UREND_METTH
ID UREND_METTH Reviewed; 257 AA.
AC O26314;
DT 26-FEB-2020, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 122.
DE RecName: Full=DNA uridine endonuclease {ECO:0000303|PubMed:17012282, ECO:0000303|PubMed:19240141};
DE Short=DNA U-endo {ECO:0000303|PubMed:17012282};
DE Short=DNA U-endonuclease {ECO:0000303|PubMed:19240141};
DE AltName: Full=AP endonuclease {ECO:0000303|PubMed:15725624};
DE EC=4.2.99.18 {ECO:0000269|PubMed:15725624, ECO:0000269|PubMed:17012282};
DE AltName: Full=ExoMt {ECO:0000303|PubMed:15725624};
DE EC=3.1.11.2 {ECO:0000269|PubMed:15725624, ECO:0000269|PubMed:17012282};
GN OrderedLocusNames=MTH_212 {ECO:0000312|EMBL:AAB84718.1};
OS Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM
OS 10044 / NBRC 100330 / Delta H) (Methanobacterium thermoautotrophicum).
OC Archaea; Euryarchaeota; Methanomada group; Methanobacteria;
OC Methanobacteriales; Methanobacteriaceae; Methanothermobacter.
OX NCBI_TaxID=187420;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H;
RX PubMed=9371463; DOI=10.1128/jb.179.22.7135-7155.1997;
RA Smith D.R., Doucette-Stamm L.A., Deloughery C., Lee H.-M., Dubois J.,
RA Aldredge T., Bashirzadeh R., Blakely D., Cook R., Gilbert K., Harrison D.,
RA Hoang L., Keagle P., Lumm W., Pothier B., Qiu D., Spadafora R., Vicare R.,
RA Wang Y., Wierzbowski J., Gibson R., Jiwani N., Caruso A., Bush D.,
RA Safer H., Patwell D., Prabhakar S., McDougall S., Shimer G., Goyal A.,
RA Pietrovski S., Church G.M., Daniels C.J., Mao J.-I., Rice P., Noelling J.,
RA Reeve J.N.;
RT "Complete genome sequence of Methanobacterium thermoautotrophicum deltaH:
RT functional analysis and comparative genomics.";
RL J. Bacteriol. 179:7135-7155(1997).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, AND COFACTOR.
RC STRAIN=ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H;
RX PubMed=15725624; DOI=10.1016/j.dnarep.2004.11.008;
RA Pfeifer S., Greiner-Stoeffele T.;
RT "A recombinant exonuclease III homologue of the thermophilic archaeon
RT Methanothermobacter thermautotrophicus.";
RL DNA Repair 4:433-444(2005).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, AND MUTAGENESIS OF ASP-151.
RC STRAIN=ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H;
RX PubMed=17012282; DOI=10.1093/nar/gkl604;
RA Georg J., Schomacher L., Chong J.P., Majernik A.I., Raabe M., Urlaub H.,
RA Mueller S., Ciirdaeva E., Kramer W., Fritz H.J.;
RT "The Methanothermobacter thermautotrophicus ExoIII homologue Mth212 is a
RT DNA uridine endonuclease.";
RL Nucleic Acids Res. 34:5325-5336(2006).
RN [4]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H;
RX PubMed=19240141; DOI=10.1093/nar/gkp102;
RA Schomacher L., Chong J.P., McDermott P., Kramer W., Fritz H.J.;
RT "DNA uracil repair initiated by the archaeal ExoIII homologue Mth212 via
RT direct strand incision.";
RL Nucleic Acids Res. 37:2283-2293(2009).
RN [5]
RP FUNCTION IN DNA URACIL REPAIR.
RC STRAIN=ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H;
RX PubMed=20129830; DOI=10.1016/j.dnarep.2010.01.004;
RA Schomacher L., Schuerer K.A., Ciirdaeva E., McDermott P., Chong J.P.,
RA Kramer W., Fritz H.J.;
RT "Archaeal DNA uracil repair via direct strand incision: A minimal system
RT reconstituted from purified components.";
RL DNA Repair 9:438-447(2010).
RN [6] {ECO:0007744|PDB:3FZI, ECO:0007744|PDB:3G00, ECO:0007744|PDB:3G0A, ECO:0007744|PDB:3G0R, ECO:0007744|PDB:3G1K, ECO:0007744|PDB:3G2C, ECO:0007744|PDB:3G2D, ECO:0007744|PDB:3G38, ECO:0007744|PDB:3G3C, ECO:0007744|PDB:3G3Y, ECO:0007744|PDB:3G4T}
RP X-RAY CRYSTALLOGRAPHY (1.23 ANGSTROMS) OF WILD-TYPE AND MUTANT ASN-151 IN
RP APO FORM AND IN COMPLEXES WITH DNA AND DIVALENT METAL IONS, AND ACTIVE
RP SITE.
RX PubMed=20434457; DOI=10.1016/j.jmb.2010.04.044;
RA Lakomek K., Dickmanns A., Ciirdaeva E., Schomacher L., Ficner R.;
RT "Crystal structure analysis of DNA uridine endonuclease Mth212 bound to
RT DNA.";
RL J. Mol. Biol. 399:604-617(2010).
RN [7] {ECO:0007744|PDB:3W2X, ECO:0007744|PDB:3W2Y}
RP X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) OF WILD-TYPE AND MUTANT SER-205 IN
RP COMPLEXES WITH MAGNESIUM.
RA Tabata N., Shida T., Arai R.;
RT "Crystal structure of DNA uridine endonuclease Mth212.";
RL Submitted (DEC-2012) to the PDB data bank.
CC -!- FUNCTION: Involved in DNA uracil repair (PubMed:17012282,
CC PubMed:19240141, PubMed:20129830). Recognizes DNA uracil residues
CC within double-stranded DNA and initiates DNA-U repair by endonucleotic
CC incision on the 5'-side of the 2'-d-uridine residue, irrespective of
CC the nature of the opposing nucleotide (PubMed:17012282,
CC PubMed:19240141, PubMed:20129830). In addition, acts as an
CC apurinic/apyrimidinic (AP) endonuclease hydrolyzing the DNA
CC phosphodiester backbone immediately at the 5'-side of AP sites, and as
CC a 3'-5' exonuclease (PubMed:15725624, PubMed:17012282). Strongly binds
CC to double-stranded DNA (PubMed:15725624). {ECO:0000269|PubMed:15725624,
CC ECO:0000269|PubMed:17012282, ECO:0000269|PubMed:19240141,
CC ECO:0000269|PubMed:20129830}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2'-deoxyribonucleotide-(2'-deoxyribose 5'-phosphate)-2'-
CC deoxyribonucleotide-DNA = a 3'-end 2'-deoxyribonucleotide-(2,3-
CC dehydro-2,3-deoxyribose 5'-phosphate)-DNA + a 5'-end 5'-monophospho-
CC 2'-deoxyribonucleoside-DNA + H(+); Xref=Rhea:RHEA:66592, Rhea:RHEA-
CC COMP:13180, Rhea:RHEA-COMP:16897, Rhea:RHEA-COMP:17067,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:136412, ChEBI:CHEBI:157695,
CC ChEBI:CHEBI:167181; EC=4.2.99.18;
CC Evidence={ECO:0000269|PubMed:15725624, ECO:0000269|PubMed:17012282};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Exonucleolytic cleavage in the 3'- to 5'-direction to yield
CC nucleoside 5'-phosphates.; EC=3.1.11.2;
CC Evidence={ECO:0000269|PubMed:15725624, ECO:0000269|PubMed:17012282};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:15725624, ECO:0000269|PubMed:17012282};
CC Note=Can also use Mn(2+), Co(2+) and Ni(2+).
CC {ECO:0000269|PubMed:15725624};
CC -!- DISRUPTION PHENOTYPE: Depletion leads to the loss of DNA-U repair.
CC {ECO:0000269|PubMed:19240141}.
CC -!- MISCELLANEOUS: The insertion of the side chain of Arg-209 into the DNA
CC helical base stack seems to be crucial for the uridine recognition.
CC {ECO:0000269|PubMed:20434457}.
CC -!- SIMILARITY: Belongs to the DNA repair enzymes AP/exoA family.
CC {ECO:0000305}.
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DR EMBL; AE000666; AAB84718.1; -; Genomic_DNA.
DR PIR; B69126; B69126.
DR RefSeq; WP_010875851.1; NC_000916.1.
DR PDB; 3FZI; X-ray; 1.90 A; A=1-257.
DR PDB; 3G00; X-ray; 1.74 A; A/B=1-257.
DR PDB; 3G0A; X-ray; 2.60 A; A=1-257.
DR PDB; 3G0R; X-ray; 2.40 A; A/B=1-257.
DR PDB; 3G1K; X-ray; 3.10 A; A/B=1-257.
DR PDB; 3G2C; X-ray; 2.30 A; A/B=1-257.
DR PDB; 3G2D; X-ray; 2.30 A; A/B=1-257.
DR PDB; 3G38; X-ray; 3.04 A; A=1-257.
DR PDB; 3G3C; X-ray; 3.04 A; A/B=1-257.
DR PDB; 3G3Y; X-ray; 2.50 A; A/B=1-257.
DR PDB; 3G4T; X-ray; 2.64 A; A/B=1-257.
DR PDB; 3G8V; X-ray; 2.40 A; A=1-257.
DR PDB; 3G91; X-ray; 1.23 A; A=1-257.
DR PDB; 3GA6; X-ray; 1.90 A; A/B=1-257.
DR PDB; 3W2X; X-ray; 1.60 A; A=1-257.
DR PDB; 3W2Y; X-ray; 1.90 A; A/D=1-257.
DR PDBsum; 3FZI; -.
DR PDBsum; 3G00; -.
DR PDBsum; 3G0A; -.
DR PDBsum; 3G0R; -.
DR PDBsum; 3G1K; -.
DR PDBsum; 3G2C; -.
DR PDBsum; 3G2D; -.
DR PDBsum; 3G38; -.
DR PDBsum; 3G3C; -.
DR PDBsum; 3G3Y; -.
DR PDBsum; 3G4T; -.
DR PDBsum; 3G8V; -.
DR PDBsum; 3G91; -.
DR PDBsum; 3GA6; -.
DR PDBsum; 3W2X; -.
DR PDBsum; 3W2Y; -.
DR AlphaFoldDB; O26314; -.
DR SMR; O26314; -.
DR STRING; 187420.MTH_212; -.
DR EnsemblBacteria; AAB84718; AAB84718; MTH_212.
DR GeneID; 1470173; -.
DR KEGG; mth:MTH_212; -.
DR PATRIC; fig|187420.15.peg.181; -.
DR HOGENOM; CLU_027539_3_1_2; -.
DR OMA; WWSYRGR; -.
DR EvolutionaryTrace; O26314; -.
DR Proteomes; UP000005223; Chromosome.
DR GO; GO:0140078; F:class I DNA-(apurinic or apyrimidinic site) endonuclease activity; IEA:UniProtKB-EC.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0004519; F:endonuclease activity; IEA:InterPro.
DR GO; GO:0008853; F:exodeoxyribonuclease III activity; IEA:UniProtKB-EC.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006281; P:DNA repair; IEA:UniProtKB-KW.
DR Gene3D; 3.60.10.10; -; 1.
DR InterPro; IPR004808; AP_endonuc_1.
DR InterPro; IPR020847; AP_endonuclease_F1_BS.
DR InterPro; IPR036691; Endo/exonu/phosph_ase_sf.
DR InterPro; IPR005135; Endo/exonuclease/phosphatase.
DR PANTHER; PTHR22748; PTHR22748; 1.
DR Pfam; PF03372; Exo_endo_phos; 1.
DR SUPFAM; SSF56219; SSF56219; 1.
DR TIGRFAMs; TIGR00633; xth; 1.
DR PROSITE; PS00726; AP_NUCLEASE_F1_1; 1.
DR PROSITE; PS51435; AP_NUCLEASE_F1_4; 1.
PE 1: Evidence at protein level;
KW 3D-structure; DNA damage; DNA repair; DNA-binding; Hydrolase; Lyase;
KW Magnesium; Metal-binding; Reference proteome.
FT CHAIN 1..257
FT /note="DNA uridine endonuclease"
FT /id="PRO_0000449236"
FT ACT_SITE 151
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000305|PubMed:20434457"
FT BINDING 12
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:20434457, ECO:0000269|Ref.7"
FT BINDING 38
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:20434457, ECO:0000269|Ref.7"
FT BINDING 151
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:20434457"
FT BINDING 153
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:20434457"
FT BINDING 248
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:20434457"
FT MUTAGEN 151
FT /note="D->N: Loss of DNA uridine endonuclease and 3'-5'
FT exonuclease activities. Has weak AP endonuclease activity."
FT /evidence="ECO:0000269|PubMed:17012282"
FT STRAND 3..10
FT /evidence="ECO:0007829|PDB:3G91"
FT HELIX 14..19
FT /evidence="ECO:0007829|PDB:3G91"
FT HELIX 22..29
FT /evidence="ECO:0007829|PDB:3G91"
FT STRAND 32..37
FT /evidence="ECO:0007829|PDB:3G91"
FT HELIX 43..45
FT /evidence="ECO:0007829|PDB:3G91"
FT HELIX 48..51
FT /evidence="ECO:0007829|PDB:3G91"
FT STRAND 57..61
FT /evidence="ECO:0007829|PDB:3G91"
FT STRAND 63..65
FT /evidence="ECO:0007829|PDB:3G91"
FT STRAND 71..77
FT /evidence="ECO:0007829|PDB:3G91"
FT STRAND 80..83
FT /evidence="ECO:0007829|PDB:3G91"
FT HELIX 89..92
FT /evidence="ECO:0007829|PDB:3G91"
FT STRAND 93..95
FT /evidence="ECO:0007829|PDB:3G91"
FT STRAND 97..101
FT /evidence="ECO:0007829|PDB:3G91"
FT STRAND 106..111
FT /evidence="ECO:0007829|PDB:3G91"
FT HELIX 119..141
FT /evidence="ECO:0007829|PDB:3G91"
FT STRAND 146..151
FT /evidence="ECO:0007829|PDB:3G91"
FT HELIX 158..160
FT /evidence="ECO:0007829|PDB:3G91"
FT HELIX 165..167
FT /evidence="ECO:0007829|PDB:3G91"
FT TURN 171..173
FT /evidence="ECO:0007829|PDB:3G8V"
FT HELIX 175..186
FT /evidence="ECO:0007829|PDB:3G91"
FT STRAND 189..191
FT /evidence="ECO:0007829|PDB:3G91"
FT HELIX 193..196
FT /evidence="ECO:0007829|PDB:3G91"
FT STRAND 204..206
FT /evidence="ECO:0007829|PDB:3W2X"
FT TURN 210..216
FT /evidence="ECO:0007829|PDB:3G91"
FT STRAND 222..227
FT /evidence="ECO:0007829|PDB:3G91"
FT HELIX 228..233
FT /evidence="ECO:0007829|PDB:3G91"
FT STRAND 234..239
FT /evidence="ECO:0007829|PDB:3G91"
FT STRAND 245..248
FT /evidence="ECO:0007829|PDB:3G91"
FT STRAND 251..256
FT /evidence="ECO:0007829|PDB:3G91"
SQ SEQUENCE 257 AA; 30347 MW; 3E3E77714C5151BF CRC64;
MTVLKIISWN VNGLRAVHRK GFLKWFMEEK PDILCLQEIK AAPEQLPRKL RHVEGYRSFF
TPAERKGYSG VAMYTKVPPS SLREGFGVER FDTEGRIQIA DFDDFLLYNI YFPNGKMSEE
RLKYKLEFYD AFLEDVNRER DSGRNVIICG DFNTAHREID LARPKENSNV SGFLPVERAW
IDKFIENGYV DTFRMFNSDP GQYTWWSYRT RARERNVGWR LDYFFVNEEF KGKVKRSWIL
SDVMGSDHCP IGLEIEL
