in total)
• Functional Keywords: nuclease, cas2, dsst motif, hydrolase
• Biological source: Burkholderia pseudomallei K96243
• Total number of polymer chains: 2
• Total formula weight: 24261.71

Authors

Shaibullah, S.,Mohd-Sharif, M.,Ho, K.L.,Firdaus-Raih, M.,Nathan, S.,Mohamed, R.,Teh, A.K.,Waterman, J.,Ng, C.L. (deposition date: 2021-11-13, release date: 2023-08-16, Last modification date: 2023-09-20)

Primary citation

Shaibullah, S.,Shuhaimi, N.,Ker, D.S.,Mohd-Sharif, N.,Ho, K.L.,Teh, A.H.,Waterman, J.,Tang, T.H.,Wong, R.R.,Nathan, S.,Mohamed, R.,Ng, M.J.,Fung, S.Y.,Jonet, M.A.,Firdaus-Raih, M.,Ng, C.L.
Structural and functional analyses of Burkholderia pseudomallei BPSL1038 reveal a Cas-2/VapD nuclease sub-family.
Commun Biol, 6:920-920, 2023

PubMed Abstract: Burkholderia pseudomallei is a highly versatile pathogen with ~25% of its genome annotated to encode hypothetical proteins. One such hypothetical protein, BPSL1038, is conserved across seven bacterial genera and 654 Burkholderia spp. Here, we present a 1.55 Å resolution crystal structure of BPSL1038. The overall structure folded into a modified βαββαβα ferredoxin fold similar to known Cas2 nucleases. The Cas2 equivalent catalytic aspartate (D11) pairs are conserved in BPSL1038 although B. pseudomallei has no known CRISPR associated system. Functional analysis revealed that BPSL1038 is a nuclease with endonuclease activity towards double-stranded DNA. The DNase activity is divalent ion independent and optimum at pH 6. The concentration of monovalent ions (Na and K) is crucial for nuclease activity. An active site with a unique D(X20)SST motif was identified and proposed for BPSL1038 and its orthologs. Structure modelling indicates the catalytic role of the D(X20)SST motif and that the arginine residues R10 and R30 may interact with the nucleic acid backbone. The structural similarity of BPSL1038 to Cas2 proteins suggests that BPSL1038 may represent a sub-family of nucleases that share a common ancestor with Cas2.

PubMed: 37684342
DOI: 10.1038/s42003-023-05265-4

Experimental method

X-RAY DIFFRACTION (1.55 Å)