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0  structures 719  species 0  interactions 737  sequences 1  architecture

Family: MatP (PF06303)

Summary: Organiser of macrodomain of Terminus of chromosome

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Organiser of macrodomain of Terminus of chromosome Provide feedback

This family, many of whose members are YcbG, organises the macrodomain Ter of the chromosome of bacteria such as E coli. In these bacteria, insulated macrodomains influence the segregation of sister chromatids and the mobility of chromosomal DNA. Organisation of the Terminus region (Ter) into a macrodomain relies on the presence of a 13 bp motif called matS repeated 23 times in the 800-kb-long domain. MatS sites are the main targets in the E. coli chromosome of YcbG or MatP (macrodomain Ter protein). MatP accumulates in the cell as a discrete focus that co-localises with the Ter macrodomain. The effects of MatP inactivation reveal its role as the main organiser of the Ter macrodomain: in the absence of MatP, DNA is less compacted, the mobility of markers is increased, and segregation of the Ter macrodomain occurs early in the cell cycle. A specific organisational system is required in the Terminus region for bacterial chromosome management during the cell cycle.

Literature references

  1. Mercier R, Petit MA, Schbath S, Robin S, El Karoui M, Boccard F, Espeli O; , Cell. 2008;135:475-485.: The MatP/matS site-specific system organizes the terminus region of the E. coli chromosome into a macrodomain. PUBMED:18984159 EPMC:18984159


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR009390

Many bacteria have circular genomes that are large in comparison to their cellular dimensions; this imposes the necessity for compaction of the chromosome during cellular growth, replication, transcription, and segregation. Compaction of chromosomes results in the formation of structures called nucleoids. Nucleoids can be generated by a number of different processes: they include unrestrained DNA supercoiling, formation of a chromatin-like structure through the interaction of DNA binding proteins, condensation by structural maintenance of chromosomes (SMC)-like proteins, and macromolecular crowding [PUBMED:16860572]. Chromosome replication and segregation are intimately linked and tightly controlled to ensure that daughter cells each receive a complete copy of the genome. Chromosomes have replication origin (Ori) and termination (Ter) regions that are diametrically opposed. During the process of chromosome replication and cell division the Ori and Ter regions form two macrodomains (MDs), the Ori MD is centred on migS, a 25 bp sequence, that acts as the cis-acting site for the bipolar positioning of oriC [PUBMED:14685268]. The Ter MD is centred on dif (deletion-induced filamentation), which is a resolvase site that reduces chromosome multimers to monomers [PUBMED:7877981]. The Ori and Ter MDs are insulated from one and other by non-structural regions and other nucleoids. Chromosome replication initiates bidirectionally from oriC. Within the Ori MD with sister chromatids being located in separate cell halves and with the Ter macrodomain anchored to the cell pole. Cell division occurs with the completion of replication of the Ter region and the subsequent separation of the two sister chromatids [PUBMED:17020576, PUBMED:18984159].

This entry contains MatP (YcbG), which is a component of the MatP/MatS site-specific system that organises the Ter macrodomain (MD) in Escherichia coli (strain K12) and related enterobacteria during replication of the chromosome. In E. coli there are 23 matS sequences, located in the Ter region which is centred on dif. The matS consensus is a palindromic sequence 5'-GTGAC[AG][CT]GTCAC, which is the recognition sequence for MatP. MatP binds to the matS sequences; and is critical for Ter MD formation. Inactivation of matP causes severe defects in chromosome segregation and cell division revealing its role as a major organiser of the Ter MD [PUBMED:18984159].

Domain organisation

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  Seed
(13)
Full
(737)
Representative proteomes NCBI
(231)
Meta
(1)
RP15
(5)
RP35
(19)
RP55
(47)
RP75
(67)
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  Seed
(13)
Full
(737)
Representative proteomes NCBI
(231)
Meta
(1)
RP15
(5)
RP35
(19)
RP55
(47)
RP75
(67)
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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.

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Curation and family details

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Curation View help on the curation process

Seed source: Pfam-B_12243 (release 9.0)
Previous IDs: DUF1047;
Type: Family
Author: Moxon SJ
Number in seed: 13
Number in full: 737
Average length of the domain: 145.90 aa
Average identity of full alignment: 71 %
Average coverage of the sequence by the domain: 97.72 %

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 20.0 20.0
Trusted cut-off 21.7 21.1
Noise cut-off 19.5 19.0
Model length: 148
Family (HMM) version: 7
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