Research The =/> fold uracil DNA glycosylases: a common origin with diverse fates

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1 Research The =/> fold uracil DNA glycosylases: a common origin with diverse A8 E )@@HAII =JE = +A JAHB H*E JA?D CO1 B H =JE =JE = 1 IJEJKJAI B0A= JD *AJDAI@=, &'" 75) + - =E ED C L Published: 13 October 2000 Genome Biology 2000, 1(4):research The electronic version of this article is the complete one and can be found online at GenomeBiology.com (Print ISSN ; Online ISSN ) Abstract Background: Uracil DNA glycosylases (UDGs) are major repair enzymes that protect DNA from mutational damage caused by uracil incorporated as a result of a polymerase error or deamination of cytosine. Four distinct families of UDGs have been identified, which show very limited sequence similarity to each other, although two of them have been shown to possess the same structural fold. The structural and evolutionary relationships between the rest of the UDGs remain uncertain. Results: Using sequence profile searches, multiple alignment analysis and protein structure comparisons, we show here that all known UDGs possess the same fold and must have evolved from a common ancestor. Although all UDGs catalyze essentially the same reaction, significant changes in the configuration of the catalytic residues were detected within their common fold, which probably results in differences in the biochemistry of these enzymes. The extreme sequence divergence of the UDGs, which is unusual for enzymes with the same principal activity, is probably due to the major role of the uracil-flipping caused by the conformational strain enacted by the enzyme on uracil-containing DNA, as compared with the catalytic action of individual polar residues. We predict two previously undetected families of UDGs and delineate a hypothetical scenario for their evolution. Conclusions: UDGs form a single protein superfamily with a distinct structural fold and a common evolutionary origin. Differences in the catalytic mechanism of the different families combined with the construction of the catalytic pocket have, however, resulted in extreme sequence divergence of these enzymes. Background KJ=CA E?KH=?E =FFA=HIE, ) FF IEJAJ CK= E A=I= HAIK J B EIE? HF H=JE H E =JE B?OJ IE A 5E E =H O E =JE FH?AII CA AH=JAI JDO E A FF IEJACK= E AE JD IA HC= EI IE A AJDO =JE, ) EI I=BACK=H@A@ BH JDA? IA GKA?AI BJDAIAALA JI>OJDA=?JELEJO BKH=?E, )C O? IO =IAI 7,/I MDE?D HA LA KH=?E I AJE AI Received: 28 June 2000 Revised: 29 August 2000 Accepted: 6 September 2000 JDO E ABH JDAIKC=H>=? > A B, )MEJD KJ>HA= E C JDA FD E JDA >=? > A 6DAHA JJOFAI BJDAIAA O AIE JDAJDHAAIKFAH E C@ I B EBA 6DA >AIJ IJK@EA@ B= E O B 7,/I JOFEBEA@ >O JDA -I?DAHE?DE=? E 7 C FH JAE EI =HCA O IFA?EBE? B H KH=?E JE =L=HEAJO B>=?JAHE= AK =HO =HCA AK =HO JE?, ) LEHKIAI! " 6DA EI =J?D IFA?EBE? KH=?E, ) C O? IO =IAI 7/I D=LA >AA E@A JEBEA@ E comment reviews reports deposited research refereed research interactions information

2 2 Genome Biology Vol 1 No E AK =HO K E AJDA7 C B= E O A O AI =HA =@@EJE = O =?JELA / 6 EI =J?DAI # $ + F=HEI BJDA?HOIJ= IJHK?JKHAI BJDAIAJM A O AI D=I ID M JD=J JDAO =HA IJHK?JKH= O LAHO IE E JDA M IAGKA?A IE E =HEJO # 5K>IAGKA J O JM JDAH? =IIAI B 7,/I D=LA >AA?D=H=?JAHE A@ A BH JDAH FDE E? =H?D=A= IALAH= >=?JAHE= % & DAHAE =BJAH?= JDAHBH LAHJA>H=JAI5 7/ ' 6DA =JJAH A O A D=I = DECD IFA?EBE?EJO B H KH=?E B H IE C A IK>IJH=JAI 6DA IE C A IFA?EBE? 7,/I II7,/I =HA >A EALA@ J >A BK?JE = O IE E =H J JDA7 7/I>A?=KIAJDAOF IIAII JEBIIE E =HJ JDA?=J= OJE? JEBI BJDA =JJAHA O AI@AIFEJAIKFF IA@ O =? E CIEC EBE?= JIAGKA?AIE E =HEJOJ JDA ' 1? JH=IJ JDA IJHK?JKH= AL KJE =HO =BBE EJEAI B JDA )7,/I =HA K?AHJ=E & 6DKI? IE@AH=> A ANEIJ= CJDA7,/I JDAEHCA AH= O IE E =H?=J= OJE?=?JELEJEAI C 0AHA KIE C IAGKA?A FH BE A IA=H?DAI K JEF A = EC A J = = OIEI IJHK?JKH=? F=HEI I MA K EBO = M 7,/I E J = IE C A FH JAE IKFAHB= E O FHA@E?J =? = > B H JDA 9A =@@EJE = IALAH= AMFH >=> A7,/IJD=J=HA@EIJE?JBH JDA= HA=@O?D=H =?JAHE A@ B= E EAI ANF HA JDA AL KJE =HO I?A =HE I JD=J? JA@E JDA >IAHLA@FDO AJE?@EIJHE>KJE BJDAIAA O AI Results and discussion Characterization of the UDG superfamily using iterative database searches ) EJAH=JELA251 * )56IA=H?D?KJ BBB HE? KIE B IAGKA?AI E J JDA F IEJE IFA?EBE? I? HE C =JHEN A E EJE=JA@MEJDJDAIAGKA?A BJDA6 #FH JAE JDAFH J JOFA A >AH B JDA )7,/ B= E O HAJHEALA@ MEJD IJ=JEIJE?= O IEC EBE?= J A L= KAI J O EJI HJD CI DECD O? IAHLA@F=H= CIBH =L=HEAJO B HC= EI I >KJ= I JDA? =IIE?= 7/I JDA,H I FDE = II7,/ 1 =@@EJE JDAIA IA=H?DAI HAIK JA@ E B K?D=H=?JAHE A@ 7,/D CIBH I += FO >=?JAH A K E AEIIAHE= A E CEJE@EI 6DA ANJ H B EJAH=JELA IA=H?DAI E EJE=JA@ MEJD JDA IAGKA?AI B JDA AM O@AJA?JA@7,/D CIHAIK JA@E JDAHAJHEAL= BJDA7 CB= E O B7,/IMEJD KJ= OB= IAF IEJELAI 6DKI >OKIE C K JEF AFH BE AIA=H?DAI EJM=IF IIE> AJ? A?J = M 7,/I =I MA =I IALAH= FKJ=JELA AM AI JDH KCDIJ=JEIJE?= OIEC EBE?= JIAGKA?AIE E =HEJO + KIJAH E C BJDAFH JAE I BJDAA AHCE C7,/IKFAHB= E OKIE C HA?EFH?= HAJHEAL= E * )562IA=H?DAI=I=?HEJAHE A@J JDA E@A JEBE?=JE B B= E EAI 6DAIA =HA 7 / HJD CI B-? E 7 C 7/ HJD CI B-? E KC )7,/ II7,/ =FHALE KI E OJD=JE? K@AI A >AHIBH JDACA KI AEIIAHE= O? >=?JAHEK AFH=A + A K E O =I >E EI 7,/: = JDAH AM B= E O E? K@E C A >AHI BH, I F EI,47,/ 2H JAE IBH A=?D B JDAIAB= E EAIMAHA= EC A@IAF=H=JA O I? H CJ? IJHK?JKHAA A A JIMAHA E@A JEBEA@ 6DA =L=E => A A IE = IJHK?JKHAI B 7 C KC MAHA IKFAHE F IA@ JDA HAIK JE C IJHK? JKH= = EC A J M=I KIA@ J? >E A JDA K JEF A = EC A JI B= IEN7,/B= E EAI.ECKHA + F=HEI BJDA K JEF A = EC A J MEJD JDA =L=E => A IJHK?JKHAI ID MA@? IAHL=JE BJDAFHE?EF= IJHK?JKH= A A A JI.ECKHA CJD=J= FH JAE I BJDA7,/IKFAHB= E O=@ FJJDA I= A = > =I 7 C KC 6DEI FHA@E?JA@ IJHK?JKH= K EJO B JDA 7,/I = C MEJD JDA IK>J A >KJ IEC EBE?= J IAGKA?AIE E =HEJO IKCCAIJI=? AL KJE =HO HECE B HJDAA JEHAIKFAHB= E O 6DA IAGKA?A? IAHL=JE E JDA 7,/ IKFAHB= E O EI??A JH=JA@ FHE =HE O E JDHAA JEBI MEJD JDA JM JEBI?=JA@ A=H JDA = E NO JAH E E? C J JDAIK>IJH=JA CF? AJ.ECKHAI 6DA=?AIJH=? BJDA7,/IKFAHB= E O? IEIJI B=?A JH= F=H= A B KH IDAAJMEJD=! "J F CO MDE?DEI=II?E =JA@MEJDB KHDA E?AI JDAIK>IJH=JA CF? AJEIB H A@ @".ECKHA 6DA?A JH=? IAHLA@ JEB? J = ID=HF JKH >AJMAA JDA =@ =?A J DA EN! MDE?D EI A B JDA IJ?D=H=?JAHEIJE?IJHK?JKH= BA=JKHAI BJDA7,/IKFAH B= E >=> OHAGKEHA@J IKFF HJJDAA O A? B H =JE AA@A@ J JDA, ) 1 > JD IJHK?JKH= O?D=H=?JAHE A@ A >AHI BJDEIIKFAHB= E O7@C KC =? IAHLA@=H =JE?HAIE@KA?=JA@E JDA F Figure 1 (on the following page) Multiple alignment of the UDG superfamily. The secondary-structure elements of the core UDG fold are shown in color above the multiple alignment. Some nonconserved elements in the MUG structure from E. coli are indicated in gray. The coloring of the alignment positions is according to the 85% consensus that includes the following categories of amino acid residues: h, hydrophobic, l, aliphatic, a, aromatic, shaded yellow (YFWLIVMA); s, small, individual letters colored green (SAGTVPNHD); p, polar, colored purple (STQNEDRKH); u, tiny, shaded green (GAS); and b, big, shaded gray (KREQWFYLMI). Af, Archaeoglobus fulgidus; Bb, Borrelia burgdorferi; Bs, Bacillus subtilis; Cj, Campylobacter jejuni; Ct, Chlamydia trachomatis; Dm, Drosophila melanogaster; Dr, Deinococcus radiodurans; Ec, Escherichia coli; Hi, Haemophilus influenzae; Hp, Helicobacter pylori; Hs, Homo sapiens; Mtu, Mycobacterium tuberculosis; Ph, Pyrococcus horikoshii; Rp, Rickettsia prowazekii; Sc, Saccharomyces cerevisiae; Scoel, Streptomyces coelicolor; Sp, Schizosaccharomyces pombe; Ssp, Synechocystis sp.; Tp, Treponema pallidum; Uu, Ureaplasma urealyticum; Yp, Yersinia pestis. The numbers at each end of each sequence are amino-acid positions and indicate the extent of the domain in each protein. The numbers within the alignment indicate inserts that have not been shown. The conserved motifs discussed in the text are designated I, II and III; the conserved aromatic (aliphatic) residue involved in the stacking interaction with uracil is indicated by an asterisk.

3 MOTIF-I * UNG_Dr_ RYTPLGEVKVLILGQDPYHG-PNQAHGLSFSV 7 PSLRNIYKELTEDIP-----GFVAPK-----HGYLRSWAEQGVLLLNA-----VLTVRAGQANS--HQGKGWEHFTD---- UNG_Ec_ RFTELGDVKVVILGQDPYHG-PGQAHGLAFSV 7 PSLLNMYKELENTIP-----GFTRPN-----HGYLESWARQGVLLLNT-----VLTVRAGQAHS--HASLGWETFTD---- UNG_Bs_ HYTSYDDVKVVILGQDPYHG-PGQAQGLSFSV 7 PSLKNIFLELQQDI------GCSIPN-----HGSLVSWAKQGVLLLNT-----VLTVRRGQANS--HKGKGWERLTD---- UNG_Ct_ QSTPFDQVRVVILGQDPYHG-EGQAHGLSFSV 7 PSLRNIFQELHTDL------GIRNE------SGCLQAWADQGVLLLNT-----VLTVRAGEAFS--HAGRGWERFTD---- UNG_Bb_ NSLPFKDIKVVIIGQDPYHG-KNQANGLAFSV 7 PSLQNIFKEIEKSL-----KIKTIP------NGDLKRWAIQGVFLINT-----ILTVEEGKPSS--HKAIGWEIFTD---- UNG_Hs_ QMCDIKDVKVVILGQDPYHG-PNQAHGLCFSV 7 PSLENIYKELSTDIED-----FVHPG-----HGDLSGWAKQGVLLLNA-----VLTVRAHQANS--HKERGWEQFTD---- UNG_Sp_ HHTPLHKTKVILLGQDPYHN-IGQAHGLCFSV 7 PSLVNIYKAIKIDYPD-----FVIPK-----TGYLVPWADQGILMLNA-----SLTVRAHQAAS--HSGKGWETFTS---- UNG_EBV_ RFCDPSDIKVVILGQDPYHG--GQANGLAFSV 7 PSLRNIYAELHRSLPE-----FSPPD-----HGCLDAWASQGVLLLNT-----ILTVQKGKPGS--HADIGWAWFTD---- MSV208_MSV_ KYFNPEHTNVVILGYRPFSL---IQDGLAFSC PIENKLFINEIFSNYN-----RLDKISDKMHKSSLECLAKQGVLLLNV-----NLTIGSNIND---HSDIGWEYLTN---- MUG_Ec_ EDILAPGLRVVFCGINPGLS--SAGTGFPFAH PA-NRFWKVIYQAGFTD--RQLKPQEAQ HLLDYRCGVTK------LVDRPTVQAN---EVSKQELHAGG---- MUG_Sm_ MELLAPNLRVVFCGINPGLS--SAHQGYPFAN GS-NRFWKVIHQAGFTE--SQLAPEQWQ QLKDNGCGITA------LVARPTVAAS---ELSRDELRSGG---- MUG_Dr_ PDVLQPGLTLVLVGTAPSGI--SARARAYYAN PE-NKFWRTLHAVGLTP--RQLVPQEYA TLPQYGLGLTD------VAKRHSGVDA---ALPGEAWRP MUG_Cord? DRIPNSDLRLLIVGVNPGLW--TAAVNAPFAH PG-NRFWPSLDRAGIVT-PRFDVSHGMSDEQEK---HLAHLGIGMTN-----LVARATARADE---LTTQELIDGA----- UDG_Hs_ PDILTFNLDIVIIGINPGLM--AAYKGHHYPG PG-NHFWKCLFMSGLSE--VQLNHMDDH TLPGKYGIGFTN------MVERTTPGSK---DLSSKEFREGG---- UDG_Dm_ PDHLCDNLDIVIVGINPGLF--AAYKGHHYAG PG-NHFWKCLYLAGLTQ--EQMSADEDH KLIKQGIGFTN------MVARATKGSA---DLTRKEIKEGS---- UDG_Sp_ PDYICENPYAIIVGLNPGIT--SSLKGHAFAS PS-NRFWKMLNKSKLLE--GNAEFTYLNDK------DLPAHGLGITN------LCARPSSSGA---DLRKEEMQDGA---- Cj1254_Cj_ EPFFDKDSKILILGSFPSIK--SRQDGFYYQH PR-NRFWPILETLFNAK----LENIT------EQQAFLRKKHIALWD------VLQSCKIKNSD--DKTISYAKAND---- ORF1_Zm_ APVTNINSRLLILGSLPGVA--SLEKAQYYGH PR-NQFWRLMSDIIGED----IESAAYP----ERLEGLLRHHIGLWD------VIGTAKRQGSL--DSNIKEVSPNP---- UDGX_Pgi? PPIEDGHLEILILGSLPGDE--SIRRGQYYAH PR-NRFWPLMAKLLGKP----LPDDYA-----ERTEILLSAHIGLWD------VAHSAIRKGSA--DIQICDEEPND---- UDGX_Mav? PPVVDERARTLILGSFPSAQ--SLLTGQYYAN PR-NAFWSITGELFGFD----AAAPYP-----RRLAQLRRHRIALWD------VLHACRRAGSADSAIEPNSLVVND---- UDGX_Ccr? PPVVDAKTCVLILGSLPGDA--SLAAGQYYGH PR-NAFWRLMEGVIDAP----LVVRAYE----DRLVTLLAHGVGLWD------VIETARRPGSL--DAAIREPAAND---- UDGX_Mle? PPVIGAGSRVLILGACPSAH--SLAKQQYYAN PE-NAFWSITNEFFGFE----LNAQYD-----DRLAASLAYGVALWV------VLYSCHCVGNTDSAIEPKRLAINN---- UDGX_Hduc? PAILPKSATVAMLGTFPPTS-EKRCMEFHYPN FQ-NDMWRIMGLLFYKNLDHFRVDQEKRFDPVRIEAFLREKGIALCSS-----AQTAIRLKGNA-SDKDLKIIDAID---- NMA0903_Nm_ DSVLPPKAAVMMMGTFPPKE-DKRAMQFHYPN FQ-NDMWRVYGLVFFNDAAHFQRLSEKAFDAEKIKAFLHERGIASCPT-----VLKAAREHGNA-SDKFLKVVETVD---- AF2277_Af_ PGVGNEKAEIVFVGEAPGRD--EDLKGEPFVG AA-GKLLTEMLASI GLRREDVYITN------VLKCRPPNNR---DPTPEEVEKCG---- PH1472_Ph_ PGDGSYDTKIMFVGEAPGYW--EDQMGLPFVG KA-GKVLDELLKLI GLKRSEVYITN------IVKCRPPNNR---DPTEEEIKACA---- APE0427_Ape_ PGEGPGEAGVMVVGEAPGRM--EDRLGRPFVG PA-GKLLDSLLELA GLSRGEVYITN------VVKCRPPGNR---DPREEEIEACL---- TM0511_Tma_ VGEGNLDTRIVFVGEGPGEE--EDKTGRPFVG RA-GMLLTELLRES GIRREDVYICN------VVKCRPPNNR---TPTPEEQAACG---- aq_1693_aae_ PGDGNPYSLLVFVGEAPGEE--EDRQGKPFVG RA-GQLLNRLIEEVL GMKREDVYITN------VCKCRPPQNR---KPTPIEMRACF---- SCD35.02_Scoe_ FGAGKASARVMLVGEQPGDQ--EDRQGKPFVG PA-GHLLDRALAEA GLDPADAYVTNAVKHFKFTRAEPRKRRIHKAPTLRETAACG---- zm12orf4_zm_ CGEGSHTSPVIFVGEQPGDQ--EDLAGRPFVG PA-GQVFDEVMASI GWPREEIYLTNAVKH--FKFWLKGERRIHQTPAPEEVDCCR---- DPOL_SPO1_ KGQGSKKARIIIVQENPFDY--EYRKKKYMTG KA-GKLLKFGLAEVG IDPDEDVYYTS------IVKYPTPENR---LPTPDEIKESM---- DR1751_Dr_ VSDGDPRAPLLIVGEGPGAE--EDRDGRPFVG QA-GQLLDRILAAA SLAREEAYLTN------VTKCRAPNNR---TPLPLETATCT---- TP0229_Tp_ VGEGVADADVLVVGEAPGAE--EDRSGRPFVG RS-GKLLDAMLAAIG LSRQQNCYITN------VVKCRPPRNR---TPTPHETACCA---- RP845_Rp_ FGDGNPQANIMLIGEAPGNT--EDLKGIPFCG ES-GNLLDNMLYAI GISRNNFYITN------MVFWRPPANR---QPTLEEVDICR---- ORFX_Zm_ FSEVKISPKLMVLSESPEAE--DMAQGQLFSG KA-GRLLHAMLDTL CIKKQDIYFATMSP---IVEHIDYVKISSYAAGNSLTSHDY---- SC7H2.04c_Scoe_ PGFGPPDARLLIVGLAPAAH-GGNRTGRMFTG DRSGDVLYQALYDV------GLASQPTAVRVD---DGLELYGVRVTS------PVHCAPPAN----KPTPAERDTCR---- RV1259_Mtu_ PGWGSKRPRLLILGLAPAAH-GANRTGRMFTG DRSGDQLYAALHRA------GLVNSPVSVDAA---DGLRANRIRITA------PVRCAPPGN----SPTPAERLTCS---- NMA0583_Nm_ VPAASGITKLAVVSLCPPIE--DAVYGQLFYG KA-GVLLDNILKAVG LDAAYVHKTC------WVKTAAVGNP---MPSEAAIETAT---- HP0650_Hp_ IGLFNPTSKLTFITLTPMLD-----SQLNFLN NLKAAMLESIIQKVF NCPLKDCSILS------LLKCDSNSLN-----LEEEINACL---- Cj0963_Cj_ MEPKIKNAKLLILDVFGQKS--ENESGILLNS KK-GEKLKHYIYQIL GLCDEDFYFSY------LFKCFCNGKF-----DDFSLQSCL---- HI0220.2_Hi_ LFSAPKTARINIVGQAPGLK--AEQSRLYWND KS-GDRLREWLGVDY DYFYNSGIFAVLP-----MDFYYPGYGK----SGDLPPRQGF---- sll1217_ssp_ LFGGNLGSQLCFFGRDLGAD--EVRQGQPLIG AA-GRLVRKGFFEAWQ----GRVPRGQDD------LQTVCQRILLTN------TVPYKPPENK----AYSVKVKERF---- DPOLIIIA_Yp_ PSIGIKPKIMVILDNANGND---GRTGYFMEN -GY-DDFKAKLLTAG DLRMGDLYVTG------VCKKVKDKEK---DYTKDEIGQFT---- DR0022_Dr_ PAGGGVNSRILCLLEAPGPQAAQSRGGSGFIS 4 DHTAHTMFQLIADS GVRREQLLLWN------IVPWYVGDDHRIRGVKQGEIQEGA---- O2_Rcoc_ PDDGGDAARCLVLLESPGPK-TIRPGGTNMCS 4 DRTNPVLKSVFADA GIDRVQCVKWN------IVPWAVLDDAGHPVSPTASVLGEA---- CG5285_Dm_ RRYMDGPKKLVFVGMNPGPN-GMAQTGIPFGN 36 PSGVRLWELFLRLA GSMQTFSQQCFVHNF----CPLAFFGADGR---NITPSEIRGAYKNQL SSUDG_Hs_ TRYCQGPKEVLFLGMNPGPF-GMAQTGVPFGE 36 VSGARFWGFFRNLC GQPEVFFHHCFVHNL----CPLLFLAPSGR---NLTPAELPAKQREQL consensus/85%...lhhlu..p...s..ass...hh..h...h.h.s...hh...s...b...s... MOTIF-II MOTIF-III UNG_Dr_ AVIKAVNAKEER--VVFILWG-SYARKKKKLITG KNHVVIESGHPS PLSEQY FFGTRPFSKTNEALE 229\ UNG_Ec_ KVISLINQHREG--VVFLLWG-SHAQKKGAIIDK QRHHVLKAPHPSPLSAHRG FFGCNHFVLANQWLE 211 UNG_Bs_ RIIDVLSERERP--VIFILWG-RHAQMKKERIDT SKHFIIESTHPSPFSARNG FFGSRPFSRANAYLE 211 UNG_Ct_ AIVTKLIQNRTH--VIFVLWG-NAARQKCNLLFQTK HQHAVLACPHPSPLAAHRG FFGCCHFSKINYLLK 217 UNG_Bb_ EVIKIISKNLKN--IVFMLWG-NLARSKKGLIDPTK HLILETSHPSPYSANNG FLGSNHFSSALDYLK 213 UNG UNG_Hs_ AVVSWLNQNSNG--LVFLLWG-SYAQKKGSAIDR KRHHVLQTAHPSPLSVYRG FFGCRHFSKTNELLQ 211 UNG_Sp_ AVLQVALNRNRK-GLVILAWG-TPAAKRLQGLPL KAHYVLRSVHPSPLSAHRG FFECHHFKKTNEWLE 290 UNG_EBV_ HVISLLSERLKA--CVFMLWG-AKAGDKASLINS KKHLVLTSQHPSPLAQNSTRKSAQQK-FLGNNHFVLANNFLR 244 MSV208_MSV_ DIIKKISINNDN--IVFILIG-SKMHDKCNIIHNI DNHFIIKTSYPSYQTLYSENSKYNVIPFINSKCFIKANEYLK 218/ MUG_Ec_ RKLIEKIEDYQP--QALAILG-KQAYEQGFSQRGAQ WGKQTLTI GSTQIWVLPNPSGLS RVSLEKLVEAYRELD 160\ MUG_Sm_ EALQEKILRYQP--RALAILG-KQAFTTAFGVKNAP WGKQTLTL GETEVWVLPNPSGLN RATLEQLTASYRELF 158 MUG_Dr_ DELRRKVEHYRP--RIVAFTS-KRGASETLGVPTGK-----LPYGPQPQPLD WPAETELWVLPSTSPLGHNHFR LEPWQALGDRVRELR 184 MUG_Cord -----QRVIHLANALRP--RVVAVVG-ITAYRAGFQHRKAV-----LGKQDPTLIAD WPEDVALWVVPQPSGLNAHET VETLAQRWRDVWDDS? MUG UDG_Hs_ RILVQKLQKYQP--RIAVFNG-KCIYEIFSKEVFGVKVKN-LEFGLQPHKIPD TETLCYVMPSSSARCAQF PRAQDKVHYYIKLKDL 295 UDG_Dm_ RILLEKLQRFRP--KVAVFNG-KLIFEVFSGKKE FHFGRQPDRVD GTDTFIWVMPSSSARCAQLP RAADKVPFYAALKKF 943 UDG_Sp_ RILYEKVKRYRP--QVGLFISGKGIWEEMYKMLTGKKLPKTFVFGWQPEKF GDANVFVGISSSGRAAGYS DEKKQNLWNLFAEEV 314/ Cj1254_Cj_ LNLILSQTKI----QAIFTTG-QSAYRFF VKFHP RLEAIALPSTSPANLN FSFEQLLQNYEIIKKFTK 160\ ORF1_Zm_ LGDLIGKLPNL----KALAFNG-QKAAQLG IKELQK IGAKLPYYILPSTSPAHA VAYDVKKAAWIKLQEI 160 UDGX_Pgi ----IRSLIERNPRL----HTIAFNG-RKAEAMF RKHFPE TLAIRCLLMPSTSPANA GKTLDLLVKDWNRIFSL? UDGX_Mav ----FGEFFAEHPGI----TRVYFNG-AKAAELY RRLATA PDHVCFQRLPSTSPAHV MAPGAKLAAWAVLRNS? UDGX UDGX_Ccr ----LMALIDTLPAL----RLVAFNG-GTAGRLG GRLIGT RVSTLALPSSSPAYAA RTFAQKAAAWAALRDG? UDGX_Mle ----FSELFTDYSTT----TFVYFNS-AKAAKLY YRLADHHLARLADPVPAAA INQHGSRHAARDQPA? UDGX_Hduc ----MQALLTELPQL----KWLFTTG-GLATETL LSLLPEKSKLPKTNEWINYPYTTDRTLYLYRLPSTSRAYP LSLAKKVEAYRQFFV? NMA0903_Nm_ LAAVLAKIPDC----RHICTTG-GKATEIL-----LDIQGG-GIKMPKTGETVPFPF AGRDLTLTRLPSTSRAYP LSLAKKAAAYRAFFE 222/ AF2277_Af_ DYLVRQLEAIRP--NVIVCLG-RFAAQFIFNLF-DLEFTT---ISRVKGKVYEVERWG KKVKVIAIYHPAAVLYR PQLREEYESDFKKIGE 186\ PH1472_Ph_ PYLDAQIDIIKP--KVIVTLG-RFSTAYIMKKY-GFNVEP---ISKIHGRVFEARTLF GKIYIVPMYHPAVALYR PQLRRELEEDFKKLKS 193 APE0427_Ape_ PYLVEQISLIRP--RLVIAVG-RHAGRTLFRLA-GLRWPG---LARARGRVWRGRIGG VELLIAVTYHPAAALYN PGLRGELERDFSGFIR 176 TM0511_Tma_ HFLLAQIEIINP--DVIVALG-ATALSFFVD---GKKVS----ITKVRGN---PIDWL GGKKVIPTFHPSYLLRNRS NELRRIVLEDIEKAKS 186 aq_1693_aae_ PYLKKEIEIIQP--KVICCLG-ATAGEGIL----GKSLR----ITKVRGQVF-PYPYN PRIKVFLTYHPAYVLRNP KEETTIIKDFEKLKE 190 SCD35.02_Scoe_ PWLAAELDRVEP--ELIVVLG-ATAGKALL----GSSFR----VTRVRGTVLEEEI HGRPQRLVPTVHPSAVLRADDR------EAAYRGLLSDLEVAAR 209 zm12orf4_zm_ YWLRQEWRLLKP--RLTIALG-GTAVLALT----GKKQT----LGSLRGKIL--TL GKAAAPFIVTYHPSYILRQASEE---GRQRAYQAMQQDLTIARN 201 DPOL_SPO1_ DYMWAEIEVIDP--DIIIPTG-NLSLKFLT----KMTA-----ITKVRGKLY EIEGRKFFPMIHPNTVLKQP KYQDFFIKDLEILAS 167 DR1751_Dr_ GLWLEPQLALLRP--RVVLSLG-NTATQFLL----GTPRG----ITRLRGQWFTYRHPAW PQPALLMPLLHPAYLLRNPVRT----PGGPKSLTWRDIREVAA 210 TP0229_Tp_ RFLHAHLTLHRP--CAILVLG-RCAAQHML----QTTDG----IGKLRGRFFTY QGIPLLATYHPSALLRDE ALKRPAWEDLKTFRA 264 RP845_Rp_ PFVEKHIALINP--KLLILVG-STAATSLL----GKNAC----ITKIRQEYYFYTNKYI STPIQTTAIFHPAYLLRQ PMQKRTSWYDLLKIKE 249 AUDG ORFX_Zm_ TLIAAQHISLIKP--RYLHLLG-DAPNRALLQMN TMDARKKIHAITVN NDNIDAFALLHPKMLLETP PLKAIAWKDLRVLKG 254 SC7H2.04c_Scoe_ SWLVQELGLLRPTLRAVVVLG-AFGWQAALPAF-AGAGWT---VPRPRPAFAHGTQVTLDAAD---GPDLHLFGCFHVSQRNTFTG RLTPEMLRDVLRTAA 229 RV1259_Mtu_ PWLNAEWRLVSDHIRAIVALG-GFAWQVALR-L-AGASG----TPKPRFG--HGVVTEL GAGVRLLGCYHPSQQNMFTG RLTPTMLDDIFREAK 293 NMA0583_Nm_ VSVMQELDGCRA--PAVLFLG-QAFVNPERQ---AMIET----LCGSRP FFIIDHPARLLRQP ELKARAWQVLKQLKR 237 HP0650_Hp_ FHLTWQLDNSASK---VIVVFG-EILPKRLLN---LSKE ESFGRIV SLKTKHFLSTHALEDMLK NPTLKKEALAHFKIALQ 191 Cj0963_Cj_ PFFWNELKLIQP--AFLLCLG-EYTFKSLGFKDY HILKGEVF AYKNFFIMPSYDLDFIEK NPSYEKNFIQDLKKIKG 200 HI0220.2_Hi_ AERWHPMILGNLPNIQLTILIG-QYAQKYYLP---ENKDN----VTNTVKNYR QFLPHFMPLVHPSPRNQLWVTK----NPWFEEQVIPELQILVK 208 sll1217_ssp_ RPFVEQLLVFHWQG-KQIITLG-TEAFKWFAPYAPKGQLDEFFQGGDRYECSLDVLIKAKTAAGKGSQKIVRLMPLPHPSPLNKRY YGQFPTMLQRRLTEIAF 225 DPOLIIIA_Yp_ DFMREEINLVRP--TYVLTCG-SRATSLFN----NKSK-----PSDLVGRK-EYLP ELDVTVFYGFNPNILYFR PEEGEKLEAILAEVAE 1131/ DR0022_Dr_ DLLAELIELLPEL-AVVVTLG-RAAASGW ARVKGR-AVSR TVTLNSWHPSGQALNGH-----PERYEHLLMTLRLAQQIS 186\DRUDG O2_Rcoc_ GPYVGELMALLPKL-EVVFVLG-AKALDGY MRVITASAPTR LLPVIAAPHPSARNAHAP------AAARQRLINAALSVATH 199/ CG5285_Dm_ GDLCLHTLEEQLKLLQP--DVIVAVG-EYVHSALKRS--GYAK SNCVSVLRLPHPSPRSTN NTNWPEKAQAFLEEHN 271\ssUDG SSUDG_Hs_ LGICDAALCRQVQLLGV--RLVVGVG-RLAEQRARRA--LAGL MPEVQVEGLLHPSPRNPQ ANKGWEAVAKERLNELG 263/ consensus/85%...l..b...hhh..g...s.p...hh...psu...h... comment reviews reports deposited research refereed research interactions information

4 4 Genome Biology Vol 1 No E,E IJ7,/:I J? IAHLA@E >=?JAHE= 7/I E IJ JDAHI 7H=?E IFA?EBE?EJO,E 7 /ICA AH= >=IA J? IAHLA@E JDAHI 0 0! 0E IJ A?AII=HOB H IJ=>E E =JE BHA=?JE E JAH A@E=JA 5E = 7/ 7,/:I 5 5 5! 5" 5N 0 0" 0 -E IALAH= ) JAH =JELACA AH= >=IA J? IAHLA@E JDAHI IAHLA@=H =JE?HAIE@KA A?AII=HOB HKH=?E C Figure 2 The topology of the UDG superfamily core fold, with the conserved and unique features of different families. The core secondary-structure elements of the UDG fold are colored as in Figure 1 and numbered according to their order in the sequence. The elements observed only in the MUGs are shown in gray. The conserved motif I occurs after strand 1 and motif II occurs after strand 4 and forms the active-site pocket in the three-dimensional structure. FHA?A@E C JDA? IAHLA@ DA EN.ECKHAI A@E=JAI C BJDA=JJ=? A@KH=?E BH JDA, )@ K> ADA ENLE= IJ=? E C E JAH=?JE I 6DEI =H =JE? HAIE@KA EI HAF =?A@ >O= = EFD=JE?HAIE@KAE =I = IK>IAJ BJDA7,/I F =O? J=E F H O? IAHLA@ID HJDA E?AIE I A B JDA7,/I IK?D=I KC 6DEIF IEJE EIDECD O? IAHLA@E JDAA JEHA7,/IKFAHB= E O.ECKHA MDE?DIKCCAIJIJD=J= IE E =H A?D= EI BKH=?E CEIK ELAHI= E JDA7,/I Catalytic mechanism 6DAANFAHE A E =JE B=IE E =H?=J= OJE?=?JEL A >AHI BJDA7,/IKFAHB= E IAHL=JE B JDA IK>IJH=JA C IEJA IKCCAIJ = CA AH= O? IAHLA@?=J= OJE? A?D= EI 0 MALAH IALAH= B= E O IFA?EBE? BA=JKHAI FHA@E?J E JAHAIJE E JDA?=J = OJE?FH FAHJEAI B= E EAI JDA>=IEI B IJK@EAI 7 C B= E O A O AI IK?D =I JD IA BH DAH FAILEHKIAI EJD=I>AA IKCCAIJA@JD=JFH J =JE BJDA BJDAB EFFA@ KJKH=?E EI?=HHEA@ KJ>OJDA? IAHLA@DEI JE@E A E JEB 111 MDE?D =?JI =I = CA AH= =?E@! 5JK@EAI JDA -? E 7 C A O A D MALAH D=LA ID M JD=JJDEI? IAHLA@DEIJE@E A@ AI J=?J=I=CA AH= =?E@ >KJE IJA=@EI AKJH= A A?JH FDE A! " JDEI>=IEI EJD=I>AA FH F IA@JD=JJDAA A?JH FDE E?E JAH =?JE IJ=>E E AIJDA@ALA FE CA =JA JDAKH=?E E? KHIA BEJIAN?EIE! " 6DEIHA=?JE EI=IIEIJA@>OJDA? IAHLA@ =IF=HJ=JA E JEB 1 JD=J =?JI =I = CA AH= = M=JAH A?K A B H JDA K? A FDE E? =JJ=?!! 6DA AMB= E O B>=?JAHE= 7,/I 7,/:E@A JEBEA@DAHA =? > JDJDA? IAHLA@A A?JH FDE A DEIJE@E A JDA CA AH= >=IA =IF=HJ=JA.ECKHA MDE?DIKCCAIJIJD=JJDAIA=HA AIIABBE?EA JA O AI # 6DA HA =E E C 7,/ B= E EAI JOFE?= O? J=E JDA A A?JH FDE E? DEIJE@E A >KJ J JDA CA AH= >=IA =IF=HJ=JA E JEB 1.ECKHA )IK>IAJ AM OE@A JEBEA@,47,/B= E O D MALAH? J=E =C KJ= =JA AF IEJE KFIJHA= B JDA =IF=HJ=JA FHAIA J E JEB 1 B JDA 7 /I.ECKHA JDEI C KJ= =JA? =?J =I = = JAH =JELA CA AH= >=IAB HJDEIIK>IAJ B7,/I )@@EJE = O JDA F B H A@>O JEB111= I DA FIE? = FE C JDAFD IFD=JA

5 >=? > A J = M HA? C EJE B JDA J=HCAJ K? A JE@A >O JDA=?JELAIEJA 6DA@EI?HE E =JE BKH=?E LAH?OJ IE A E A O AI B JDA 7 / B= JDA =IF=H=CE A?=JA@ A=H JDA B JDA? HA ) =IF=H=CE A H =IF=HJ=JA EI? IAHLA@ E JDA = HEJO BJDA7,/IKFAHB= E OA O AIE JDEIF IE JE MEJD JDA AN?AFJE B I A A >AHI B JDA 7/ )7,/ 7,/: B= E EAI * JD -? E KC EJI DK = HJD C 6,/ D=LA >AA ID M J =?J F MAH BK O KJ=CA E? = O =JA@ >=IAI IK?D =I AJDA?OJ IE A # KJ=JE = HAF =?A A J B=IF=H=CE A>O=IF=HJ=JAE JDA DK = KH=?E, ) C O? IO =IA 7 / HAIK JI E EJI =?GKEHE C?OJ IE AC O? IO =IA=?JELEJO $ 6DEIIK>IJE JKJE MDE?D??KHI =JKH= O E IALAH= 7,/: B= E O : 0, I JK>AH?K IEI,47,/ 5I7,/ 5 7/ 7/ 6,/ 7,/: 7 / )7,/ *=?JAHE= * IK>JE EI 5?AHALEI=A + A K E -? E 5 F >A 6 F= E@K FH JAE I = C MEJD JDAH HAF =?A A JI B =IF=H=CE A E JDEI F IEJE J A >AHI B JDEI IKFAHB= E O.ECKHA EIFH >=> O= =@=FJ=JE B HHA L= B KJ= CA E?= O =JA@>=IAIIK?D=IAJDA?OJ IE A Evolution JDA >=IEI B JDA? IAHL=JE B BK?JE = O E F HJ= J HAIE@KAIE JDA7,/IKFAHB= E O =F=HIE E KI = JD KCD IFA?K =JELA I?DA AB HJDAAL KJE BJDAIAA O AI?= >A FH F IA@.ECKHA! 6DA =?AIJH= KH=?E, ) C O? IO =IAFH >=> OF IIAIIA@JDA? =IF=H=CE A=J A=JJDAA IJ? IA O HAIA >A@ JDA )7,/ B= E EAI.H JDEI=?AIJH= B H JDADECD =?JELEJOB H IIK?D=IJDA -K =HO= : : 5 0 I=FEA I, A = C=IJAH + A AC= I 2 B=?EF=HK ) FAH EN ) BK CE@KI = =I?DEE Figure 3 A hypothetical evolutionary scenario for the UDG superfamily. The different families are shown in different colors and potential order and lineage of derivation is indicated on the standard phylogenetic model for the three domains of life. The representation of the active-site pocket residues typical of that set is shown next to each class at the point of derivation. The first position is the general base represented by an aspartate in the UNGs, the second position is the uracil/cytosine discrimination site occurring after the core strand 2, and the third position is typically represented by a histidine that acts as an electrophile. The X at a given position denotes lack of conservation. In some of the AUDGs and the DRUDGs, a glutamate could function as alternative general base. ) =A E?KI, 0 : 0 : 0 )H?D=A= comment reviews reports deposited research refereed research interactions information

6 6 Genome Biology Vol 1 No E 7 /? =II? LA@>O=?GKEHE CJDACA AH= >=IA E JEB1 6DA=?GKEIEJE BJDAC KJ= =JAE JEB1 BJDA )7,/I HAFHAIA J AL K JE B JDA I= A JOFA B DECD =?JELEJO A O A 6DA MAH =?JELEJO B H I IK?D =I JDA 7/I JDA 7,/:I? D=LA AL LA@ >O HAF =?A A J B JDA =?AIJH= A A?JH FDE E? DEIJE@E AJD=JIJ=>E E A@JDAHA=?JE E JAH A@E=JA>O= JDAH F =HHAIE@KAIK?D=IIAHE A H=IF=H=CE A 6DA?= E =JE BJDA=?JELAIEJAB H A@>O C FI JDAI= AIE@A B JDA 7,/ A?K AI FH >=> O HAIK JA@ E HA =N=JE B JDA IA A?JELA? IJH=E JI =E JA =?A BJDACA AH= ID=FA CF? AJ HA LAH ALA JDA?D=HCA@ HAIE@KAI E JDA C F? AJ =HA J A JEHA O? IJH=E A@ >A?=KIAJDAA O A A?D= EI IAA HA?HEJE?= O JDAIJAHE?IJH=E?=KIA@>O>=IA B EFFE CJD= JDA>=IA H JDAHHAIE@KAIJD=JIJ=>E E AJDA E JAH A@E=JA 6DAIA BA=JKHAI B JDA 7,/I FH >=> O? JHE>KJA@ J JDA AL KJE B = LAHO DECD ALA B MEJD KJ = IE C A HAIE@KA? IAHLA@ JDH KCD KJ JDAIKFAHB= E O MDE?DEIK KIK= B HD C KIA O AI JD=J?=J= O AAIIA JE= OJDAI= AHA=?JE 6DAFDO AJE?@EIJHE>KJE BJDA7,/IID MIF=HJE=? F A A J=HEJO J B= E EAI MDE?D IKCCAIJI JD=J JDAOFAHB H =J A=IJF=HJE= O LAH =FFE CBK?JE A J HC= EI I 6=> A -=?D? F AJA O IAGKA?A@ CA A MEJD JDA =FF=HA J AN?AFJE B JDA =H?D=A= AJD=???KI = =I?DEE AJD= >=?JAHEK JDAH =KJ JH FDE?K A=IJ A A >AH BJDA7,/ IKFAHB= E O MEJD= =NE K BB KH A >AHIE JDA?=IA B JDAH=@E HAIEIJ= J>=?JAHEK, I6=> A -=?D BJDAIAB= E EAI MEJDJDAAN?AFJE BJDAII7,/I MDE?DI B=H=HA E EJA@J = E = I ID MI=F=J?DOIFHA=@ LAH=ME@A FDO CA AJE?H= CA MDE?DIKCCAIJIE F HJ= JH AIB HD HE J= CA AJH= E A=CA IFA?EBE?CA A IIE JDAAL KJE B JDA 7,/I 6DA FHAIA?A B )7,/ E =J A=IJ A >=?JAHE B7 /IE =HCAAK =HO JE?, )LEHKIAI 6=> A F E JJ AF IIE> AJOFA BLADE? AB HD HE E =JE BJDAIAA O AI 6DAFDO AJE?@EIJHE>KJE B JDA 7,/I IKCCAIJI JD=J JDA )7,/I? >A JDA =?AIJH= B H F IIE> OE DAHEJA@BH JDA =IJ? =?AIJ H B= ANJ= J EBAB H I 6DEIIAA IJ >A? F=JE> AMEJDJDA=FF=H A J=?AIJH= =O KJ BJDA=?JELA?A JAH BJDAIAA O AIIAA => LA 6DA 7 /I =FFA=H J >A = FHE EJELA >=?JAHE= B H MDAHA=IJDA 7/ 7,/:CH =JAH IJ=CA B >=?JAHE= AL KJE 6DA IAF=H=JE >AJMAA 7 7/ >OIA A?JE B H@EIJE?JBK?JE = E?DAI =KH=?E IFA?EBE?A O AE JDA?=IA BJDAB H 7 6 EI =J?DHAF=EHA O AE JDA =JJAH 7/B= E EAIID M=? IAHHA = JE IDEFJ A=?D JDAHJD= J JDAHB= E EAI BJDAIKFAHB= E O IKCCAIJE C = HA =JELA O HA?A = IE E =H EI =J?DHAF=EHBK?JE 6DA,47,/I=FFA=HJ >AIFA?E= E JD=J A AHCA@ MEJDE A >=?JAHE= E A=CA B MA@ >O E =J A=IJ E JDA?KHHA J O I= F A@ >=?JAHE= J=N= JDEI I?A =HE )7,/I D=LA Table 1 Phyletic distributions of the six families of UNGs Species/family UNG* AUDG* MUG SsUDG* DRUDG* + UDGX* Bacteria Escherichia coli 1 1 (MUG) Haemophilus influenzae 1 1 Neisseria meningitidis (UDGX) Rickettsia prowazekii 1 Campylobacter jejuni (UDGX) Helicobacter pylori 1 1 Bacillus subtilis 1 Mycoplasma genitalium 1 Mycoplasma pneumoniae 1 Ureaplasma urealyticum 1 Deinococcus radiodurans (MUG) 1 Mycobacterium tuberculosis 1 1 Streptomyces coelicolor 1 2 Synechocystis sp. 1 Chlamydia trachomatis 1 Chlamydophila pneumoniae 1 Treponema pallidum 1 Borrelia burgdorferi 1 1(d) Aquifex aeolicus 1 Thermotoga maritima 1 Archaea Aeropyrum pernix 1 Archaeoglobus fulgidus 1 Pyrococcus horikoshii 1 Methanobacterium thermoautotrophicum Methanococcus jannaschii Eukaryota Saccharomyces cerevisiae 1 (r) Schizosaccharomyces pombe1 1(MUG) Caenorhabditis elegans 1 Drosophila melanogaster (?) 1(MUG) 1 Homo sapiens 1 1(MUG) 1 Large DNA viruses Poxviruses 1 Herpesviruses 1 Bacteriophages SPO1 1 *The number of detected representatives of each family is indicated for each species. Note that duplication is uncharacteristic of the UNGs. (d) indicates a possibly disrupted version in which the amino-terminal conserved motifs are not detectable; (r) indicates an apparent recent loss in S. cerevisiae, as the gene is retained in the related yeast Candida albicans; (?) indicates the unusual lack of a detectable UNG in both the genome and EST sequences. =?A@ E I A B JDA >=?JAHE= F IIE> O E JDA =?AIJH= AK =HO JAI >OJDA7 7/I 6DA)7,/I=HABKIA@J )F O AH=IAI =, )F O AH=IA111= IK>K EJE ;AHIE E=FAIJEI O AH=IA BJDA)B= E OD C B>=?JAHE= 2 1E >=?JA HE FD=CA 52 6DEI BKIE EI JDA?=KIA B = O AHH A KI

7 = J=JE I B )7,/ B= E O A >AHI =I [FKJ=JELA FD=CA JOFA, ) F O AH=IAI\ JD=J =HA B E?KHHA J 6DABKIE MEJDJDAF O AH=IAIIKCCAIJIJD=JJDA BK?JE E C BJDA)7,/I IIE> O JDAH7,/I? >AJECDJ O? KF A@J JD=J BJDA, )HAF E?=JE =FF=H=JKI 6DEI =O >A F=HJE?K =H O E F HJ= J E JDA =H?D=A= MD IA F O AH=IAI IJ= =J KHE@E AI E JDA JA F =JA % /ELA JDEIF IIE> ABK?JE B)7,/IE HAF E?=JE A J= H A B7,/IE HAF=EH JDA=FF=HA J=>IA?A B JDAIAA O AIE JM =H?D=A= AJD= CA IEIK ANFA?JA@ ) JD KCD JDAIA =H?D=A= CA AI? ANJHA A J A >AHI B JDA 7,/ IKFAHB= E O JD=J ALA E JDA FHAIA A@ = = OIEI EJ IAA I HA E A O JD=J E JDAIA =H?D=A= JDA 7,/I D=LA F =?A@ >O K HA =JA@ A O AI B JDA = DA E?= KJ; IKFAH B= E O & -K =HO / 7/ B= E OA O AIJD=J=HA JB IA OHA =JA@J JDAEH>=?JAHE= HJD CI 6DEI IJH C O IKCCAIJI =?GKEIEJE BH >=?JAHE= IO >E JI E? K@E C B MA@ F =?A A J BJDA7,/E DAHEJA@BH JDA? =?AIJ H MEJD =H?D=A= FH >=> O )7,/ 6DA 7/ B= E O A O AI BH = E = I D=LA M? F ANEJO IAC A JI AEJDAH IE@A B JDA, ) C O? IO =E 1 JDA?=IA B,H I FDE = JDAIA=HAF=HJE?K E HCH LA, ) C JEBI JDA)6D I ' 6DEI JEB EI B E = O?DH I = FH JAE I DA F E JDA JH= I?=JE B JDA A O A J IFA?EBE? IEJAI E?DH =JE IK?D=I =JHEN=JJ=?D A JHACE I 1 JAHAIJE C J AK =HO JE? E A=CAI ID M J=> E JDAEHHAFAHJ EHAI B7,/I MEJD O= 7 / B= E OA O A I B=H@AJA?JA@E JDA A HD=>@EJEIA AC= I 6DA FDO CA AJE? =BBE EJO B JDA II7,/I MDE?D D=LA KF J M O E? A =JAI EI D=H@ >A?=KIAJDAOD=LAAL LA@@EIJE?JIJHK?JKH= BA=JKHAI IK?D =I CE IAHJI JD=J=HA JIAA E JDA JDAH A >AHI BJDA 7,/ IKFAHB= E O 6DA FHAIA?A B = DEIJE@E A E JEB 111 IKCCAIJIJD=JJDAII7,/I? LA@BH =7 / E A A O A >O 6DA AL KJE CA?A JDA HECE B =?GKEIEJE B ) C O? IO =IA =O? HHA =JAMEJDJDA AA@B H= A O AJD=J?= AAJ JDA F=HJE?K =H, ) HAF=EH AA@I B K JE?A K =H = E = I IK?D=IJDAHAF=EH BBHAGKA J OJH= I?HE>A@, ) Conclusions 7IE CIAGKA?AFH BE AIA=H?DAI K JEF A= EC A J= = OIEI JAE IJHK?JKHA? F=HEI I MAD=LAID M JD=J= M 7,/IB H =IE C AFH JAE IKFAHB= E OMEJD=@EI AL KJE =HO HECE 6DA ANJHA AIAGKA?A@ELAHCA?A B@EBBAHA JB= E EAI B7,/IEI FH >=> JDAEH>E?DA EIJHO MEJD O JDA CA AH= ID=FA B JDA FH JAE A?K A JDA C F? AJ>AE CAIIA JE= B HJDA, )C O? IO =IAHA=?JE FAH IA ) JD KCD JDA 7,/ IKFAHB= E O EI A=H O K>EGKEJ KI = C?A K =H EBA B H I JDA B= E EAI ID M E FDO I 6DA A AHCE C AL KJE =HOI?A =HE B HJDA7,/IE L LAI K JEF AALA JI B =JAH= CA A JH= IBAH E A=CA IFA?EBE? CA A II 1 =@@EJE MA FHA@E?J JM FHALE KI O B= E EAI B 7,/I JDA ANFAHE A J= E LAIJEC=JE B JDAEH BK?JE I EI ANFA?JA@J >H =@A JDA?KHHA JFAHIFA?JELA JDAIA?HEJE?= HAF=EHA O AI Materials and methods KIA@ E JDEI IJK@O MAHA JDA J K? A JE@A 2H JAE JDA -NFHAIIA@ 5AGKA?A 6=CI =JE = +A JAH B H *E JA?D CO 1 B H =JE JDA FH JAE B? F AJA O F=HJE= O IAGKA?A@ CA AI?= = EC A J IA=H?DAI MAHA FAHB H A@ KIE C JDA C=FFA@ LAHIE BJDA* )56FH CH= I* )562/2B HFH JAE 6* )56 /2 B H JH= I =JE C IA=H?DAI B K? A >=IAI 5AGKA?AFH BE AIA=H?DAIMAHAFAHB H A@KIE C JDA 251 * )56 FH CH= H KIE C JDA 0 5-)4+0 FH CH= MEJDE FKJDE@@A =H ICA AH=JA@BH K JEF A = EC A JI KIE C JDA 0 *71, FH CH= 6DA K JEF A = EC A JI MAHA CA AH=JA@ KIE C =? >E = JE B 251 * ) ) 9 6DA IJ=JEIJE?= O IEC EBE?= J JEBI KIE C JDA /E>>I I= F E C FJE B JDA )+)9 FH CH=! " 6DA A IE = IJHK?JKHALEIK= E =JE = EC E CMAHA?=HHEA@ KJKIE CJDA ,* 8EAMAHFH CH= # References 1. Krokan HE, Standal R, Slupphaug G: DNA glycosylases in the base excision repair of DNA. Biochem J 1997, 325: Friedberg EC, Walker GC, Siede W: DNA Repair and Mutagenesis. Washington, DC: American Society for Microbiology; Savva R, McAuley-Hecht K, Brown T, Pearl L: The structural basis of specific base-excision repair by uracil-dna glycosylase. Nature 1995, 373: Mol CD, Arvai AS, Slupphaug G, Kavli B, Alseth I, Krokan HE, Tainer JA: Crystal structure and mutational analysis of human uracil-dna glycosylase: structural basis for specificity and catalysis. Cell 1995, 80: Barrett TE, Savva R, Panayotou G, Barlow T, Brown T, Jiricny J, Pearl LH: Crystal structure of a G:T/U mismatch-specific DNA glycosylase: mismatch recognition by complementarystrand interactions. Cell 1998, 92: Gallinari P, Jiricny J: A new class of uracil-dna glycosylases related to human thymine-dna glycosylase. Nature 1996, 383: Sandigursky M, Franklin WA: Uracil-DNA glycosylase in the extreme thermophile Archaeoglobus fulgidus. J Biol Chem 2000, 275: Sandigursky M, Franklin WA: Thermostable uracil-dna glycosylase from Thermotoga maritima, a member of a novel class of DNA repair enzymes. Curr Biol 1999, 9: Haushalter KA, Todd Stukenberg MW, Kirschner MW, Verdine GL: Identification of a new uracil-dna glycosylase family by expression cloning using synthetic inhibitors. Curr Biol 1999, 9: Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25: comment reviews reports deposited research refereed research interactions information

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