ID   ATL_VIBPQ               Reviewed;         100 AA.
AC   A6B4U8;
DT   01-APR-2015, integrated into UniProtKB/Swiss-Prot.
DT   24-JUL-2007, sequence version 1.
DT   25-MAY-2022, entry version 52.
DE   RecName: Full=DNA base-flipping protein {ECO:0000250|UniProtKB:P0AFP2};
DE   AltName: Full=Alkyltransferase-like protein ATL {ECO:0000250|UniProtKB:P0AFP2};
DE   AltName: Full=vpAtl {ECO:0000303|PubMed:20212037};
GN   ORFNames=A79_1377 {ECO:0000312|EMBL:EDM58796.1},
GN   D030_1023 {ECO:0000312|EMBL:EXF71745.1};
OS   Vibrio parahaemolyticus serotype O3:K6 (strain AQ3810).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae;
OC   Vibrio.
OX   NCBI_TaxID=419109;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=AQ3810;
RA   Heidelberg J., Sebastian Y.;
RT   "Annotation of Vibrio parahaemolyticus AQ3810.";
RL   Submitted (JAN-2007) to the EMBL/GenBank/DDBJ databases.
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=AQ3810;
RA   Eppinger M., Hasan N.A., Sengamalay N., Hine E., Su Q., Daugherty S.C.,
RA   Choi S.Y., Sadzewicz L., Tallon L., Cebula T.A., Ravel J., Colwell R.R.;
RL   Submitted (DEC-2013) to the EMBL/GenBank/DDBJ databases.
RN   [3]
RP   STRUCTURE BY NMR, FUNCTION, AND MUTAGENESIS OF TYR-23; ARG-37 AND TRP-54.
RX   PubMed=20212037; DOI=10.1074/jbc.m109.093591;
RA   Aramini J.M., Tubbs J.L., Kanugula S., Rossi P., Ertekin A., Maglaqui M.,
RA   Hamilton K., Ciccosanti C.T., Jiang M., Xiao R., Soong T.T., Rost B.,
RA   Acton T.B., Everett J.K., Pegg A.E., Tainer J.A., Montelione G.T.;
RT   "Structural basis of O6-alkylguanine recognition by a bacterial
RT   alkyltransferase-like DNA repair protein.";
RL   J. Biol. Chem. 285:13736-13741(2010).
CC   -!- FUNCTION: Involved in DNA damage recognition. Binds DNA containing
CC       O(6)-methylguanine (PubMed:20212037). Binds to the damaged base and
CC       flips the base out of the DNA duplex into an extrahelical conformation,
CC       which allows processing by repair proteins (By similarity).
CC       {ECO:0000250|UniProtKB:P0AFP2, ECO:0000269|PubMed:20212037}.
CC   -!- SIMILARITY: Belongs to the MGMT family. ATL subfamily. {ECO:0000305}.
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DR   EMBL; AAWQ01000051; EDM58796.1; -; Genomic_DNA.
DR   EMBL; AZJP01000183; EXF71745.1; -; Genomic_DNA.
DR   RefSeq; WP_005461131.1; NZ_KK073771.1.
DR   PDB; 2KIF; NMR; -; A=1-100.
DR   PDB; 2KIM; NMR; -; A=1-100.
DR   PDBsum; 2KIF; -.
DR   PDBsum; 2KIM; -.
DR   AlphaFoldDB; A6B4U8; -.
DR   BMRB; A6B4U8; -.
DR   SMR; A6B4U8; -.
DR   PATRIC; fig|419109.25.peg.1095; -.
DR   HOGENOM; CLU_000445_52_5_6; -.
DR   EvolutionaryTrace; A6B4U8; -.
DR   GO; GO:0003824; F:catalytic activity; IEA:InterPro.
DR   GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0006281; P:DNA repair; IEA:InterPro.
DR   CDD; cd06445; ATase; 1.
DR   Gene3D; 1.10.10.10; -; 1.
DR   InterPro; IPR014048; MethylDNA_cys_MeTrfase_DNA-bd.
DR   InterPro; IPR036217; MethylDNA_cys_MeTrfase_DNAb.
DR   InterPro; IPR036388; WH-like_DNA-bd_sf.
DR   Pfam; PF01035; DNA_binding_1; 1.
DR   SUPFAM; SSF46767; SSF46767; 1.
PE   1: Evidence at protein level;
KW   3D-structure; DNA damage; DNA-binding.
FT   CHAIN           1..100
FT                   /note="DNA base-flipping protein"
FT                   /id="PRO_0000432552"
FT   SITE            23
FT                   /note="Required for phosphate rotation/nucleotide flipping"
FT                   /evidence="ECO:0000250|UniProtKB:Q9UTN9"
FT   SITE            37
FT                   /note="Arg finger, required for nucleotide flipping"
FT                   /evidence="ECO:0000250|UniProtKB:Q9UTN9"
FT   MUTAGEN         23
FT                   /note="Y->A: Severely impairs ability to bind alkylated
FT                   DNA."
FT                   /evidence="ECO:0000269|PubMed:20212037"
FT   MUTAGEN         23
FT                   /note="Y->F: Slightly impairs ability to bind alkylated
FT                   DNA."
FT                   /evidence="ECO:0000269|PubMed:20212037"
FT   MUTAGEN         37
FT                   /note="R->A: Severely impairs ability to bind alkylated
FT                   DNA."
FT                   /evidence="ECO:0000269|PubMed:20212037"
FT   MUTAGEN         54
FT                   /note="W->A: Exhibits some affinity for methylated DNA."
FT                   /evidence="ECO:0000269|PubMed:20212037"
FT   HELIX           3..12
FT                   /evidence="ECO:0007829|PDB:2KIF"
FT   STRAND          20..22
FT                   /evidence="ECO:0007829|PDB:2KIF"
FT   HELIX           23..30
FT                   /evidence="ECO:0007829|PDB:2KIF"
FT   HELIX           36..45
FT                   /evidence="ECO:0007829|PDB:2KIF"
FT   HELIX           54..56
FT                   /evidence="ECO:0007829|PDB:2KIM"
FT   HELIX           69..79
FT                   /evidence="ECO:0007829|PDB:2KIF"
FT   TURN            80..82
FT                   /evidence="ECO:0007829|PDB:2KIF"
FT   TURN            87..89
FT                   /evidence="ECO:0007829|PDB:2KIF"
FT   HELIX           93..96
FT                   /evidence="ECO:0007829|PDB:2KIF"
SQ   SEQUENCE   100 AA;  11251 MW;  2CF15E0684DFF9A0 CRC64;
     MDQFLVQIFA VIHQIPKGKV STYGEIAKMA GYPGYARHVG KALGNLPEGS KLPWFRVINS
     QGKISLKGRD LDRQKQKLEA EGIEVSEIGK IALRKYKWQP