Summary: SeqA protein C-terminal domain
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SeqA protein domain Edit Wikipedia article
|SeqA, C-terminal domain|
Crystal structure of the E.coli SeqA protein complexed with n6-methyladenine- guanine mismatch DNA
In molecular biology the protein domain SeqA is one found in bacteria and archaea. The function of this protein domain is highly important in DNA replication. The protein negatively regulates the initiation of DNA replication at the origin of replication, in Escherichia coli, OriC. Additionally the protein plays a further role in sequestration. The importance of this protein is vital, without its help in DNA replication, cell division and other crucial processes could not occur. This protein domain is thought to be part of a much larger protein complex which includes other proteins such as SeqB.
DNA replication is an energy consuming process and hence in bacteria the process only occurs at a specific checkpoint in the cell cycle. The binding of SeqA protein to hemimethylated GATC sequences is important in the negative modulation of chromosomal initiation at oriC, and in the formation of SeqA foci necessary for Escherichia coli chromosome segregation.
SeqA tetramers are able to aggregate or multimerize in a reversible, concentration-dependent manner. Apart from its function in the control of DNA replication, SeqA may also be a specific transcription factor.
N terminal domain
C terminal domain
The C-terminal protein domain has an important role in binding to DNA. It binds to fully methylated and hemimethylated GATC sequences at oriC. The structure of the C-terminal domain consists of seven alpha-helices and a three-stranded beta-sheet.
- Slater S, Wold S, Lu M, Boye E, Skarstad K, Kleckner N (September 1995). "E. coli SeqA protein binds oriC in two different methyl-modulated reactions appropriate to its roles in DNA replication initiation and origin sequestration". Cell. 82 (6): 927–36. doi:10.1016/0092-8674(95)90272-4. PMID 7553853.
- Shakibai N, Ishidate K, Reshetnyak E, Gunji S, Kohiyama M, Rothfield L (September 1998). "High-affinity binding of hemimethylated oriC by Escherichia coli membranes is mediated by a multiprotein system that includes SeqA and a newly identified factor, SeqB". Proceedings of the National Academy of Sciences of the United States of America. 95 (19): 11117–21. doi:10.1073/pnas.95.19.11117. PMC . PMID 9736699.
- Lee H, Kang S, Bae SH, Choi BS, Hwang DS (September 2001). "SeqA protein aggregation is necessary for SeqA function". The Journal of Biological Chemistry. 276 (37): 34600–6. doi:10.1074/jbc.M101339200. PMID 11457824.
- Slomińska M, Wegrzyn A, Konopa G, Skarstad K, Wegrzyn G (June 2001). "SeqA, the Escherichia coli origin sequestration protein, is also a specific transcription factor". Molecular Microbiology. 40 (6): 1371–9. doi:10.1046/j.1365-2958.2001.02480.x. PMID 11442835.
- Waldminghaus T, Skarstad K (May 2009). "The Escherichia coli SeqA protein". Plasmid. 61 (3): 141–50. doi:10.1016/j.plasmid.2009.02.004. PMID 19254745.
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SeqA protein C-terminal domain Provide feedback
The binding of SeqA protein to hemimethylated GATC sequences is important in the negative modulation of chromosomal initiation at oriC, and in the formation of SeqA foci necessary for Escherichia coli chromosome segregation . SeqA tetramers are able to aggregate or multimerise in a reversible, concentration-dependent manner . Apart from its function in the control of DNA replication, SeqA may also be a specific transcription factor .
Shakibai N, Ishidate K, Reshetnyak E, Gunji S, Kohiyama M, Rothfield L; , Proc Natl Acad Sci U S A 1998;95:11117-11121.: High-affinity binding of hemimethylated oriC by Escherichia coli membranes is mediated by a multiprotein system that includes SeqA and a newly identified factor, SeqB. PUBMED:9736699 EPMC:9736699
Slater S, Wold S, Lu M, Boye E, Skarstad K, Kleckner N; , Cell 1995;82:927-936.: E. coli SeqA protein binds oriC in two different methyl-modulated reactions appropriate to its roles in DNA replication initiation and origin sequestration. PUBMED:7553853 EPMC:7553853
Slominska M, Wegrzyn A, Konopa G, Skarstad K, Wegrzyn G; , Mol Microbiol 2001;40:1371-1379.: SeqA, the Escherichia coli origin sequestration protein, is also a specific transcription factor. PUBMED:11442835 EPMC:11442835
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR026577
The C-terminal domain binds DNA, binding to hemimethylated GATC sequences at oriC [ PUBMED:12379844 , PUBMED:14704346 ]. The structure of the C-terminal domain consists of seven alpha-helices and three-stranded beta-sheet.
The binding of the negative modulator of initiation of replication (SeqA) protein to hemimethylated GATC sequences is important in the negative modulation of chromosomal initiation at oriC, and in the formation of SeqA foci necessary for Escherichia coli chromosome segregation [ PUBMED:11457824 ]. SeqA tetramers are able to aggregate or multimerize in a reversible, concentration-dependent manner [ PUBMED:11457824 ]. Apart from its function in the control of DNA replication, SeqA may also be a specific transcription factor [ PUBMED:11442835 ].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||DNA binding (GO:0003677)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
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|Number in seed:||30|
|Number in full:||357|
|Average length of the domain:||109.60 aa|
|Average identity of full alignment:||45 %|
|Average coverage of the sequence by the domain:||58.64 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||16|
|Download:||download the raw HMM for this family|
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Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
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Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
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The tree shows the occurrence of this domain across different species. More...
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For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
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Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the SeqA domain has been found. There are 9 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
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