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37  structures 11  species 1  interaction 13  sequences 2  architectures

Family: Bse634I (PF07832)

Summary: Cfr10I/Bse634I restriction endonuclease

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This is the Wikipedia entry entitled "Cfr10I/Bse634I". More...

Cfr10I/Bse634I Edit Wikipedia article

Bse634I
PDB 1cfr EBI.jpg
crystal structure of citrobacter freundii restriction endonuclease cfr10i at 2.15 angstroms resolution.
Identifiers
Symbol Bse634I
Pfam PF07832
InterPro IPR012415

In molecular biology, the Cfr10I/Bse634I family of restriction endonucleases includes the type II restriction endonucleases Cfr10I and Bse634I. They exhibit a conserved tetrameric architecture that is of functional importance, wherein two dimers are arranged, back-to-back, with their putative DNA-binding clefts facing opposite directions. These clefts are formed between two monomers that interact, mainly via hydrophobic interactions supported by a few hydrogen bonds, to form a U-shaped dimer. Each monomer is folded to form a compact alpha-beta structure, whose core is made up of a five-stranded mixed beta-sheet. The monomer may be split into separate N-terminal and C-terminal subdomains at a hinge located in helix alpha3.[1] Both Cfr10I and Bse634I recognise the double-stranded sequence RCCGGY and cleave after the purine R.[2]

Recognition sequence     Cut
5' RCCGGY                5' ---R   CCGGY--- 3'
3' YGGCCR                3' ---YGGCC   R--- 5'

References[edit]

  1. ^ Grazulis S, Deibert M, Rimseliene R, Skirgaila R, Sasnauskas G, Lagunavicius A, Repin V, Urbanke C, Huber R, Siksnys V (February 2002). "Crystal structure of the Bse634I restriction endonuclease: comparison of two enzymes recognizing the same DNA sequence". Nucleic Acids Res. 30 (4): 876–85. doi:10.1093/nar/30.4.876. PMC 100338. PMID 11842098. 
  2. ^ Bozic D, Grazulis S, Siksnys V, Huber R (January 1996). "Crystal structure of Citrobacter freundii restriction endonuclease Cfr10I at 2.15 A resolution". J. Mol. Biol. 255 (1): 176–86. doi:10.1006/jmbi.1996.0015. PMID 8568865. 

This article incorporates text from the public domain Pfam and InterPro IPR012415

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Cfr10I/Bse634I restriction endonuclease Provide feedback

Cfr10I (P56200) and Bse634I (Q8RT53) are two Type II restriction endonucleases. They exhibit a conserved tetrameric architecture that is of functional importance, wherein two dimers are arranged 'back-to-back' with their putative DNA-binding clefts facing opposite directions. These clefts are formed between two monomers that interact, mainly via hydrophobic interactions supported by a few hydrogen bonds, to form a U-shaped dimer. Each monomer is folded to form a compact alpha-beta structure, whose core is made up of a five-stranded mixed beta-sheet.The monomer may be split into separate N-terminal and C-terminal subdomains at a hinge located in helix alpha3 [1].

Literature references

  1. Grazulis S, Deibert M, Rimseliene R, Skirgaila R, Sasnauskas G, Lagunavicius A, Repin V, Urbanke C, Huber R, Siksnys V; , Nucleic Acids Res 2002;30:876-885.: Crystal structure of the Bse634I restriction endonuclease: comparison of two enzymes recognizing the same DNA sequence. PUBMED:11842098 EPMC:11842098

  2. Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K;, Nucleic Acids Res. 2012;40:7016-7045.: Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. PUBMED:22638584 EPMC:22638584


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR012415

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 II restriction endonucleases (EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin [PUBMED:15770420]. However, there is still considerable diversity amongst restriction endonucleases [PUBMED:14576294, PUBMED:11827971]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone [PUBMED:11557805].

This entry represents Cfr10I and Bse634I restriction endonucleases. They exhibit a conserved tetrameric architecture that is of functional importance, wherein two dimers are arranged, back-to-back, with their putative DNA-binding clefts facing opposite directions. These clefts are formed between two monomers that interact, mainly via hydrophobic interactions supported by a few hydrogen bonds, to form a U-shaped dimer. Each monomer is folded to form a compact alpha-beta structure, whose core is made up of a five-stranded mixed beta-sheet. The monomer may be split into separate N-terminal and C-terminal subdomains at a hinge located in helix alpha3 [PUBMED:11842098]. Both Cfr10I and Bse634I recognise the double-stranded sequence RCCGGY and cleave after the purine R [PUBMED:8568865].

Domain organisation

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Seed source: Pfam-B_46671 (release 14.0)
Previous IDs: none
Type: Domain
Author: Fenech M
Number in seed: 4
Number in full: 13
Average length of the domain: 267.20 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 86.22 %

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Model details:
Parameter Sequence Domain
Gathering cut-off 20.7 20.7
Trusted cut-off 22.8 21.6
Noise cut-off 20.4 20.2
Model length: 280
Family (HMM) version: 6
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Interactions

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Bse634I

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 Bse634I domain has been found. There are 37 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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