4JDG image
Deposition Date 2013-02-25
Release Date 2014-02-26
Last Version Date 2024-10-30
Entry Detail
PDB ID:
4JDG
Keywords:
Title:
Structure of Tomato Bifunctional Nuclease TBN1, variant N211D
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.74 Å
R-Value Free:
0.26
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
H 3
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Nuclease
Gene (Uniprot):tbn1
Mutations:N211D
Chain IDs:A
Chain Length:277
Number of Molecules:1
Biological Source:Solanum lycopersicum
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
ASN A ASN GLYCOSYLATION SITE
Primary Citation
Phosphate binding in the active centre of tomato multifunctional nuclease TBN1 and analysis of superhelix formation by the enzyme
Acta Crystallogr.,Sect.F 71 1408 1415 (2015)
PMID: 26527269 DOI: 10.1107/S2053230X15018324

Abstact

Tomato multifunctional nuclease TBN1 belongs to the type I nuclease family, which plays an important role in apoptotic processes and cell senescence in plants. The newly solved structure of the N211D mutant is reported. Although the main crystal-packing motif (the formation of superhelices) is conserved, the details differ among the known structures. A phosphate ion was localized in the active site of the enzyme. The binding of the surface loop to the active centre is stabilized by the phosphate ion, which correlates with the observed aggregation of TBN1 in phosphate buffer. The conserved binding of the surface loop to the active centre suggests biological relevance of the contact in a regulatory function or in the formation of oligomers.

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Primary Citation of related structures