Database accession: MF7000981
Name: BPSL1038 (Burkholderia pseudomallei)
PDB ID: 7vxr
Experimental method: X-ray (1.55 Å)
Assembly: Homodimer
Source organism: Burkholderia pseudomallei
Primary publication of the structure:
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
Structural and functional analyses of Burkholderia pseudomallei BPSL1038 reveal a Cas-2/VapD nuclease sub-family.
(2023) Commun Biol 6: 920
PMID: 37684342
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 D11(X20)SST motif was identified and proposed for BPSL1038 and its orthologs. Structure modelling indicates the catalytic role of the D11(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.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown.Molecular function: not assigned
Biological process: not assigned
Cellular component: not assigned
Structural annotations of the participating protein chains.Entry contents: 2 distinct polypeptide molecules
Chains: A, B
Notes: All chains according to the most probable oligomerization state stored in PDBe were considered.
Number of unique protein segments: 1
Name: Uncharacterized protein
Source organism: Burkholderia pseudomallei
Length: 88 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMAGNLVIVCRDQDADAFDQLMQEYGSFQTRLSSTAWYLNMNIVPETLQEDILERVGKYTTLYIFEATSVTYNTIDSNAAETLSTLFGE
UniProtKB AC: Q63W52 (positions: 1-87)
Coverage: 98%
Name: Uncharacterized protein
Source organism: Burkholderia pseudomallei
Length: 88 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMAGNLVIVCRDQDADAFDQLMQEYGSFQTRLSSTAWYLNMNIVPETLQEDILERVGKYTTLYIFEATSVTYNTIDSNAAETLSTLFGE
UniProtKB AC: Q63W52 (positions: 2-87)
Coverage: 97%
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Representative domain in related structures: BPSL1038 modified ferredoxin fold
Evidence level: Insufficient evidence (candidate)
Evidence coverage: The full structure participates in mutual synergistic folding.
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 A:
N/A
Chain B:
N/A
Surface and contacts features:
Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap). Download the CIF file (.cif)
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