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PDBsum entry 7cc9
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DNA binding protein/DNA
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PDB id
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7cc9
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PDB id:
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| Name: |
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DNA binding protein/DNA
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Title:
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Sulfur binding domain of sprmcra complexed with phosphorothioated DNA
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Structure:
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Hnhc domain-containing protein. Chain: a, b, c. Fragment: sulfur binding domain. Engineered: yes. DNA (5'-d( Gp Gp Cp Gp Gs Cp Cp C)-3'). Chain: d, f, h. Engineered: yes. DNA (5'-d( Gp Gp Gp Cp Cp Gp Cp C)-3'). Chain: e, g, i.
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Source:
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Streptomyces pristinaespiralis. Organism_taxid: 38300. Gene: spri_5136. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Streptomyces lividans 1326. Organism_taxid: 1200984. Organism_taxid: 1200984
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Resolution:
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2.06Å
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R-factor:
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0.212
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R-free:
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0.231
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Authors:
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H.Yu,G.Zhao,J.Gan,G.Liu,G.Wu,X.He
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Key ref:
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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:
DOI:
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Date:
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16-Jun-20
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Release date:
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08-Jul-20
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PROCHECK
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Headers
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References
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A0A0M4DML1
(A0A0M4DML1_STRPR) -
HNH nuclease domain-containing protein from Streptomyces pristinaespiralis
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Seq:
Struc:
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326 a.a.
163 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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G-G-C-G-_GS-C-C-C
8 bases
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G-G-G-C-C-G-C-C
8 bases
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G-G-C-G-_GS-C-C-C
8 bases
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G-G-G-C-C-G-C-C
8 bases
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G-G-C-G-_GS-C-C-C
8 bases
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G-G-G-C-C-G-C-C
8 bases
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DOI no:
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Nucleic Acids Res
48:8755-8766
(2020)
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PubMed id:
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DNA backbone interactions impact the sequence specificity of DNA sulfur-binding domains: revelations from structural analyses.
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H.Yu,
J.Li,
G.Liu,
G.Zhao,
Y.Wang,
W.Hu,
Z.Deng,
G.Wu,
J.Gan,
Y.L.Zhao,
X.He.
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ABSTRACT
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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.
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