MINT MINT, Dpt of Biology, University of Rome Tor Vergata MINT http://mint.bio.uniroma2.it/mint url>http://mint.bio.uniroma2.it/mint/ https://mint.bio.uniroma2.it MINT-[0-9]+ https://mint.bio.uniroma2.it/index.php/results-interactions/?id=${ac} The Molecular INTeraction database (MINT) is a relational database designed to store interactions between biological molecules. http://mint.bio.uniroma2.it http://mint.bio.uniroma2.it/mint sung-2014-4 DNA end recognition by the Mre11 nuclease dimer: insights into resection and repair of damaged DNA. yeast Saccharomyces cerevisiae Baker's yeast anti tag coip anti tag coimmunoprecipitation anti tag coip anti tag western anti tag western blot anti tag western Sung S., Li F., Park Y.B., Kim J.S., Kim A.K., Song O.K., Kim J., Che J., Lee S.E., Cho Y. lees4@uthscsa.edu; yunje@postech.ac.kr EMBO J. (0261-4189) 2014 Only protein-protein interactions imex curation sung-2014-5 DNA end recognition by the Mre11 nuclease dimer: insights into resection and repair of damaged DNA. yeast Saccharomyces cerevisiae Baker's yeast 2 hybrid two hybrid 2H 2h Gal4 transcription regeneration two-hybrid yeast two hybrid 2-hybrid classical two hybrid classical two hybrid 2H two-hybrid 2-hybrid Gal4 transcription regeneration 2h yeast two hybrid Y2H Y-2H 2 hybrid predetermined predetermined participant predetermined Sung S., Li F., Park Y.B., Kim J.S., Kim A.K., Song O.K., Kim J., Che J., Lee S.E., Cho Y. lees4@uthscsa.edu; yunje@postech.ac.kr EMBO J. (0261-4189) 2014 Only protein-protein interactions imex curation sung-2014-1 DNA end recognition by the Mre11 nuclease dimer: insights into resection and repair of damaged DNA. in vitro In vitro x-ray diffraction x-ray crystallography X-ray X-ray x-ray diffraction predetermined predetermined participant predetermined Sung S., Li F., Park Y.B., Kim J.S., Kim A.K., Song O.K., Kim J., Che J., Lee S.E., Cho Y. lees4@uthscsa.edu; yunje@postech.ac.kr EMBO J. (0261-4189) 2014 Only protein-protein interactions imex curation sung-2014-2 DNA end recognition by the Mre11 nuclease dimer: insights into resection and repair of damaged DNA. in vitro In vitro molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column predetermined predetermined participant predetermined Sung S., Li F., Park Y.B., Kim J.S., Kim A.K., Song O.K., Kim J., Che J., Lee S.E., Cho Y. lees4@uthscsa.edu; yunje@postech.ac.kr EMBO J. (0261-4189) 2014 Only protein-protein interactions imex curation sung-2014-3 DNA end recognition by the Mre11 nuclease dimer: insights into resection and repair of damaged DNA. in vitro In vitro crosslink cross-linking study crosslink weight by comassie molecular weight estimation by coomasie staining weight by comassie Sung S., Li F., Park Y.B., Kim J.S., Kim A.K., Song O.K., Kim J., Che J., Lee S.E., Cho Y. lees4@uthscsa.edu; yunje@postech.ac.kr EMBO J. (0261-4189) 2014 Only protein-protein interactions imex curation xrs2_yeast DNA repair protein XRS2 XRS2 D9481.13 YDR369C protein protein yeast Saccharomyces cerevisiae Baker's yeast MWVVRYQNTLEDGSISFISCCLQAFKTYSIGRSSKNPLIIKNDKSISRQHITFKWEINNSSDLKHSSLCLVNKGKLTSLNKKFMKVGETFTINASDVLKSTIIELGTTPIRIEFEWINEVWNIPPHLTQFRTMLSEYGISTEISINDIPANLMISDYPKSEDNSIRELYALVSTIPMKKSRFLMELCNTLLPTSKTNLKFDEMWNDMISNPEYNVFDFDPNILLSKFMRLNNIRVLTTIKSEPRLSSLLRTFNINLFAFDNIDSLYKYVDSLEASTEYLILTTTDKKENGKILCTIKTMLTSIIDGTLSAVINMKGASSRTLDNGKFDQISEGMSTILKTSRAPEVEASPVVSKKRKLNRRRVLPLDSLDFFAGGLSTKTLSENRSLTDAKRLNCGAESKTVISSPNIAEADEKHAPFLQNALKPTEDIGKKSGHSSPGAIIVSSPNLGTVNTSEDSLDKSLQSHKLPQPSLPEVAGIGSQTISSNSADYETAAVNSMDDAEVTKNFRVNHHQNIEQPSKNIRKLSNYSREISSPLQENCKSPVKELSIKEKSGTPHAFVEAIQETKNREVKRVKSTIVELKDEELSEEAINQLKNLAIVEPSNNLLRKSFDSEGNKTSRTTEKWENSLMEPEWHKRKNFKTFVKVRPKSKAHKEEGKNNTQSSDFIRNAAFLITRNYVPLKKYSKKDTTTKWGTEENEDMFALTEMERFGSNTFMSDNINSNTIQKRSQALNRFTNEDSSNEGEEDSFSFSRCSGTAASVQPLKNKIFITDEDDLGDIDDKSDRLNHRENNRNLFVVKEMNLRPNLSEECSKQSRHSRSATSRSRGSFGASNNGDGDDDDDDGPKFTFKRRKG 833DAD6D20F6693E mre11_yeast Double-strand break repair protein MRE11 YM9959.06C YMR224C MRE11 protein protein yeast Saccharomyces cerevisiae Baker's yeast MDYPDPDTIRILITTDNHVGYNENDPITGDDSWKTFHEVMMLAKNNNVDMVVQSGDLFHVNKPSKKSLYQVLKTLRLCCMGDKPCELELLSDPSQVFHYDEFTNVNYEDPNFNISIPVFGISGNHDDASGDSLLCPMDILHATGLINHFGKVIESDKIKVVPLLFQKGSTKLALYGLAAVRDERLFRTFKDGGVTFEVPTMREGEWFNLMCVHQNHTGHTNTAFLPEQFLPDFLDMVIWGHEHECIPNLVHNPIKNFDVLQPGSSVATSLCEAEAQPKYVFILDIKYGEAPKMTPIPLETIRTFKMKSISLQDVPHLRPHDKDATSKYLIEQVEEMIRDANEETKQKLADDGEGDMVAELPKPLIRLRVDYSAPSNTQSPIDYQVENPRRFSNRFVGRVANGNNVVQFYKKRSPVTRSKKSGINGTSISDRDVEKLFSESGGELEVQTLVNDLLNKMQLSLLPEVGLNEAVKKFVDKDEKTALKEFISHEISNEVGILSTNEEFLRTDDAEEMKALIKQVKRANSVRPTPPKENDETNFAFNGNGLDSFRSSNREVRTGSPDITQSHVDNESRITHISQAESSKPTSKPKRVRTATKKKIPAFSDSTVISDAENELGDNNDAQDDVDIDENDIIMVSTDEEDASYGLLNGRKTKTKTRPAASTKTASRRGKGRASRTPKTDILGSLLAKKRK D58433E32E852B73 rad50_yeast DNA repair protein RAD50 RAD50 YNL250W N0872 153 kDa protein protein protein yeast Saccharomyces cerevisiae Baker's yeast MSAIYKLSIQGIRSFDSNDRETIEFGKPLTLIVGMNGSGKTTIIECLKYATTGDLPPNSKGGVFIHDPKITGEKDIRAQVKLAFTSANGLNMIVTRNIQLLMKKTTTTFKTLEGQLVAINNSGDRSTLSTRSLELDAQVPLYLGVPKAILEYVIFCHQEDSLWPLSEPSNLKKKFDEIFQAMKFTKALDNLKSIKKDMSVDIKLLKQSVEHLKLDKDRSKAMKLNIHQLQTKIDQYNEEVSEIESQLNEITEKSDKLFKSNQDFQKILSKVENLKNTKLSISDQVKRLSNSIDILDLSKPDLQNLLANFSKVLMDKNNQLRDLETDISSLKDRQSSLQSLSNSLIRRQGELEAGKETYEKNRNHLSSLKEAFQHKFQGLSNIENSDMAQVNHEMSQFKAFISQDLTDTIDQFAKDIQLKETNLSDLIKSITVDSQNLEYNKKDRSKLIHDSEELAEKLKSFKSLSTQDSLNHELENLKTYKEKLQSWESENIIPKLNQKIEEKNNEMIILENQIEKFQDRIMKTNQQADLYAKLGLIKKSINTKLDELQKITEKLQNDSRIRQVFPLTQEFQRADLEMDFQKLFINMQKNIAINNKKMHELDRRYTNALYNLNTIEKDLQDNQKSKEKVIQLLSENLPEDCTIDEYNDVLEETELSYKTALENLKMHQTTLEFNRKALEIAERDSCCYLCSRKFENESFKSKLLQELKTKTDANFEKTLKDTVQNEKEYLHSLRLLEKHIITLNSINEKIDNSQKCLEKAKEETKTSKSKLDELEVDSTKLKDEKELAESEIRPLIEKFTYLEKELKDLENSSKTISEELSIYNTSEDGIQTVDELRDQQRKMNDSLRELRKTISDLQMEKDEKVRENSRMINLIKEKELTVSEIESSLTQKQNIDDSIRSKRENINDIDSRVKELEARIISLKNKKDEAQSVLDKVKNERDIQVRNKQKTVADINRLIDRFQTIYNEVVDFEAKGFDELQTTIKELELNKAQMLELKEQLDLKSNEVNEEKRKLADSNNEEKNLKQNLELIELKSQLQHIESEISRLDVQNAEAERDKYQEESLRLRTRFEKLSSENAGKLGEMKQLQNQIDSLTHQLRTDYKDIEKNYHKEWVELQTRSFVTDDIDVYSKALDSAIMKYHGLKMQDINRIIDELWKRTYSGTDIDTIKIRSDEVSSTVKGKSYNYRVVMYKQDVELDMRGRCSAGQKVLASIIIRLALSETFGANCGVIALDEPTTNLDEENIESLAKSLHNIINMRRHQKNFQLIVITHDEKFLGHMNAAAFTDHFFKVKRDDRQKSQIEWVDINRVTY 58A0AA173AC5677E mre11_metja DNA double-strand break repair protein Mre11 mre11 MJ1323 protein protein metja Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) Methanococcus jannaschii MMFVHIADNHLGYRQYNLDDREKDIYDSFKLCIKKILEIKPDVVLHSGDLFNDLRPPVKALRIAMQAFKKLHENNIKVYIVAGNHEMPRRLGEESPLALLKDYVKILDGKDVINVNGEEIFICGTYYHKKSKREEMLDKLKNFESEAKNYKKKILMLHQGINPYIPLDYELEHFDLPKFSYYALGHIHKRILERFNDGILAYSGSTEIIYRNEYEDYKKEGKGFYLVDFSGNDLDISDIEKIDIECREFVEVNIKDKKSFNEAVNKIERCKNKPVVFGKIKREFKPWFDTLKDKILINKAIIVDDEFIDMPDNVDIESLNIKELLVDYANRQGIDGDLVLSLYKALLNNENWKELLDEYYNTKFRG xrs2-mre11-4 1778099 n/a 1778104 anti tag western anti tag western blot anti tag western unspecified role unspecified role bait bait over-expressed over expressed level over-expressed living cell living cell myc tag myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false n/a 1778105 anti tag western anti tag western blot anti tag western unspecified role unspecified role prey prey over-expressed over expressed level over-expressed living cell living cell ha tag ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false physical association physical association false false false f6a xrs2-mre11-5 1778099 n/a 1778105 anti tag western anti tag western blot anti tag western unspecified role unspecified role prey prey over-expressed over expressed level over-expressed living cell living cell ha tag ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false n/a 1778106 anti tag western anti tag western blot anti tag western unspecified role unspecified role bait bait over-expressed over expressed level over-expressed living cell living cell myc tag myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false physical association physical association false false false f6a mre11-xrs2-5 1778100 n/a 1778104 predetermined predetermined participant predetermined unspecified role unspecified role prey prey over-expressed over expressed level over-expressed living cell living cell n/a 1778105 predetermined predetermined participant predetermined unspecified role unspecified role bait bait over-expressed over expressed level over-expressed living cell living cell physical association physical association false false false f6b mre11-xrs2-6 1778100 n/a 1778106 predetermined predetermined participant predetermined unspecified role unspecified role prey prey over-expressed over expressed level over-expressed living cell living cell n/a 1778105 predetermined predetermined participant predetermined unspecified role unspecified role bait bait over-expressed over expressed level over-expressed living cell living cell physical association physical association false false false f6b mre11-1 1778101 n/a 1778107 predetermined predetermined participant predetermined unspecified role unspecified role neutral component neutral component purified purified range binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false Stoichiometry: 2.0 direct interaction direct interaction false false false st1 f1b f4a f4b sf2 To obtain Mre11–DNA crystals, we used MjMre11 core (residues 1–313) and two different DNA substrates: a 22-bp dsDNA with one blunt end and 4-base 30 and 50 overhangs on the other end (DNA1), or a 17-bp dsDNA with one blunt end and a 5-base 30 overhang on the other end (DNA2) (Fig 1A). We determined the structures of both MjMre11–DNA complexes in the presence of Mg2+ at 3.55 A ̊ (Mre11–DNA1) and 3.59 A ̊ (Mre11– DNA2) mre11-1 1778102 n/a 1778107 predetermined predetermined participant predetermined unspecified role unspecified role neutral component neutral component purified purified range binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false Stoichiometry: 2.0 direct interaction direct interaction false false false f3e The R55S mutant exhibited signifi- cantly decreased exo- and endonuclease activities (Fig 3D, lane 4 and 5, Supplementary Fig S5). This mutant forms a stable dimer, suggesting that the diminished DNA binding and cleavage is unli- kely to be due to perturbation of dimerization (Fig 3E). mre11-1 1778103 n/a 1778107 predetermined predetermined participant predetermined unspecified role unspecified role neutral component neutral component purified purified range binding region binding-associated region binding region certain certain sequence position certain certain certain sequence position certain false Q58719:p.[Val58Cys;Leu99Cys] mutation disrupting mutation disrupting interaction mutation disrupting certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false Stoichiometry: 2.0 direct interaction direct interaction false false false f4c Mobility-shift analysis confirmed that the K59C/E94C mutant formed a disulfide, whereas the V58C/L99C mutant did not form a disulfide link in the presence of an oxidizing agent (Fig 4C).