The Crystallography Open Database (COD), which is a project that aims to gather all available inorganic, metal-organic and small organic molecule structural data in one database, is described. The database adopts an openaccess model. The COD currently contains 80 000 entries in crystallographic information file format, with nearly full coverage of the International Union of Crystallography publications, and is growing in size and quality.

Using an open-access distribution model, the Crystallography Open Database (COD, http://www.crystallography.net) collects all known ‘small molecule / small to medium sized unit cell’ crystal structures and makes them available freely on the Internet. As of today, the COD has aggregated ∼150 000 structures, offering basic search capabilities and the possibility to download the whole database, or parts thereof using a variety of standard open communication protocols. A newly developed website provides capabilities for all registered users to deposit published and so far unpublished structures as personal communications or pre-publication depositions. Such a setup enables extension of the COD database by many users simultaneously. This increases the possibilities for growth of the COD database, and is the first step towards establishing a world wide Internet-based collaborative platform dedicated to the collection and curation of structural knowledge.

The crystal structure of the NgoMIV restriction endonuclease in complex with cleaved DNA has been determined at 1.6 A resolution. The crystallographic asymmetric unit contains a protein tetramer and two DNA molecules cleaved at their recognition sites. This is the first structure of a tetrameric restriction enzyme-DNA complex. In the tetramer, two primary dimers are arranged back to back with two oligonucleotides bound in clefts on opposite sides of the tetramer. The DNA molecules retain a B-type conformation and have an enclosed angle between their helical axes of 60 degrees. Sequence-specific interactions occur in both the major and minor grooves. Two Mg2+ ions are located close to the cleaved phosphate at the active site of NgoMIV. Biochemical experiments show that interactions between the recognition sites within the tetramer greatly increase DNA cleavage efficiency.

Among all restriction endonucleases known to date, BfiI is unique in cleaving DNA in the absence of metal ions. BfiI represents a different evolutionary lineage of restriction enzymes, as shown by its crystal structure at 1.9-Å resolution. The protein consists of two structural domains. The N-terminal catalytic domain is similar to Nuc, an EDTA-resistant nuclease from the phospholipase D superfamily. The C-terminal DNA-binding domain of BfiI exhibits a ␤-barrel-like structure very similar to the effector DNA-binding domain of the Mg 2؉ -dependent restriction enzyme EcoRII and to the B3-like DNA-binding domain of plant transcription factors. BfiI presumably evolved through domain fusion of a DNA-recognition element to a nonspecific nuclease akin to Nuc and elaborated a mechanism to limit DNA cleavage to a single double-strand break near the specific recognition sequence. The crystal structure suggests that the interdomain linker may act as an autoinhibitor controlling BfiI catalytic activity in the absence of a specific DNA sequence. A PSI-BLAST search identified a BfiI homologue in a Mesorhizobium sp. BNC1 bacteria strain, a plant symbiont isolated from an EDTA-rich environment.restriction endonuclease ͉ x-ray crystallography R estriction endonucleases (REases) protect bacteria by hydrolyzing invading viral or other foreign DNA. Type II REases perform their function by catalyzing the sequencespecific cleavage of double-stranded DNA molecules in the presence of Mg 2ϩ ions within or close to their recognition sites (1). Surprisingly, orthodox REases and bacteriophage -exonuclease that binds a free end of double-stranded DNA and processively degrades one strand in the 5Ј to 3Ј direction share a similar catalytic mechanism and a common structural ancestor (2). A -exonuclease-like domain has been identified in many Mg 2ϩ -dependent nucleases involved in DNA recombination and repair (3-5), suggesting that it has been remolded during evolution to perform different functions. To constrain cleavage at specific sites, REases had to develop effective means to control nucleolytic activity of -exonuclease-like catalytic domain.A variety of mechanisms have evolved to maintain REases in inactive configuration to avoid uncontrolled DNA cleavage and couple it to the recognition of specific nucleotide sequence. Orthodox REases, like EcoRI or BamHI, are homodimers that make largely symmetrical interactions with palindromic DNA sequences and contain two distinct sites each responsible for catalyzing cleavage in one DNA strand (1). In orthodox restriction enzymes, structural elements involved in sequence recognition are grafted on the conserved -exonuclease-like scaffold that makes a catalytic core (6). Structural analysis indicates that EcoRI amino acid residues involved in specific DNA binding are coupled to the catalytic residues through the intricate network of interactions (7). Therefore, any perturbation in the recognition site (for example, an incorrect base pair) would propagate via the network to the cleavage site and thus ...