7VXR

Crystal structure of BPSL1038 from Burkholderia pseudomallei


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.118 
  • R-Value Observed: 0.120 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural and functional analyses of Burkholderia pseudomallei BPSL1038 reveal a Cas-2/VapD nuclease sub-family.

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.

(2023) Commun Biol 6: 920-920

  • DOI: https://doi.org/10.1038/s42003-023-05265-4
  • Primary Citation of Related Structures:  
    7VXR, 7VXT

  • 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 11 (X20)SST motif was identified and proposed for BPSL1038 and its orthologs. Structure modelling indicates the catalytic role of the D 11 (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.


  • Organizational Affiliation

    Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, 43600, Selangor, Malaysia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BPSL1038
A, B
108Burkholderia pseudomallei K96243Mutation(s): 0 
Gene Names: BPSL1038
UniProt
Find proteins for Q63W52 (Burkholderia pseudomallei (strain K96243))
Explore Q63W52 
Go to UniProtKB:  Q63W52
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ63W52
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.118 
  • R-Value Observed: 0.120 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.36α = 90
b = 115.63β = 90
c = 46.73γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Universiti Kebangsaan MalaysiaMalaysiaGGPM- 2012-069
Universiti Kebangsaan MalaysiaMalaysiaGUP-2017-070
Universiti Kebangsaan MalaysiaMalaysiaDIP-2012-13
Ministry of Higher Education, MalaysiaMalaysiaERGS/1/2011/STG/UKM/01/15

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-16
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Database references, Structure summary