3ZI5

Crystal STRUCTURE OF RESTRICTION ENDONUCLEASE BFII C-TERMINAL RECOGNITION DOMAIN IN COMPLEX WITH COGNATE DNA

Summary for 3ZI5

• Entry DOI: 10.2210/pdb3zi5/pdb
• Descriptor: RESTRICTION ENDONUCLEASE, 5'-D(*AP*GP*CP*AP*CP*TP*GP*GP*GP*TP*CP*GP)-3', 5'-D(*CP*GP*AP*CP*CP*CP*AP*GP*TP*GP*CP*TP)-3', ... (4 entities in total)
• Functional Keywords: hydrolase-dna complex, dna-binding pseudobarrel fold, dna recognition, hydrolase/dna
• Biological source: BACILLUS FIRMUS; More
• Total number of polymer chains: 6
• Total formula weight: 52063.21

Authors

Golovenko, D.,Manakova, E.,Zakrys, L.,Zaremba, M.,Sasnauskas, G.,Grazulis, S.,Siksnys, V. (deposition date: 2013-01-03, release date: 2014-01-15, Last modification date: 2023-12-20)

Primary citation

Golovenko, D.,Grazulis, S.,Manakova, E.,Sasnauskas, G.,Siksnys, V.,Zakrys, L.,Zaremba, M.
Structural Insight Into the Specificity of the B3 DNA-Binding Domains Provided by the Co-Crystal Structure of the C-Terminal Fragment of Bfii Restriction Enzyme
Nucleic Acids Res., 42:4113-, 2014

PubMed Abstract: The B3 DNA-binding domains (DBDs) of plant transcription factors (TF) and DBDs of EcoRII and BfiI restriction endonucleases (EcoRII-N and BfiI-C) share a common structural fold, classified as the DNA-binding pseudobarrel. The B3 DBDs in the plant TFs recognize a diverse set of target sequences. The only available co-crystal structure of the B3-like DBD is that of EcoRII-N (recognition sequence 5'-CCTGG-3'). In order to understand the structural and molecular mechanisms of specificity of B3 DBDs, we have solved the crystal structure of BfiI-C (recognition sequence 5'-ACTGGG-3') complexed with 12-bp cognate oligoduplex. Structural comparison of BfiI-C-DNA and EcoRII-N-DNA complexes reveals a conserved DNA-binding mode and a conserved pattern of interactions with the phosphodiester backbone. The determinants of the target specificity are located in the loops that emanate from the conserved structural core. The BfiI-C-DNA structure presented here expands a range of templates for modeling of the DNA-bound complexes of the B3 family of plant TFs.

PubMed: 24423868
DOI: 10.1093/NAR/GKT1368

Experimental method

X-RAY DIFFRACTION (3.2 Å)