The crystal structure of the hyperthermophile chromosomal protein Sso7d bound to DNA

Gao, Yu; Su, Shenjian; Robinson, Howard; Padmanabhan, Savita; Lim, Louis W.; McCrary, Bradford S.; Edmondson, Stephen P.; Shriver, John W.; Wang, Andrew H.‐J.

doi:10.1038/1822

Cited by 150 publications

(160 citation statements)

References 32 publications

(6 reference statements)

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“…We have compared the distance separating the tether attachment points for distal site disulfide crosslinking, namely the N 6 of adenine 5 and the ␤-carbon of residue 292, between the reported structures of hOGG1 that illuminate many of the base extrusion intermediates, from those that occur "early" to "late" in the pathway (Fig. 6A) (18,22,24,26). From this comparison we found that this distance varies as a function of progression along the nucleobase extrusion pathway.…”

Section: Resultsmentioning

confidence: 99%

“…When proteins interact with DNA lacking any specific recognition feature, the two macromolecules form large ensembles of rapidly interconverting complexes, and this inherent heterogeneity has hampered attempts to characterize nonspecific protein-DNA interactions at atomic resolution (21)(22)(23)(24)(25)(26)(27)(28)(29)(30)(31)(32). We have overcome this problem by developing a straightforward means by which to drastically limit the region a protein can explore while diffusing along DNA, through the introduction of an intermolecular disulfide cross-link (DXL) between protein and DNA.…”

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confidence: 99%

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Enforced Presentation of an Extrahelical Guanine to the Lesion Recognition Pocket of Human 8-Oxoguanine Glycosylase, hOGG1

Crenshaw

Nam

et al. 2012

Journal of Biological Chemistry

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Background: Considerable interest surrounds how 8-oxoguanine DNA glycosylase (hOGG1) distinguishes rare oxoG lesions from undamaged G residues. Results: Even when G is forcibly inserted into the lesion-recognition pocket on the enzyme, it is not cleaved. Conclusion:The hOGG1 active site can discriminate G from oxoG at the stage of catalysis. Significance: HOGG1 has a catalytic checkpoint that prevents accidental cleavage of undamaged DNA.

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Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

Enforced Presentation of an Extrahelical Guanine to the Lesion Recognition Pocket of Human 8-Oxoguanine Glycosylase, hOGG1

Crenshaw

Nam

et al. 2012

Journal of Biological Chemistry

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“…Two structures of DNA-bound to Src homology 3 (SH3)-like folds are known (41)(42)(43). The proteins involved, Sso7d and Sac7d, bind in the minor groove of double-stranded DNA in a sequenceindependent manner.…”

Section: Discussionmentioning

confidence: 99%

Crystal structure of the HIV-1 integrase catalytic core and C-terminal domains: A model for viral DNA binding

Chen

Krucinski

Miercke

et al. 2000

Proc. Natl. Acad. Sci. U.S.A.

385

445

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“…Recently, we examined the photoreactions of 5-iodouracil ( I U)-containing 5Ј-d(GTAAT-I UAC)-3Ј and the Sso7d chromosomal protein from the hyperthermophilic archaeabacteria Sulfolobus solfataricus (8,9) and demonstrated that the uracil-5-yl radical abstracts hydrogen from the methyl group of T 5 at the sharp kink (16).…”

Section: Resultsmentioning

confidence: 99%

Photoreactivation of DNA by an Archaeal nucleoprotein Sso7d

Tashiro

Wang

Sugiyama

2006

Proc. Natl. Acad. Sci. U.S.A.

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Archaea ͉ DNA repair ͉ electron transfer ͉ thymine dimer U ltraviolet light from the sun causes various types of DNA damage that induce mutations, carcinogenesis, and cell death. Pyrimidine-pyrimidine photodimers are typical products of photoinduced damage (1). Photolyase repairs thymine dimers by using electron transfer from cofactor domains under light. Recently, Barton and colleagues (2-4) proposed an attractive hypothesis that some repair enzymes use electron transfer from redox cofactors for detection of oxidatively generated DNA damage. Evidence that photolyase can also repair thymine dimers without the involvement of a cofactor (1, 5) suggests that the amino acid itself has the potential to repair DNA by a photoinduced electron transfer mechanism. In the living cell, DNA is usually associated with various types of nucleoproteins, which implies the existence of DNA repair activities in nucleoproteins. In fact, Cullis et al. (6) demonstrated that the guanine radical formed in DNA is reduced by electron transfer from histone, even though the detailed mechanisms is not known. The Archaea, as representatives of one of the oldest lineages, offer special insight into the origin of cellular life and the ancestry of eukaryotes (7). Sso7d and Sac7d are nucleohistone-like proteins of archaea, and structures of their DNA complexes have been solved by x-ray crystallography and NMR (refs. 8-10 and Fig. 1). In this article, we demonstrate electron transfer from the archaeal nucleosomal protein Sso7d to DNA by using 5-bromouracil ( Br U) residue. We also demonstrate that the electron transfer from Sso7d effectively repairs a TϽϾT dimer. Results and DiscussionDetection of Electron Transfer from Sso7d to DNA by Using Br U.5-Halouracil, a photoreactive analogue of thymine, has been widely used for biological assays and studies of DNA chemistry (11-14).Recently, Br U has been used as an electron trap in DNA-mediated excess electron transfer processes (12, 13), because the formation of the anion radical of Br U rapidly eliminates bromo anions, to generate the uracil-5-yl radical (14,15). Recently, we examined the photoreactions of 5-iodouracil ( I U)-containing 5Ј-d(GTAAT-I UAC)-3Ј and the Sso7d chromosomal protein from the hyperthermophilic archaeabacteria Sulfolobus solfataricus (8, 9) and demonstrated that the uracil-5-yl radical abstracts hydrogen from the methyl group of T 5 at the sharp kink (16).Because we recently found that photoinduced electron transfer occurs from guanine (G) to Br U through an A͞T bridge in duplex DNA (17), evaluation of the contribution of the electron transfer process in this system might be important. Therefore, we examined the photoreactivity of 5Ј-d(GTAAT Br UAC)-3Ј (ODN1) in the presence and absence of Sso7d.HPLC product analysis indicated that photoirradiation of ODN1 alone mainly gave 2-deoxyribonolactone-containing octamers, 1 (Fig. 2A). This result is consistent with previous observations (16,17). Upon addition of Sso7d to the reaction mixture, the photoreactivity of ODN1 was enhanced, ...

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The crystal structure of the hyperthermophile chromosomal protein Sso7d bound to DNA

Cited by 150 publications

References 32 publications

Enforced Presentation of an Extrahelical Guanine to the Lesion Recognition Pocket of Human 8-Oxoguanine Glycosylase, hOGG1

Enforced Presentation of an Extrahelical Guanine to the Lesion Recognition Pocket of Human 8-Oxoguanine Glycosylase, hOGG1

Crystal structure of the HIV-1 integrase catalytic core and C-terminal domains: A model for viral DNA binding

Photoreactivation of DNA by an Archaeal nucleoprotein Sso7d

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