The Catalytic Core Domains of Integrases

Home Page National Cancer Institute Macromolecular Crystallography Laboratory Retroviral Integrase Project NCI-Frederick MCL - Protein Structure Section
Structures determined by the Macromolecular Crystallography Laboratory, Protein Structure Section at the NCI-Frederick campus. Work performed in collaboration with the Skalka Laboratory in the Institute for Cancer Research, Fox Chase Cancer Center.






IN full length protein and catalytic core domain

All structures presented in this web site are of the catalytic core domains, characteristic of retroviral integrase proteins. A domain is a stable part of a protein. Different protein domains can carry out different functions. The IN catalytic core domain contains the active site, binds metal cations, and carries out the integration reaction. This core domain resembles that of other proteins both structurally and functionally. Flanking the catalytic core domain is the N-terminal domain, which binds zinc and appears to alter conformation, stabilize the protein, and increase activity, and the C-terminal domain, which binds DNA and has an "SH-3"-like fold (resembles a protein called SH-3).

Although many people have attempted to crystallize or otherwise solve the structure of the entire protein, these attempts have not been successful. There are several reasons for this lack of success, including the fact that full-length INs can be significantly less soluble than the catalytic core, and that the three domains are connected by flexible regions. Flexibility is undoubtedly important for enzyme function, but this very flexibility may result in more conformational variability than the conditions for protein crystallization can handle. It appears that a more rigid protein unit, such as the catalytic core domain, can pack better into a crystalline form than can the full-length protein. The structures of the two other domains, the N- and C-termini, have been solved in solution by nuclear magnetic resonance (NMR) spectroscopy. However, having all three domain structures solved separately does not allow a determination of how the entire protein fits or works together. Additional work on solving the structure of the entire protein or separate domains with inhibitors and DNA is in progress. *Core domain diagram adapted from work done for the MSL by Richard Frederickson, Publications Dept., NCI-FCRDC.



The coordinate and Rasmol image files of ASV IN core domain are available from the PDB.

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If you have questions or comments about the Integrase Project web site,
contact: Jerry N. Alexandratos at alexandr@ncifcrf.gov.