5FDK

Crystal structure of RecU(D88N) in complex with palindromic DNA duplex

Summary for 5FDK

• Entry DOI: 10.2210/pdb5fdk/pdb
• Related: 1ZP7
• Descriptor: Holliday junction resolvase RecU, palindromic DNA (2 entities in total)
• Functional Keywords: resolvase, holliday junction, recu, dna, complex, dna-binding proteins, hydrolase
• Biological source: Bacillus subtilis; More
• Cellular location: Cytoplasm : P39792
• Total number of polymer chains: 8
• Total formula weight: 108283.58

Authors

Khavnekar, S.,Rafferty, J.B.,Kale, A. (deposition date: 2015-12-16, release date: 2016-12-07, Last modification date: 2024-05-08)

Primary citation

Khavnekar, S.,Dantu, S.C.,Sedelnikova, S.,Ayora, S.,Rafferty, J.,Kale, A.
Structural insights into dynamics of RecU-HJ complex formation elucidates key role of NTR and stalk region toward formation of reactive state.
Nucleic Acids Res., 45:975-986, 2017

PubMed Abstract: Holliday junction (HJ) resolving enzyme RecU is involved in DNA repair and recombination. We have determined the crystal structure of inactive mutant (D88N) of RecU from Bacillus subtilis in complex with a 12 base palindromic DNA fragment at a resolution of 3.2 Å. This structure shows the stalk region and the essential N-terminal region (NTR) previously unseen in our DNA unbound structure. The flexible nature of the NTR in solution was confirmed using SAXS. Thermofluor studies performed to assess the stability of RecU in complex with the arms of an HJ indicate that it confers stability. Further, we performed molecular dynamics (MD) simulations of wild type and an NTR deletion variant of RecU, with and without HJ. The NTR is observed to be highly flexible in simulations of the unbound RecU, in agreement with SAXS observations. These simulations revealed domain dynamics of RecU and their role in the formation of complex with HJ. The MD simulations also elucidate key roles of the NTR, stalk region, and breathing motion of RecU in the formation of the reactive state.

PubMed: 27903910
DOI: 10.1093/nar/gkw1165

Experimental method

X-RAY DIFFRACTION (3.208 Å)