3ODH

Structure of OkrAI/DNA complex

Summary for 3ODH

• Entry DOI: 10.2210/pdb3odh/pdb
• Descriptor: OkrAI endonuclease, DNA (5'-D(*TP*AP*TP*GP*GP*AP*TP*CP*CP*AP*TP*A)-3'), CALCIUM ION, ... (4 entities in total)
• Functional Keywords: alpha and beta proteins (a/b), restriction endonuclease-like, phosphodiesterase, hydrolase-dna complex, hydrolase/dna
• Biological source: Oceanobacter kriegii
• Total number of polymer chains: 8
• Total formula weight: 102380.27

Authors

Vanamee, E.S.,Aggarwal, A.K. (deposition date: 2010-08-11, release date: 2010-10-06, Last modification date: 2024-02-21)

Primary citation

Vanamee, E.S.,Viadiu, H.,Chan, S.H.,Ummat, A.,Hartline, A.M.,Xu, S.Y.,Aggarwal, A.K.
Asymmetric DNA recognition by the OkrAI endonuclease, an isoschizomer of BamHI.
Nucleic Acids Res., 39:712-719, 2011

PubMed Abstract: Restriction enzymes share little or no sequence homology with the exception of isoschizomers, or enzymes that recognize and cleave the same DNA sequence. We present here the structure of a BamHI isoschizomer, OkrAI, bound to the same DNA sequence (TATGGATCCATA) as that cocrystallized with BamHI. We show that OkrAI is a more minimal version of BamHI, lacking not only the N- and C-terminal helices but also an internal 3(10) helix and containing β-strands that are shorter than those in BamHI. Despite these structural differences, OkrAI recognizes the DNA in a remarkably similar manner to BamHI, including asymmetric contacts via C-terminal 'arms' that appear to 'compete' for the minor groove. However, the arms are shorter than in BamHI. We observe similar DNA-binding affinities between OkrAI and BamHI but OkrAI has higher star activity (at 37°C) compared to BamHI. Together, the OkrAI and BamHI structures offer a rare opportunity to compare two restriction enzymes that work on exactly the same DNA substrate.

PubMed: 20833632
DOI: 10.1093/nar/gkq779

Experimental method

X-RAY DIFFRACTION (2.3 Å)