Structural Biology of the Nudix Proteins from the Extremely Radiation-Resistant Bacterium Deinococcus radiodurans
EMSL Project ID
2331
Abstract
Deinococcus radiodurans is a bacterium that is extremely resistant to the lethal and mutagenic effects of ionizing radiation, ultraviolet radiation, and other physical and chemical DNA-damaging agents. It has been suggested that this resistance is due to unusually efficient DNA repair mechanisms. Analysis of the complete genome sequence of D. radiodurans reveals a full suite of genes with potential DNA repair activities, essentially all of which have functional homologues in other procaryotic systems. Furthermore, D. radiodurans displays a high amount of redundancy in these hypothetical DNA repair genes. One of the mechanisms that have evolved to reduce the mutation rate in cells is to remove modified nucleotide triphosphates from the NTP pool in the cell and prevent their use for DNA synthesis. One of the best characterized of these is MutT, a protein that hydrolyses 7,8-dihydro-8-oxoguanosine triphosphates. 7,8-Dihydro-8-oxoguanosine is a known mutatgen that acts to increase base mispairing during DNA replication; an A instead of a C often being inserted opposite the modified guanosine. Upon mispairing the error is perpetuated in subsequent rounds of DNA replication. MutT is a member of a large family of proteins, often referred to as the Nudix (nucleotide diphosphate linked to x) hydrolases. A requirement for nucleotide diphosphates appears to be the common feature of Nudix substrates. Nudix proteins can be recognized in genome sequences by a fairly short region of sequence homology in a region involved in contacting the nucleotide diphosphate. Analysis of the D. radiodurans sequences identifies 20 Nudix proteins in the bacterium's genome, far more than in any other bacterium genome studied. The only structure for a member of the class of Nudix proteins is MutT. Our project focuses on determining the structures of the D. radiodurans Nudix proteins and determining their substrate specificity. Because these proteins are relatively small (Table 1), they are good candidates for NMR-based structural studies.
Project Details
Project type
Capability Research
Start Date
2001-10-01
End Date
2002-11-18
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members
Related Publications
Buchko, GW (2010) "Circular dichroism studies on the Deinococcus radiodurans Nudix hydrolase DR_0079: An atypical thermal melt." Protein and Peptide Letters. 17:831-835.
Buchko GW, O Litvinova, H Robinson, AF Yakunin, and MA Kennedy. 2008. "Functional and structural characterization of DR_0079 from Deinococcus radiodurans, a novel Nudix hydrolase with a preference for cytosine (deoxy) ribonucleoside 5'-di- and triphosphates." Biochemistry 47(25):6571-6582.
Buchko GW, S Ni, SR Holbrook, and MA Kennedy. 2003. "H-1, C-13, and N-15 NMR assignments of the hypothetical Nudix protein DR0079 from the extremely radiation-resistant bacterium Deinococcus radiodurans.." Journal of Biomolecular NMR 25(2):169-170.
Buchko GW, S Ni, SR Holbrook, and MA Kennedy. 2004. "Solution Structure of Hypothetical Nudix Hydrolase DR0079 from Extremely Radiation-Resistant Deinococcus radiodurans Bacterium." Proteins. Structure, Function, and Bioinformatics 56(1):28-39.
E.L. Holbrook, U. Schulze-Gahmen, G.W. Buchko, S. Ni, M.A. Kennedy, and S.R. Holbrook. (2003) Purification, crystallization and preliminary X-ray analysis of two Nudix hydrolases from Deinococcus radiodurans. Acta Crystallogr. D Biol. Crystallogr., 59:737-740.