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13  structures 780  species 0  interactions 801  sequences 3  architectures

Family: SeqA (PF03925)

Summary: SeqA protein

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SeqA protein domain Edit Wikipedia article

SeqA, C-terminal domain
PDB 1j3e EBI.jpg
Crystal structure of the E.coli SeqA protein complexed with n6-methyladenine- guanine mismatch DNA
Identifiers
Symbol SeqA
Pfam PF03925
InterPro IPR005621
SCOP 1lrr
SUPERFAMILY 1lrr

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.[1] 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.[2]

Function

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.[3]

SeqA tetramers are able to aggregate or multimerize in a reversible, concentration-dependent manner.[3] Apart from its function in the control of DNA replication, SeqA may also be a specific transcription factor.[4]

Additionally, SeqA is also thought to have a role in chromosome organisation and gene regulation.[5]

Localisation

Most of the SeqA in the cell is found bound to new DNA, at the replication fork.[5]

Structure

N terminal domain

The N-terminal domain folds into two alpha-helices and one beta-strand. This protein domain is vital in assisting multimerisation.[5]

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.[5]

References

  1. ^ Slater S, Wold S, Lu M, Boye E, Skarstad K, Kleckner N (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. 
  2. ^ Shakibai N, Ishidate K, Reshetnyak E, Gunji S, Kohiyama M, Rothfield L (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.". Proc Natl Acad Sci U S A 95 (19): 11117–21. doi:10.1073/pnas.95.19.11117. PMC 21605. PMID 9736699. 
  3. ^ a b Lee H, Kang S, Bae SH, Choi BS, Hwang DS (September 2001). "SeqA protein aggregation is necessary for SeqA function". J. Biol. Chem. 276 (37): 34600–6. doi:10.1074/jbc.M101339200. PMID 11457824. 
  4. ^ 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". Mol. Microbiol. 40 (6): 1371–9. doi:10.1046/j.1365-2958.2001.02480.x. PMID 11442835. 
  5. ^ a b c d Waldminghaus T, Skarstad K (2009). "The Escherichia coli SeqA protein.". Plasmid 61 (3): 141–50. doi:10.1016/j.plasmid.2009.02.004. PMID 19254745. 

This article incorporates text from the public domain Pfam and InterPro IPR005621


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SeqA protein 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 [3]. SeqA tetramers are able to aggregate or multimerise in a reversible, concentration-dependent manner [3]. Apart from its function in the control of DNA replication, SeqA may also be a specific transcription factor [4].

Literature references

  1. 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

  2. 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

  3. Lee H, Kang S, Bae SH, Choi BS, Hwang DS; , J Biol Chem 2001;276:34600-34606.: SeqA protein aggregation is necessary for SeqA function. PUBMED:11457824 EPMC:11457824

  4. 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 IPR005621

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 [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 C-terminal domain binds DNA, binding to fully methylated and hemimethylated GATC sequences at oriC. The structure of the C-terminal domain consists of seven alpha-helices and three-stranded beta-sheet.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

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(37)
Full
(801)
Representative proteomes NCBI
(335)
Meta
(9)
RP15
(13)
RP35
(36)
RP55
(70)
RP75
(101)
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  Seed
(37)
Full
(801)
Representative proteomes NCBI
(335)
Meta
(9)
RP15
(13)
RP35
(36)
RP55
(70)
RP75
(101)
Alignment:
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  Seed
(37)
Full
(801)
Representative proteomes NCBI
(335)
Meta
(9)
RP15
(13)
RP35
(36)
RP55
(70)
RP75
(101)
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

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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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: COG3057
Previous IDs: none
Type: Family
Author: Bateman A
Number in seed: 37
Number in full: 801
Average length of the domain: 177.20 aa
Average identity of full alignment: 64 %
Average coverage of the sequence by the domain: 98.90 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.7 22.7
Trusted cut-off 23.0 22.7
Noise cut-off 22.6 22.6
Model length: 190
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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Structures

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 13 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 seqence.

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