7VXT

Crystal structure of a selenomethionine-labeled BPSL1038 from Burkholderia pseudomallei

PDB DOI: https://doi.org/10.2210/pdb7VXT/pdb

Classification: HYDROLASE
Organism(s): Burkholderia pseudomallei K96243
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-11-13 Released: 2023-08-16
Deposition Author(s): Shaibullah, S., Mohd-Sharif, M., Ho, K.L., Firdaus-Raih, M., Nathan, S., Mohamed, R., Teh, A.K., Waterman, J., Ng, C.L.
Funding Organization(s): Universiti Kebangsaan Malaysia, Ministry of Higher Education, Malaysia

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free:
0.178 (Depositor), 0.180 (DCC)
R-Value Work:
0.148 (Depositor), 0.150 (DCC)
R-Value Observed:
0.149 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 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

PubMed: 37684342 Search on PubMedSearch on PubMed Central
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.

Macromolecule Content

Total Structure Weight: 25.05 kDa
Atom Count: 1,729
Modelled Residue Count: 187
Deposited Residue Count: 216
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BPSL1038	A, B	108	Burkholderia pseudomallei K96243	Mutation(s): 0 Gene Names: BPSL1038
UniProt
Find proteins for Q63W52 (Burkholderia pseudomallei (strain K96243)) Explore Q63W52 Go to UniProtKB: Q63W52
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q63W52
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BME Query on BME Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B]	C [auth A], D [auth A], F [auth B], G [auth B], H [auth B]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B]	E [auth A], I [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.178 (Depositor), 0.180 (DCC)
R-Value Work: 0.148 (Depositor), 0.150 (DCC)
R-Value Observed: 0.149 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.726	α = 90
b = 115.891	β = 90
c = 46.812	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-08-16

Deposition Author(s):

Funding Organization	Location	Grant Number
Universiti Kebangsaan Malaysia	Malaysia	DIP-2012-13
Universiti Kebangsaan Malaysia	Malaysia	GGPM- 2012-069
Universiti Kebangsaan Malaysia	Malaysia	GUP-2017-070
Ministry of Higher Education, Malaysia	Malaysia	ERGS/1/2011/STG/UKM/01/15