Brand  (β version)

PDB ID: 4KPY

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Ligands
Code Name Style Show Link
TMP Thymidine-5'-phosphate PoSSuM
MN Manganese (II) ion PoSSuM
Non-standard Residues
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Glycosylation
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Structure summary

Code : 4KPY   PDBj   RCSB PDB   PDBe
Header : DNA BINDING PROTEIN/DNA
Title : DNA binding protein and DNA complex structure
Release Data : 2014-01-29
Compound :
mol_id molecule chains
1 Uncharacterized protein A,B
mol_id molecule chains
2 DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)-3') C,E
mol_id molecule chains
3 DNA (5'-D(P*TP*AP*CP*TP*AP*CP*CP*TP*CP*G)-3') D,F
mol_id molecule chains
4 DNA (5'-D(*TP*AP*TP*AP*CP*AP*AP*CP*C)-3') M,N
Source :
mol_id organism_scientific expression_system
1 Thermus thermophilus  (taxid:262724) Escherichia coli  (taxid:562)
strain: HB27
gene: TT_P0026
expression_system_strain: Rosetta
expression_system_vector_type: plasmid
expression_system_plasmid: pET-sumo
mol_id organism_scientific
2 Synthetic construct  (taxid:32630)
synthetic: yes
mol_id organism_scientific
3 Synthetic construct  (taxid:32630)
synthetic: yes
mol_id organism_scientific
4 Synthetic construct  (taxid:32630)
synthetic: yes
Authors : Sheng, G., Zhao, H., Wang, J., Rao, Y., Wang, Y.
Keywords : Argonaute, RNA interference, DNA interference, DNA BINDING PROTEIN-DNA complex
Exp. method : X-RAY DIFFRACTION ( 2.4060 Å )
Citation :

Structure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage.

Sheng, G.,Zhao, H.,Wang, J.  et al.
(2014)  Proc.Natl.Acad.Sci.USA  111 : 652 - 657

PubMed: 24374628
DOI: 10.1073/pnas.1321032111

Reaction

Chain : A, B
UniProt : Q746M7 (AGO_THET2)
Reaction : -
Cofactor: Evidence: Note:
Mn(2+) ECO:0000269 | PubMed:18754009
ECO:0000269 | PubMed:19812667
ECO:0000269 | PubMed:24374628
ECO:0000269 | PubMed:24531762
ECO:0000269 | PubMed:32846159
Binds 3 Mn(2+) per subunit (Probable) (PubMed:24374628). Target RNA cleavage occurs in the presence of Mn(2+) (PubMed:18754009, PubMed:19812667). Prefers Mn(2+) over Mg(2+) for tDNA cleavage (PubMed:24531762). tDNA cleavage occurs in the presence of Mn(2+) or Mg(2+) with a slight preference for Mn(2+), no cleavage occurs in the presence of Ca(2+) (PubMed:19812667, PubMed:24374628).