SEQA_ECOLI
ID SEQA_ECOLI Reviewed; 181 AA.
AC P0AFY8; P36658;
DT 20-DEC-2005, integrated into UniProtKB/Swiss-Prot.
DT 20-DEC-2005, sequence version 1.
DT 03-AUG-2022, entry version 129.
DE RecName: Full=Negative modulator of initiation of replication {ECO:0000255|HAMAP-Rule:MF_00908};
GN Name=seqA {ECO:0000255|HAMAP-Rule:MF_00908};
GN OrderedLocusNames=b0687, JW0674;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND FUNCTION.
RC STRAIN=K12;
RX PubMed=8011018; DOI=10.1016/0092-8674(94)90156-2;
RA Lu M., Campbell J.L., Boye E., Kleckner N.;
RT "SeqA: a negative modulator of replication initiation in E. coli.";
RL Cell 77:413-426(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=8905232; DOI=10.1093/dnares/3.3.137;
RA Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K.,
RA Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S.,
RA Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K., Mori H.,
RA Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G.,
RA Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M.,
RA Horiuchi T.;
RT "A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 12.7-28.0 min region on the linkage map.";
RL DNA Res. 3:137-155(1996).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP FUNCTION.
RX PubMed=7891562; DOI=10.1111/j.1365-2958.1994.tb01313.x;
RA von Freiesleben U., Rasmussen K.V., Schaechter M.;
RT "SeqA limits DnaA activity in replication from oriC in Escherichia coli.";
RL Mol. Microbiol. 14:763-772(1994).
RN [6]
RP REVIEW.
RX PubMed=7850437; DOI=10.1016/s0960-9822(00)00214-1;
RA Baker T.A.;
RT "Replication initiation. A new controller in Escherichia coli.";
RL Curr. Biol. 4:945-946(1994).
RN [7]
RP CHARACTERIZATION, AND FUNCTION.
RX PubMed=7553853; DOI=10.1016/0092-8674(95)90272-4;
RA Slater S., Wold S., Lu M., Boye E., Skarstad K., Kleckner N.;
RT "E. coli seqA protein binds oriC in two different methyl-modulated
RT reactions appropriate to its roles in DNA replication initiation and origin
RT sequestration.";
RL Cell 82:927-936(1995).
RN [8]
RP SUBCELLULAR LOCATION.
RC STRAIN=K12;
RX PubMed=9660922; DOI=10.1016/s1097-2765(00)80038-6;
RA Hiraga S., Ichinose C., Niki H., Yamazoe M.;
RT "Cell cycle-dependent duplication and bidirectional migration of SeqA-
RT associated DNA-protein complexes in E. coli.";
RL Mol. Cell 1:381-387(1998).
RN [9]
RP CHARACTERIZATION.
RX PubMed=9736699; DOI=10.1073/pnas.95.19.11117;
RA Shakibai N., Ishidate K., Reshetnyak E., Gunji S., Kohiyama M.,
RA Rothfield L.;
RT "High-affinity binding of hemimethylated oriC by Escherichia coli membranes
RT is mediated by a multiprotein system that includes seqA and a newly
RT identified factor, seqB.";
RL Proc. Natl. Acad. Sci. U.S.A. 95:11117-11121(1998).
RN [10]
RP FUNCTION, AND DNA-BINDING.
RX PubMed=11080170; DOI=10.1093/emboj/19.22.6249;
RA Brendler T., Sawitzke J., Sergueev K., Austin S.;
RT "A case for sliding SeqA tracts at anchored replication forks during
RT Escherichia coli chromosome replication and segregation.";
RL EMBO J. 19:6249-6258(2000).
RN [11]
RP FUNCTION, AND DNA-BINDING.
RX PubMed=10931282; DOI=10.1046/j.1365-2958.2000.01943.x;
RA Skarstad K., Lueder G., Lurz R., Speck C., Messer W.;
RT "The Escherichia coli SeqA protein binds specifically and co-operatively to
RT two sites in hemimethylated and fully methylated oriC.";
RL Mol. Microbiol. 36:1319-1326(2000).
RN [12]
RP DOMAIN.
RX PubMed=12507506; DOI=10.1016/s0006-291x(02)02891-7;
RA Fujikawa N., Kurumizaka H., Yamazoe M., Hiraga S., Yokoyama S.;
RT "Identification of functional domains of the Escherichia coli SeqA
RT protein.";
RL Biochem. Biophys. Res. Commun. 300:699-705(2003).
RN [13]
RP REVIEW.
RX PubMed=19254745; DOI=10.1016/j.plasmid.2009.02.004;
RA Waldminghaus T., Skarstad K.;
RT "The Escherichia coli SeqA protein.";
RL Plasmid 61:141-150(2009).
RN [14]
RP FUNCTION, AND DNA-BINDING.
RC STRAIN=K12 / CMT940;
RX PubMed=20689753; DOI=10.1128/mbio.00012-10;
RA Sanchez-Romero M.A., Busby S.J., Dyer N.P., Ott S., Millard A.D.,
RA Grainger D.C.;
RT "Dynamic distribution of SeqA protein across the chromosome of Escherichia
RT coli K-12.";
RL MBio 1:E12-E12(2010).
RN [15]
RP X-RAY CRYSTALLOGRAPHY (2.65 ANGSTROMS) OF 51-181 IN COMPLEX WITH
RP HEMIMETHYLATED DNA, DNA-BINDING, SUBUNIT, AND DOMAIN.
RX PubMed=12379844; DOI=10.1038/nsb857;
RA Guarne A., Zhao Q., Ghirlando R., Yang W.;
RT "Insights into negative modulation of E. coli replication initiation from
RT the structure of SeqA-hemimethylated DNA complex.";
RL Nat. Struct. Biol. 9:839-843(2002).
RN [16]
RP X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 71-181 IN COMPLEX WITH
RP HEMIMETHYLATED DNA, MUTAGENESIS OF ARG-116; ARG-118; THR-149; ASN-150;
RP THR-151; ASN-152; ARG-155 AND LYS-156, AND DNA-BINDING.
RX PubMed=14704346; DOI=10.1093/nar/gkh173;
RA Fujikawa N., Kurumizaka H., Nureki O., Tanaka Y., Yamazoe M., Hiraga S.,
RA Yokoyama S.;
RT "Structural and biochemical analyses of hemimethylated DNA binding by the
RT SeqA protein.";
RL Nucleic Acids Res. 32:82-92(2004).
RN [17]
RP X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS) OF 1-50, AND SUBUNIT.
RX PubMed=15933720; DOI=10.1038/sj.emboj.7600634;
RA Guarne A., Brendler T., Zhao Q., Ghirlando R., Austin S., Yang W.;
RT "Crystal structure of a SeqA-N filament: implications for DNA replication
RT and chromosome organization.";
RL EMBO J. 24:1502-1511(2005).
RN [18]
RP X-RAY CRYSTALLOGRAPHY (2.98 ANGSTROMS) IN COMPLEX WITH HEMIMETHYLATED DNA,
RP DNA-BINDING, AND DOMAIN.
RX PubMed=19304745; DOI=10.1093/nar/gkp151;
RA Chung Y.S., Brendler T., Austin S., Guarne A.;
RT "Structural insights into the cooperative binding of SeqA to a tandem GATC
RT repeat.";
RL Nucleic Acids Res. 37:3143-3152(2009).
RN [19]
RP 3D-STRUCTURE MODELING.
RX PubMed=18849124; DOI=10.1016/j.patbio.2008.03.013;
RA Daghfous D., Chatti A., Hammami R., Landoulsi A.;
RT "Modeling of the full-length Escherichia coli SeqA protein, in complex with
RT DNA.";
RL Pathol. Biol. 57:E61-E66(2009).
CC -!- FUNCTION: Negative regulator of replication initiation, which
CC contributes to regulation of DNA replication and ensures that
CC replication initiation occurs exactly once per chromosome per cell
CC cycle. Binds to pairs of hemimethylated GATC sequences in the oriC
CC region, thus preventing assembly of replication proteins and re-
CC initiation at newly replicated origins. Repression is relieved when the
CC region becomes fully methylated. Can also bind to hemimethylated GATC
CC sequences outside of oriC region. Binds, with less affinity, to fully
CC methylated GATC sites and affects timing of replication. May play a
CC role in chromosome organization and gene regulation.
CC {ECO:0000255|HAMAP-Rule:MF_00908, ECO:0000269|PubMed:10931282,
CC ECO:0000269|PubMed:11080170, ECO:0000269|PubMed:20689753,
CC ECO:0000269|PubMed:7553853, ECO:0000269|PubMed:7891562,
CC ECO:0000269|PubMed:8011018}.
CC -!- SUBUNIT: Homodimer. Polymerizes to form helical filaments. Dimerization
CC is sufficient for DNA-binding, but oligomerization is essential for
CC function. {ECO:0000255|HAMAP-Rule:MF_00908,
CC ECO:0000269|PubMed:12379844, ECO:0000269|PubMed:14704346,
CC ECO:0000269|PubMed:15933720, ECO:0000269|PubMed:19304745}.
CC -!- INTERACTION:
CC P0AFY8; P0AFY8: seqA; NbExp=13; IntAct=EBI-552553, EBI-552553;
CC P0AFY8; P0A8F8: uvrB; NbExp=2; IntAct=EBI-552553, EBI-552176;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00908,
CC ECO:0000269|PubMed:9660922}. Note=Localization is cell cycle-dependent.
CC Localizes at midcell in newborn cells, then migrates in opposite
CC directions toward cell quarter sites and remains tethered there until
CC the cell divides.
CC -!- DOMAIN: The N-terminal domain is required for multimerization. The C-
CC terminal domain is involved in DNA-binding.
CC {ECO:0000269|PubMed:12379844, ECO:0000269|PubMed:12507506,
CC ECO:0000269|PubMed:19304745}.
CC -!- SIMILARITY: Belongs to the SeqA family. {ECO:0000255|HAMAP-
CC Rule:MF_00908}.
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DR EMBL; U07651; AAA19855.1; -; Unassigned_RNA.
DR EMBL; U00096; AAC73781.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA35336.1; -; Genomic_DNA.
DR PIR; A54296; A54296.
DR RefSeq; NP_415213.1; NC_000913.3.
DR RefSeq; WP_000848387.1; NZ_STEB01000044.1.
DR PDB; 1IU3; X-ray; 3.00 A; C/F=71-181.
DR PDB; 1J3E; X-ray; 2.50 A; A=71-181.
DR PDB; 1LRR; X-ray; 2.65 A; A/D=51-181.
DR PDB; 1XRX; X-ray; 2.15 A; A/B/C/D=1-50.
DR PDB; 3FMT; X-ray; 2.98 A; A/B/E/F=1-181.
DR PDBsum; 1IU3; -.
DR PDBsum; 1J3E; -.
DR PDBsum; 1LRR; -.
DR PDBsum; 1XRX; -.
DR PDBsum; 3FMT; -.
DR AlphaFoldDB; P0AFY8; -.
DR SMR; P0AFY8; -.
DR BioGRID; 4261907; 83.
DR BioGRID; 849651; 2.
DR ComplexPortal; CPX-1955; SeqA-DNA complex.
DR DIP; DIP-48017N; -.
DR IntAct; P0AFY8; 3.
DR STRING; 511145.b0687; -.
DR jPOST; P0AFY8; -.
DR PaxDb; P0AFY8; -.
DR PRIDE; P0AFY8; -.
DR EnsemblBacteria; AAC73781; AAC73781; b0687.
DR EnsemblBacteria; BAA35336; BAA35336; BAA35336.
DR GeneID; 66671042; -.
DR GeneID; 945272; -.
DR KEGG; ecj:JW0674; -.
DR KEGG; eco:b0687; -.
DR PATRIC; fig|1411691.4.peg.1589; -.
DR EchoBASE; EB2114; -.
DR eggNOG; COG3057; Bacteria.
DR HOGENOM; CLU_099733_0_0_6; -.
DR OMA; RTRTYFA; -.
DR PhylomeDB; P0AFY8; -.
DR BioCyc; EcoCyc:EG12197-MON; -.
DR EvolutionaryTrace; P0AFY8; -.
DR PRO; PR:P0AFY8; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0032991; C:protein-containing complex; IDA:EcoCyc.
DR GO; GO:1990097; C:SeqA-DNA complex; IDA:EcoCyc.
DR GO; GO:0003688; F:DNA replication origin binding; IDA:EcoCyc.
DR GO; GO:0010385; F:double-stranded methylated DNA binding; IDA:EcoCyc.
DR GO; GO:0044729; F:hemi-methylated DNA-binding; IDA:EcoCyc.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0032297; P:negative regulation of DNA-templated DNA replication initiation; IMP:EcoCyc.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; IEA:InterPro.
DR GO; GO:0009314; P:response to radiation; IMP:EcoCyc.
DR Gene3D; 1.10.1220.10; -; 1.
DR Gene3D; 1.20.1380.10; -; 1.
DR HAMAP; MF_00908; SeqA; 1.
DR InterPro; IPR013321; Arc_rbn_hlx_hlx.
DR InterPro; IPR010985; Ribbon_hlx_hlx.
DR InterPro; IPR005621; SeqA.
DR InterPro; IPR026577; SeqA_DNA-bd_C.
DR InterPro; IPR036835; SeqA_DNA-bd_C_sf.
DR InterPro; IPR033761; SeqA_N.
DR Pfam; PF03925; SeqA; 1.
DR Pfam; PF17206; SeqA_N; 1.
DR PIRSF; PIRSF019401; SeqA; 1.
DR SUPFAM; SSF47598; SSF47598; 1.
DR SUPFAM; SSF82808; SSF82808; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; DNA replication inhibitor; DNA-binding;
KW Reference proteome.
FT CHAIN 1..181
FT /note="Negative modulator of initiation of replication"
FT /id="PRO_0000097684"
FT REGION 87..88
FT /note="Interaction with DNA"
FT REGION 116..120
FT /note="Interaction with DNA"
FT REGION 150..156
FT /note="Interaction with DNA"
FT MUTAGEN 116
FT /note="R->A: Strongly reduced DNA binding."
FT /evidence="ECO:0000269|PubMed:14704346"
FT MUTAGEN 118
FT /note="R->A: Strongly reduced DNA binding."
FT /evidence="ECO:0000269|PubMed:14704346"
FT MUTAGEN 149
FT /note="T->A: Strongly reduced DNA binding."
FT /evidence="ECO:0000269|PubMed:14704346"
FT MUTAGEN 150
FT /note="N->A,D: Strongly reduced DNA binding."
FT /evidence="ECO:0000269|PubMed:14704346"
FT MUTAGEN 151
FT /note="T->A: Reduced DNA binding."
FT /evidence="ECO:0000269|PubMed:14704346"
FT MUTAGEN 152
FT /note="N->D: Strongly reduced DNA binding."
FT /evidence="ECO:0000269|PubMed:14704346"
FT MUTAGEN 155
FT /note="R->A: Strongly reduced DNA binding."
FT /evidence="ECO:0000269|PubMed:14704346"
FT MUTAGEN 156
FT /note="K->A: Strongly reduced DNA binding."
FT /evidence="ECO:0000269|PubMed:14704346"
FT STRAND 2..6
FT /evidence="ECO:0007829|PDB:1XRX"
FT HELIX 8..15
FT /evidence="ECO:0007829|PDB:1XRX"
FT HELIX 25..33
FT /evidence="ECO:0007829|PDB:1XRX"
FT HELIX 36..38
FT /evidence="ECO:0007829|PDB:3FMT"
FT HELIX 71..77
FT /evidence="ECO:0007829|PDB:1J3E"
FT HELIX 79..83
FT /evidence="ECO:0007829|PDB:1J3E"
FT HELIX 87..101
FT /evidence="ECO:0007829|PDB:1J3E"
FT HELIX 103..111
FT /evidence="ECO:0007829|PDB:1J3E"
FT STRAND 116..119
FT /evidence="ECO:0007829|PDB:1J3E"
FT STRAND 121..125
FT /evidence="ECO:0007829|PDB:1J3E"
FT HELIX 126..130
FT /evidence="ECO:0007829|PDB:1J3E"
FT STRAND 131..134
FT /evidence="ECO:0007829|PDB:1J3E"
FT STRAND 137..139
FT /evidence="ECO:0007829|PDB:3FMT"
FT STRAND 142..144
FT /evidence="ECO:0007829|PDB:1IU3"
FT STRAND 146..148
FT /evidence="ECO:0007829|PDB:3FMT"
FT HELIX 153..166
FT /evidence="ECO:0007829|PDB:1J3E"
FT HELIX 171..178
FT /evidence="ECO:0007829|PDB:1J3E"
SQ SEQUENCE 181 AA; 20315 MW; 37D9078CA3D7229B CRC64;
MKTIEVDDEL YSYIASHTKH IGESASDILR RMLKFSAASQ PAAPVTKEVR VASPAIVEAK
PVKTIKDKVR AMRELLLSDE YAEQKRAVNR FMLLLSTLYS LDAQAFAEAT ESLHGRTRVY
FAADEQTLLK NGNQTKPKHV PGTPYWVITN TNTGRKCSMI EHIMQSMQFP AELIEKVCGT
I
