Summary: Cfr10I/Bse634I restriction endonuclease

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Cfr10I/Bse634I Edit Wikipedia article

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Bse634I

crystal structure of citrobacter freundii restriction endonuclease cfr10i at 2.15 angstroms resolution.

Identifiers

Symbol

Bse634I

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

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'

[edit] References

^ 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): 876Ã¢ÂÂ85. doi:10.1093/nar/30.4.876. PMC 100338. PMID 11842098. //www.ncbi.nlm.nih.gov/pmc/articles/PMC100338/.
^ 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): 176Ã¢ÂÂ86. 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

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

PANDIT:	PF07832
Pseudofam:	PF07832
SYSTERS:	Bse634I

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

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

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Pfam Clan

This family is a member of clan PDDEXK (CL0236), which contains the following 123 members:

BamHI BpuSI_N Bse634I BsuBI_PstI_RE Cas_APE2256 Cas_Cas02710 Cas_Cas4 Cas_Csm6 Cas_NE0113 CoiA Dna2 DpnII DRP DUF1016 DUF1052 DUF1064 DUF1626 DUF1703 DUF1780 DUF1853 DUF1887 DUF2034 DUF2130 DUF234 DUF2726 DUF2800 DUF2887 DUF3799 DUF3883 DUF4143 DUF4263 DUF4420 DUF506 DUF524 DUF559 DUF790 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 Herpes_alk_exo Herpes_UL24 Hjc HSDR_N HSDR_N_2 L_protein_N McrBC Mrr_cat Mrr_cat_2 MutH MvaI_BcnI NaeI NARG2_C NERD NgoMIV_restric NotI PDDEXK_1 PDDEXK_2 PDDEXK_3 PDDEXK_4 PDDEXK_5 Pet127 Phage_endo_I R-HINP1I 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 TBPIP_N ThaI Tn7_Tnp_TnsA_N Transposase_31 tRNA_int_endo Tsp45I Uma2 UPF0102 VirArc_Nuclease VRR_NUC Vsr XhoI XisH YaeQ YqaJ

Alignments

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There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.

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We make a range of alignments for each Pfam-A family:

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full: the alignment generated by searching the sequence database using the HMM
RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
NCBI: alignment generated by searching the NCBI sequence database using the family HMM
meta: alignment generated by searching the metagenomics sequence database using the family HMM

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	Seed (4)	Full (13)	Representative proteomes				NCBI (16)	Meta (0)
	Seed (4)	Full (13)	RP15 (1)	RP35 (1)	RP55 (1)	RP75 (2)	NCBI (16)	Meta (0)
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¹Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: available, not generated, — not available.

Format an alignment

	Seed (4)	Full (13)	Representative proteomes				NCBI (16)	Meta (0)
	Seed (4)	Full (13)	RP15 (1)	RP35 (1)	RP55 (1)	RP75 (2)	NCBI (16)	Meta (0)
Alignment:
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Sequence:	Inserts lower case All upper case
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

	Seed (4)	Full (13)	Representative proteomes				NCBI (16)	Meta (0)
	Seed (4)	Full (13)	RP15 (1)	RP35 (1)	RP55 (1)	RP75 (2)	NCBI (16)	Meta (0)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download
Gzipped	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.

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

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

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 %

HMM information

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	20.7	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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Species distribution

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Unmapped species names

The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.

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Interactive tree

For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.

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We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.

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Interactions

There is 1 interaction for this family. More...

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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Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: Bse634I (PF07832)

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Summary: Cfr10I/Bse634I restriction endonuclease

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Cfr10I/Bse634I Edit Wikipedia article

[edit] References

Cfr10I/Bse634I restriction endonuclease Provide feedback

Literature references

External database links

InterPro entry IPR012415

Domain organisation

Pfam Clan

Alignments

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Structures