3GOX

Crystal structure of the beta-beta-alpha-Me type II restriction endonuclease Hpy99I in the absence of EDTA

Summary for 3GOX

• Entry DOI: 10.2210/pdb3gox/pdb
• Related: 1A73 2QNC 2QNF 3FC3
• Descriptor: Restriction endonuclease Hpy99I, 5'-(*DCP*DTP*DCP*DGP*DAP*DCP*DGP*DTP*DAP*DGP*DA)-3', 5'-(*DTP*DAP*DCP*DGP*DTP*DCP*DGP*DAP*DGP*DTP*DC)-3', ... (7 entities in total)
• Functional Keywords: endonuclease-dna complex, restriction enzyme, hpy99i, pseudopalindrome, hydrolase-dna complex, hydrolase/dna
• Biological source: Helicobacter pylori; More
• Total number of polymer chains: 4
• Total formula weight: 52812.78

Authors

Sokolowska, M.,Czapinska, H.,Bochtler, M. (deposition date: 2009-03-20, release date: 2009-04-28, Last modification date: 2024-02-21)

Primary citation

Sokolowska, M.,Czapinska, H.,Bochtler, M.
Crystal structure of the beta beta alpha-Me type II restriction endonuclease Hpy99I with target DNA.
Nucleic Acids Res., 37:3799-3810, 2009

PubMed Abstract: The beta beta alpha-Me restriction endonuclease (REase) Hpy99I recognizes the CGWCG target sequence and cleaves it with unusual stagger (five nucleotide 5'-recessed ends). Here we present the crystal structure of the specific complex of the dimeric enzyme with DNA. The Hpy99I protomer consists of an antiparallel beta-barrel and two beta 4 alpha 2 repeats. Each repeat coordinates a structural zinc ion with four cysteine thiolates in two CXXC motifs. The beta beta alpha-Me region of the second beta 4 alpha 2 repeat holds the catalytic metal ion (or its sodium surrogate) via Asp148 and Asn165 and activates a water molecule with the general base His149. In the specific complex, Hpy99I forms a ring-like structure around the DNA that contacts DNA bases on the major and minor groove sides via the first and second beta 4 alpha 2 repeats, respectively. Hpy99I interacts with the central base pair of the recognition sequence only on the minor groove side, where A:T resembles T:A and G:C is similar to C:G. The Hpy99I-DNA co-crystal structure provides the first detailed illustration of the beta beta alpha-Me site in REases and complements structural information on the use of this active site motif in other groups of endonucleases such as homing endonucleases (e.g. I-PpoI) and Holliday junction resolvases (e.g. T4 endonuclease VII).

PubMed: 19380375
DOI: 10.1093/nar/gkp228

Experimental method

X-RAY DIFFRACTION (1.5 Å)