6SDK

Crystal structure of bacterial ParB dimer bound to CDP

PDB DOI: https://doi.org/10.2210/pdb6SDK/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Bacillus subtilis subsp. subtilis str. 168
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-07-28 Released: 2019-10-23
Deposition Author(s): Soh, Y.M., Basquin, J., Gruber, S.
Funding Organization(s): European Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free: 0.213
R-Value Work: 0.184
R-Value Observed: 0.185

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Self-organization ofparScentromeres by the ParB CTP hydrolase.

Soh, Y.M., Davidson, I.F., Zamuner, S., Basquin, J., Bock, F.P., Taschner, M., Veening, J.W., De Los Rios, P., Peters, J.M., Gruber, S.

(2019) Science 366: 1129-1133

PubMed: 31649139 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1126/science.aay3965
Primary Citation of Related Structures:
6SDK

PubMed Abstract:
ParABS systems facilitate chromosome segregation and plasmid partitioning in bacteria and archaea. ParB protein binds centromeric parS DNA sequences and spreads to flanking DNA. We show that ParB is an enzyme that hydrolyzes cytidine triphosphate (CTP) to cytidine diphosphate (CDP). parS DNA stimulates cooperative CTP binding by ParB and CTP hydrolysis. A nucleotide cocrystal structure elucidates the catalytic center of the dimerization-dependent ParB CTPase. Single-molecule imaging and biochemical assays recapitulate features of ParB spreading from parS in the presence but not absence of CTP. These findings suggest that centromeres assemble by self-loading of ParB DNA sliding clamps at parS ParB CTPase is not related to known nucleotide hydrolases and might be a promising target for developing new classes of antibiotics.

Organizational Affiliation

Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), Lausanne, Switzerland.

Macromolecule Content

Total Structure Weight: 93.14 kDa
Atom Count: 6,932
Modelled Residue Count: 795
Deposited Residue Count: 796
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Stage 0 sporulation protein J	A, B, C, D	199	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0 Gene Names: spo0J, BSU40960
UniProt
Find proteins for P26497 (Bacillus subtilis (strain 168)) Explore P26497 Go to UniProtKB: P26497
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P26497
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDP Query on CDP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D]	E [auth A], H [auth B], K [auth C], N [auth D]	CYTIDINE-5'-DIPHOSPHATE C₉ H₁₅ N₃ O₁₁ P₂ ZWIADYZPOWUWEW-XVFCMESISA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain O [auth D] SDF format, chain P [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D]	F [auth A] G [auth A] I [auth B] J [auth B] L [auth C] F [auth A], G [auth A], I [auth B], J [auth B], L [auth C], M [auth C], O [auth D], P [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D]