Summary: Cfr10I/Bse634I restriction endonuclease
This is the Wikipedia entry entitled "Cfr10I/Bse634I". More...
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Cfr10I/Bse634I Edit Wikipedia article
crystal structure of citrobacter freundii restriction endonuclease cfr10i at 2.15 angstroms resolution.
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. Both Cfr10I and Bse634I recognise the double-stranded sequence RCCGGY and cleave after the purine R.
Recognition sequence Cut 5' RCCGGY 5' ---R CCGGY--- 3' 3' YGGCCR 3' ---YGGCC R--- 5'
- 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): 876â85. doi:10.1093/nar/30.4.876. PMC 100338. PMID 11842098.
- 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): 176â86. doi:10.1006/jmbi.1996.0015. PMID 8568865.
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 .
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
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].
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This clan includes a large number of nuclease families related to holliday junction resolvases [1,2].
The clan contains the following 123 members:BamHI BpuJI_N BpuSI_N Bse634I BsuBI_PstI_RE Cas_APE2256 Cas_Cas02710 Cas_Cas4 Cas_Csm6 Cas_NE0113 CoiA Dna2 DpnI DpnII DUF1016 DUF1052 DUF1780 DUF1887 DUF2034 DUF2161 DUF234 DUF2357 DUF2726 DUF2800 DUF2887 DUF3799 DUF3883 DUF4143 DUF4263 DUF4420 DUF559 DUF91 DUF911 EcoRI EcoRII-C eIF-3_zeta Endonuc-BglII Endonuc-BsobI Endonuc-EcoRV Endonuc-FokI_C Endonuc-HincII Endonuc-MspI Endonuc-PvuII Endonuc_BglI Endonuc_Holl ERCC4 Exo5 Flu_PA Herpes_alk_exo Herpes_UL24 Hjc HSDR_N HSDR_N_2 L_protein_N McrBC Mrr_cat Mrr_cat_2 MutH MvaI_BcnI NaeI NERD NgoMIV_restric NotI PDDEXK_1 PDDEXK_10 PDDEXK_2 PDDEXK_3 PDDEXK_4 PDDEXK_5 PDDEXK_7 PDDEXK_9 Pet127 Phage_endo_I R-HINP1I Rad10 RAI1 RAP RE_AlwI RE_ApaLI RE_Bpu10I RE_Bsp6I RE_CfrBI RE_Eco47II RE_EcoO109I RE_HaeII RE_HindIII RE_HindVP RE_HpaII RE_LlaJI RE_LlaMI RE_MjaI RE_NgoBV RE_NgoPII RE_SacI RE_ScaI RE_SinI RE_TaqI RE_TdeIII RE_XamI RE_XcyI RecU RestrictionMunI RestrictionSfiI RmuC RNA_pol_Rpb5_N Sen15 SfsA Spo0A_C TBPIP_N ThaI Tn7_Tnp_TnsA_N Transposase_31 tRNA_int_endo Tsp45I Uma2 UPF0102 VirArc_Nuclease VRR_NUC Vsr XhoI XisH YaeQ YqaJ
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Curation and family details
|Seed source:||Pfam-B_46671 (release 14.0)|
|Number in seed:||4|
|Number in full:||23|
|Average length of the domain:||271.60 aa|
|Average identity of full alignment:||26 %|
|Average coverage of the sequence by the domain:||88.72 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||7|
|Download:||download the raw HMM for this family|
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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 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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