{"entry": {"accession": "MF7000980", "general": {"name": "Selenomethionine-labeled BPSL1038 (Burkholderia pseudomallei)", "pdb_id": "7vxt", "exp_method": "X-ray", "resolution": "1.88", "assembly": "Homodimer", "source_organism": "Burkholderia pseudomallei", "publication": {"pmid": "37684342", "authors": "Shaibullah S, Shuhaimi N, Ker DS, Mohd-Sharif N, Ho KL, Teh AH, Waterman J, Tang TH, Wong RR, Nathan S, Mohamed R, Ng MJ, Fung SY, Jonet MA, Firdaus-Raih M, Ng CL", "title": "Structural and functional analyses of Burkholderia pseudomallei BPSL1038 reveal a Cas-2/VapD nuclease sub-family.", "journal": "Commun Biol", "year": "2023", "issue": "1", "volume": "6", "pages": "920", "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\u2009\u00c5 resolution crystal structure of BPSL1038. The overall structure folded into a modified \u03b2\u03b1\u03b2\u03b2\u03b1\u03b2\u03b1 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<sub>+</sub> and K<sub>+</sub>) is crucial for nuclease activity. An active site with a unique D<sub>11</sub>(X20)SST motif was identified and proposed for BPSL1038 and its orthologs. Structure modelling indicates the catalytic role of the D<sub>11</sub>(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."}}, "function": null, "macromolecules": {"general": {"nr_of_chains": "2", "nr_of_unique_protein_segments": "1", "class": "Homooligomeric enzymes", "subclass": "Homodimeric enzymes", "note": "All chains according to the most probable oligomerization state stored in PDBe were considered."}, "chain": [{"id": "A", "name": "Uncharacterized protein", "source_organism": "Burkholderia pseudomallei", "uniprot": {"id": "Q63W52", "start": "1", "end": "87", "coverage": "98%", "sequence": "MAGNLVIVCRDQDADAFDQLMQEYGSFQTRLSSTAWYLNMNIVPETLQEDILERVGKYTTLYIFEATSVTYNTIDSNAAETLSTLFGE", "length": "88"}, "regions": {"region": [{"region_type": "secondary structure", "region_name": "helix", "region_start": "33", "region_end": "42"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "43", "region_end": "46"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "63", "region_end": "76"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "95", "region_end": "107"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "9", "region_end": "12"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "24", "region_end": "29"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "48", "region_end": "52"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "55", "region_end": "59"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "81", "region_end": "92"}]}}, {"id": "B", "name": "Uncharacterized protein", "source_organism": "Burkholderia pseudomallei", "uniprot": {"id": "Q63W52", "start": "2", "end": "87", "coverage": "97%", "sequence": "MAGNLVIVCRDQDADAFDQLMQEYGSFQTRLSSTAWYLNMNIVPETLQEDILERVGKYTTLYIFEATSVTYNTIDSNAAETLSTLFGE", "length": "88"}, "regions": {"region": [{"region_type": "secondary structure", "region_name": "helix", "region_start": "33", "region_end": "42"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "43", "region_end": "46"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "63", "region_end": "76"}, {"region_type": "secondary structure", "region_name": "helix", "region_start": "95", "region_end": "106"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "24", "region_end": "29"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "48", "region_end": "52"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "55", "region_end": "59"}, {"region_type": "secondary structure", "region_name": "strand", "region_start": "81", "region_end": "92"}]}}]}, "evidence": {"evidence_level": "Insufficient evidence (candidate)", "evidence_coverage": "The full structure participates in mutual synergistic folding.", "sequence_domain": "BPSL1038 modified ferredoxin fold", "complex_evidence": "The two monomers have a common beta sheet and a large total calculated buried interface area that involves mainly hydrophobic interactions in addition to 16 hydrogen bonds and one salt bridge. In total, 42% of the amino acids (37 residues) are associated with dimerization (PMID: 37684342).", "chain_evidence": [{"chain_id": "A", "support": "N/A"}, {"chain_id": "B", "support": "N/A"}]}, "related_structures": {"id": ["MF7000980", "MF7000981"]}}}