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8  structures 2584  species 0  interactions 3819  sequences 43  architectures

Family: HSDR_N (PF04313)

Summary: Type I restriction enzyme R protein N terminus (HSDR_N)

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Type I restriction enzyme R protein N terminus (HSDR_N) Provide feedback

This family consists of a number of N terminal regions found in type I restriction enzyme R (HSDR) proteins. Restriction and modification (R/M) systems are found in a wide variety of prokaryotes and are thought to protect the host bacterium from the uptake of foreign DNA [1]. Type I restriction and modification systems are encoded by three genes: hsdR, hsdM, and hsdS. The three polypeptides, HsdR, HsdM, and HsdS, often assemble to give an enzyme (R2M2S1) that modifies hemimethylated DNA and restricts unmethylated DNA [2].

Literature references

  1. Piekarowicz A, Klyz A, Kwiatek A, Stein DC; , Mol Microbiol 2001;41:1199-1210.: Analysis of type I restriction modification systems in the Neisseriaceae: genetic organization and properties of the gene products. PUBMED:11555298 EPMC:11555298

  2. Makovets S, Doronina VA, Murray NE; , Proc Natl Acad Sci U S A 1999;96:9757-9762.: Regulation of endonuclease activity by proteolysis prevents breakage of unmodified bacterial chromosomes by type I restriction enzymes. PUBMED:10449767 EPMC:10449767


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007409

There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [PUBMED:15121719, PUBMED:12665693], as summarised below:

  • Type I enzymes (EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (EC) activities.
  • Type II enzymes (EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase.
  • Type III enzymes (EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (EC).
  • Type IV enzymes target methylated DNA.

Type I restriction endonucleases are components of prokaryotic DNA restriction-modification mechanisms that protects the organism against invading foreign DNA. Type I enzymes have three different subunits subunits - M (modification), S (specificity) and R (restriction) - that form multifunctional enzymes with restriction (EC), methylase (EC) and ATPase activities [PUBMED:15121719, PUBMED:12595133]. The S subunit is required for both restriction and modification and is responsible for recognition of the DNA sequence specific for the system. The M subunit is necessary for modification, and the R subunit is required for restriction. These enzymes use S-Adenosyl-L-methionine (AdoMet) as the methyl group donor in the methylation reaction, and have a requirement for ATP. They recognise asymmetric DNA sequences split into two domains of specific sequence, one 3-4 bp long and another 4-5 bp long, separated by a nonspecific spacer 6-8 bp in length. Cleavage occurs a considerable distance from the recognition sites, rarely less than 400 bp away and up to 7000 bp away. Adenosyl residues are methylated, one on each strand of the recognition sequence. These enzymes are widespread in eubacteria and archaea. In enteric bacteria they have been subdivide into four families: types IA, IB, IC and ID.

Type III restriction endonucleases (EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. Type III enzymes are hetero-oligomeric, multifunctional proteins composed of two subunits, Res and Mod. The Mod subunit recognises the DNA sequence specific for the system and is a modification methyltransferase; as such it is functionally equivalent to the M and S subunits of type I restriction endonuclease. Res is required for restriction, although it has no enzymatic activity on its own. Type III enzymes recognise short 5-6 bp long asymmetric DNA sequences and cleave 25-27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction. Type III enzymes belong to the beta-subfamily of N6 adenine methyltransferases, containing the nine motifs that characterise this family, including motif I, the AdoMet binding pocket (FXGXG), and motif IV, the catalytic region (S/D/N (PP) Y/F) [PUBMED:15121719, PUBMED:12595133].

This entry represents the N-terminal domain found in both the R subunit (HsdR) of type I enzymes and the Res subunit of type III enzymes. The type I enzyme represented is EcoRI, which recognises the DNA sequence 5'-GAATTC; the R protein (HsdR) is required for both nuclease and ATPase activity [PUBMED:8412658, PUBMED:10449767, PUBMED:11555298].

This domain is often found adjacent to a methylase domain (INTERPRO) in restriction endonucleases or methylases. In one of the proteins, SWISSPROT, it is adjacent to a helicase domain (INTERPRO) in a putative restriction endonuclease.

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Domain organisation

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(576)
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  Seed
(77)
Full
(3819)
Representative proteomes NCBI
(3899)
Meta
(642)
RP15
(293)
RP35
(576)
RP55
(721)
RP75
(831)
Alignment:
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  Seed
(77)
Full
(3819)
Representative proteomes NCBI
(3899)
Meta
(642)
RP15
(293)
RP35
(576)
RP55
(721)
RP75
(831)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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Curation and family details

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Seed source: COG2810
Previous IDs: DUF450;
Type: Family
Author: Kerrison ND, Finn RD, Yeats C
Number in seed: 77
Number in full: 3819
Average length of the domain: 175.90 aa
Average identity of full alignment: 19 %
Average coverage of the sequence by the domain: 18.43 %

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 21.1 20.5
Trusted cut-off 21.1 20.5
Noise cut-off 21.0 20.4
Model length: 194
Family (HMM) version: 9
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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 HSDR_N domain has been found. There are 8 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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