PDBsum entry 7ccd

DNA binding protein/DNA

PDB id: 7ccd

Contents

Protein chains

169 a.a.

DNA/RNA

Waters ×23

PDB id:

7ccd

Name:

DNA binding protein/DNA

Title:

Sulfur binding domain of sprmcra complexed with phosphorothioated DNA

Structure:

Hnhc domain-containing protein. Chain: a, b. Fragment: sulfur binding domain. Engineered: yes. DNA (5'-d( Cp Ap Cp Gp Tp Tp Cp Gp Cp C)-3'). Chain: e, c. Engineered: yes. DNA (5'-d( Gp Gp Cp Gp As Ap Cp Gp Tp G)-3'). Chain: f, d.

Source:

Streptomyces pristinaespiralis. Organism_taxid: 38300. Gene: spri_5136. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Escherichia coli b7a. Organism_taxid: 340184. Organism_taxid: 340184

Resolution:

2.42Å R-factor: 0.204 R-free: 0.249

Authors:

H.Yu,J.Li,G.Liu,G.Zhao,Y.Wang,W.Hu,Z.Deng,J.Gan,Y.Zhao,X.He

Key ref:

H.Yu et al. (2020). DNA backbone interactions impact the sequence specificity of DNA sulfur-binding domains: revelations from structural analyses. Nucleic Acids Res, 48, 8755-8766. PubMed id: 32621606 DOI: 10.1093/nar/gkaa574

Date:

16-Jun-20 Release date: 08-Jul-20

Protein chains

A0A0M4DML1  (A0A0M4DML1_STRPR) -  HNH nuclease domain-containing protein from Streptomyces pristinaespiralis

Seq: 326 a.a.

Struc: 169 a.a.*

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

DNA/RNA chains

C-A-C-G-T-T-C-G-C-C 10 bases

G-G-C-G-_AS-A-C-G-T-G 10 bases

C-A-C-G-T-T-C-G-C-C 10 bases

G-G-C-G-_AS-A-C-G-T-G 10 bases

DOI no: 10.1093/nar/gkaa574

Nucleic Acids Res 48:8755-8766 (2020)

PubMed id: 32621606

DNA backbone interactions impact the sequence specificity of DNA sulfur-binding domains: revelations from structural analyses.

H.Yu, J.Li, G.Liu, G.Zhao, Y.Wang, W.Hu, Z.Deng, G.Wu, J.Gan, Y.L.Zhao, X.He.

ABSTRACT

The sulfur atom of phosphorothioated DNA (PT-DNA) is coordinated by a surface cavity in the conserved sulfur-binding domain (SBD) of type IV restriction enzymes. However, some SBDs cannot recognize the sulfur atom in some sequence contexts. To illustrate the structural determinants for sequence specificity, we resolved the structure of SBDSpr, from endonuclease SprMcrA, in complex with DNA of GPSGCC, GPSATC and GPSAAC contexts. Structural and computational analyses explained why it binds the above PT-DNAs with an affinity in a decreasing order. The structural analysis of SBDSpr-GPSGCC and SBDSco-GPSGCC, the latter only recognizes DNA of GPSGCC, revealed that a positively charged loop above the sulfur-coordination cavity electrostatically interacts with the neighboring DNA phosphate linkage. The structural analysis indicated that the DNA-protein hydrogen bonding pattern and weak non-bonded interaction played important roles in sequence specificity of SBD protein. Exchanges of the positively-charged amino acid residues with the negatively-charged residues in the loop would enable SBDSco to extend recognization for more PT-DNA sequences, implying that type IV endonucleases can be engineered to recognize PT-DNA in novel target sequences.