User:Dima Golovenko/R.EcoRII

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{{STRUCTURE_1na6| PDB=1na6 | SCENE= }}
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===Crystal structure of restriction endonuclease EcoRII mutant R88A===
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{{STRUCTURE_1na6 | PDB=1na6 | SCENE= }}
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{{ABSTRACT_PUBMED_14659759}}
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==About this Structure==
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1NA6 is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NA6 OCA].
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[[Restriction endonuclease]] (REase) '''EcoRII''' (pronounced "eco R two") is an [[enzyme]] of [[restriction modification system]] (RM) naturally found in ''[[Escherichia coli]]'', a [[Gram-negative bacteria]]. Its [[molecular mass]] is 45.2 [[Atomic mass unit|kDa]], being composed of 402 [[amino acids]].<ref name="title">{{cite web | url = http://rebase.neb.com/rebase/enz/EcoRII.html | title = EcoRII | accessdate = 2008-03-23 | author = Richard J. Roberts | authorlink = | coauthors = | date = | format = | work = REBASE - The Restriction Enzyme Database | publisher = | pages = | language = | archiveurl = | archivedate = | quote = }}</ref>
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==Mode of action==
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EcoRII is a [[bacterial]] Type IIE<ref name="pmid12654995">{{cite journal | author = Roberts RJ, Belfort M, Bestor T, ''et al.'' | title = A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes | journal = Nucleic Acids Res. | volume = 31 | issue = 7 | pages = 1805–12 | year = 2003 | pmid = 12654995 | doi = 10.1093/nar/gkg274 | pmc = 152790 }} [http://nar.oxfordjournals.org/cgi/reprint/31/7/1805.pdf PDF] </ref> [[restriction endonuclease|REase]] that interacts with two<ref name="pmid10903314">{{cite journal | author = Mücke M, Lurz R, Mackeldanz P, Behlke J, Krüger DH, Reuter M | title = Imaging DNA loops induced by restriction endonuclease EcoRII. A single amino acid substitution uncouples target recognition from cooperative DNA interaction and cleavage | journal = J. Biol. Chem. | volume = 275 | issue = 39 | pages = 30631–7 | year = 2000 | pmid = 10903314 | doi = 10.1074/jbc.M003904200 }}[http://www.jbc.org/cgi/reprint/275/39/30631.pdf PDF]</ref> or [http://pubs.acs.org/isubscribe/journals/bichaw/46/i39/figures/bi701123un00001.gif three]<ref name="pmid17845057">{{cite journal | author = Shlyakhtenko LS, Gilmore J, Portillo A, Tamulaitis G, Siksnys V, Lyubchenko YL | title = Direct visualization of the EcoRII-DNA triple synaptic complex by atomic force microscopy | journal = Biochemistry | volume = 46 | issue = 39 | pages = 11128–36 | year = 2007 | pmid = 17845057 | doi = 10.1021/bi701123u }}</ref> copies of the pseudopalindromic [[dsDNA|DNA]] [[Restriction_enzyme#Recognition_site|recognition sequence]] [[5' end|5']]-[[Cytosine|CC]]W[[Guanine|GG]]-[[3' end|3']] ([[W]] = [[Adenine|A]] or [[Thymine|T]]), one being the actual target of cleavage, the other(s) serving as the [[Allosteric regulation#Allosteric activation and inhibition|allosteric activator]](s). EcoRII cut target [[dsDNA|DNA]] sequence CCWGG generating [[sticky ends]].<ref name="isbn0-7167-3520-2">{{cite book | author = Griffiths, Anthony J. F. | title = An Introduction to genetic analysis | publisher = W.H. Freeman | location = San Francisco | year = 1999 | pages = | isbn = 0-7167-3520-2 | oclc = | doi = }}</ref>
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==Cut diagram==
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{| class="wikitable"
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| Recognition site
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| Cut results
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|-
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|
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5' NN'''CCWGG'''NN
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3' NN'''GGWCC'''NN
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|
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5' NN '''CCWGG'''NN
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3' NN'''GGWCC''' NN
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|}
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==Structure==
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The [[apo]] [[X-ray crystallography|crystal]] [[protein structure|structure]] of EcoRII [[Point mutation|mutant]] R88A ({{PDB|1NA6}})<ref name="Zhou_2004">{{cite journal | author = Zhou XE, Wang Y, Reuter M, Mücke M, Krüger DH, Meehan EJ, Chen L | title = Crystal structure of type IIE restriction endonuclease EcoRII reveals an autoinhibition mechanism by a novel effector-binding fold | journal = J. Mol. Biol. | volume = 335 | issue = 1 | pages = 307–19 | year = 2004 | pmid = 14659759 | doi = 10.1016/j.jmb.2003.10.030 }}</ref> has been solved at 2.1 [[Å]] [[Resolution (electron density)|resolution]]. The EcoRII [[Primary structure|monomer]] has two [[Protein domains|domains]], [[N-terminus|N-terminal]] and [[C-terminus|C-terminal]], linked through a [[hinge]] [[turn (biochemistry)|loop]].
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===Effector-binding domain===
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The N-terminal [[Effector (biology)|effector]]-[[DNA-binding domain|binding domain]] has a archetypal DNA-binding pseudobarrel fold ({{SCOP|101936}}) with a prominent [[structural motif|cleft]]. [[Structural alignment#DALI|Structural superposition]] showed it is evolutionarily related to:
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*[[B3 DNA binding domain]] ({{SCOP|117343}}) from the [[transcription factors]] in [[higher plants]] ({{PDB|1WID}})<ref name="pmid15548737">{{cite journal | author = Yamasaki K, Kigawa T, Inoue M, Tateno M, Yamasaki T, Yabuki T, Aoki M, Seki E, Matsuda T, Tomo Y, Hayami N, Terada T, Shirouzu M, Osanai T, Tanaka A, Seki M, Shinozaki K, Yokoyama S | title = Solution structure of the B3 DNA binding domain of the Arabidopsis cold-responsive transcription factor RAV1 | journal = Plant Cell | volume = 16 | issue = 12 | pages = 3448–59 | year = 2004 | pmid = 15548737 | doi = 10.1105/tpc.104.026112 | pmc = 535885 }}[http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=535885&blobtype=pdf PDF]</ref>
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*C-terminal domain of [[restriction endonuclease]] BfiI<ref name="BfiI">{{cite web | url = http://rebase.neb.com/rebase/enz/BfiI.html | title = BfiI | accessdate = 2008-03-23 | author = Richard J. Roberts | authorlink = | coauthors = | date = | format = | work = REBASE - The Restriction Enzyme Database | publisher = | pages = | language = | archiveurl = | archivedate = | quote = }}</ref> ({{PDB|2C1L}})<ref name="pmid16247004">{{cite journal | author = Grazulis S, Manakova E, Roessle M, Bochtler M, Tamulaitiene G, Huber R, Siksnys V | title = Structure of the metal-independent restriction enzyme BfiI reveals fusion of a specific DNA-binding domain with a nonspecific nuclease | journal = Proc. Natl. Acad. Sci. U.S.A. | volume = 102 | issue = 44 | pages = 15797–802 | year = 2005 | pmid = 16247004 | doi = 10.1073/pnas.0507949102 | pmc = 1266039 }} [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1266039&blobtype=pdf PDF]</ref>
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===Catalytic domain===
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<scene name='1na6/C-term/1'>The C-terminal domain</scene> has a typical<ref name="pmid17369272">{{cite journal | author = Niv MY, Ripoll DR, Vila JA, Liwo A, Vanamee ES, Aggarwal AK, Weinstein H, Scheraga HA | title = Topology of Type II REases revisited; structural classes and the common conserved core | journal = NAR | volume = 35 | issue = 7 | pages = 2227–37 | year = 2007 | pmid = 17369272 | doi = 10.1093/nar/gkm045 | pmc = 1874628}} [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1874628&blobtype=pdf PDF]</ref> restriction endonuclease-like fold ({{SCOP|52979}}) and belongs to the large (more than 30 members) [[restriction endonuclease]] superfamily ({{SCOP|52980}}).
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==Autoinhibition/activation mechanism==
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[[Structural alignment#Structural_superposition|Structure-based sequence]] alignment and [[site-directed mutagenesis]] identified the putative PD..D/EXK [[active site]]s of the EcoRII catalytic domain dimer that in apo structure are spatially blocked by the N-terminal domains.<ref name="Zhou_2004"/>
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==See also==
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*[[EcoRI]], another nuclease enzyme from ''[[Escherichia coli]]''.
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*[[EcoRV]], another nuclease enzyme from ''[[Escherichia coli]]''.
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*[[B3 DNA binding domain]] from [[higher plants]] is evolutionary related to EcoRII
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<!-- *[[BamHI]], another nuclease enzyme from ''[[Bacillus amyloliquefaciens]]''.
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*[[HindIII]], another nuclease enzyme from ''[[Haemophilus influenzae]]''.
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*[[HaeIII]], another nuclease enzyme from ''[[Haemophilus aegyptius]]''.
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*[[TaqI]], another nuclease enzyme from ''[[Thermus aquaticus]]''. -->
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*[[FokI]], another nuclease enzyme from ''[[Flavobacterium okeanokoites]]''
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==External links==
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*EcoRII in Restriction Enzyme Database [http://rebase.neb.com/rebase/enz/EcoRII.html REBASE]
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<!-- *EcoRII from [http://www.fermentas.com/catalog/re/ecorii.htm Fermentas] -->
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==References==
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{{Reflist|2}}
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<references/>
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==Reference==
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<ref group="xtra">PMID:14659759</ref><references group="xtra"/>
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[[Category: Escherichia coli]]
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[[Category: Type II site-specific deoxyribonuclease]]
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[[Category: Chen, L.]]announced
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[[Category: Kruger, D H.]]
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[[Category: Meehan, E J.]]
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[[Category: Mucke, M.]]
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[[Category: Reuter, M.]]
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[[Category: Wang, Y.]]
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[[Category: Zhou, X E.]]
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[[Category: Mutation]]
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[[Category: Replication]]
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[[Category: Site-specific restriction]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 03:36:10 2009''

Revision as of 15:28, 11 June 2010


PDB ID 1na6

Drag the structure with the mouse to rotate
1na6, resolution 2.10Å ()
Gene: EcoRII (Escherichia coli)
Activity: Type II site-specific deoxyribonuclease, with EC number 3.1.21.4
Resources: FirstGlance, OCA, PDBsum, RCSB
Coordinates: save as pdb, mmCIF, xml



Contents

Crystal structure of restriction endonuclease EcoRII mutant R88A

Publication Abstract from PubMed

EcoRII is a type IIE restriction endonuclease that interacts with two copies of the DNA recognition sequence 5'CCWGG, one being the actual target of cleavage, the other serving as the allosteric effector. The mode of enzyme activation by effector binding is unknown. To investigate the molecular basis of activation and cleavage mechanisms by EcoRII, the crystal structure of EcoRII mutant R88A has been solved at 2.1A resolution. The EcoRII monomer has two domains linked through a hinge loop. The N-terminal effector-binding domain has a novel DNA recognition fold with a prominent cleft. The C-terminal catalytic domain has a restriction endonuclease-like fold. Structure-based sequence alignment identified the putative catalytic site of EcoRII that is spatially blocked by the N-terminal domain. The structure together with the earlier characterized EcoRII enzyme activity enhancement in the absence of its N-terminal domain reveal an autoinhibition/activation mechanism of enzyme activity mediated by a novel effector-binding fold. This is the first case of autoinhibition, a mechanism described for many transcription factors and signal transducing proteins, of a restriction endonuclease.

Crystal structure of type IIE restriction endonuclease EcoRII reveals an autoinhibition mechanism by a novel effector-binding fold., Zhou XE, Wang Y, Reuter M, Mucke M, Kruger DH, Meehan EJ, Chen L, J Mol Biol. 2004 Jan 2;335(1):307-19. PMID:14659759

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

About this Structure

1NA6 is a 2 chains structure of sequences from Escherichia coli. Full crystallographic information is available from OCA.

Restriction endonuclease (REase) EcoRII (pronounced "eco R two") is an enzyme of restriction modification system (RM) naturally found in Escherichia coli, a Gram-negative bacteria. Its molecular mass is 45.2 kDa, being composed of 402 amino acids.[1]

Mode of action

EcoRII is a bacterial Type IIE[2] REase that interacts with two[3] or three[4] copies of the pseudopalindromic DNA recognition sequence 5'-CCWGG-3' (W = A or T), one being the actual target of cleavage, the other(s) serving as the allosteric activator(s). EcoRII cut target DNA sequence CCWGG generating sticky ends.[5]

Cut diagram

Recognition site Cut results 
5' NNCCWGGNN
3' NNGGWCCNN 

5' NN  CCWGGNN
3' NNGGWCC  NN

Structure

The apo crystal structure of EcoRII mutant R88A (Template:PDB)[6] has been solved at 2.1 Å resolution. The EcoRII monomer has two domains, N-terminal and C-terminal, linked through a hinge loop.

Effector-binding domain

The N-terminal effector-binding domain has a archetypal DNA-binding pseudobarrel fold (Template:SCOP) with a prominent cleft. Structural superposition showed it is evolutionarily related to:

Catalytic domain

has a typical[10] restriction endonuclease-like fold (Template:SCOP) and belongs to the large (more than 30 members) restriction endonuclease superfamily (Template:SCOP).

Autoinhibition/activation mechanism

Structure-based sequence alignment and site-directed mutagenesis identified the putative PD..D/EXK active sites of the EcoRII catalytic domain dimer that in apo structure are spatially blocked by the N-terminal domains.[6]

See also

External links

  • EcoRII in Restriction Enzyme Database REBASE

References

  1. ↑ Template:Cite web
  2. ↑ <ref>PMID:9556453</ref> PDF
  3. ↑ <ref>PMID:9556453</ref>PDF
  4. ↑ <ref>PMID:9556453</ref>
  5. ↑ Template:Cite book
  6. ↑ 6.0 6.1 <ref>PMID:9556453</ref>
  7. ↑ <ref>PMID:9556453</ref>PDF
  8. ↑ Template:Cite web
  9. ↑ <ref>PMID:9556453</ref> PDF
  10. ↑ <ref>PMID:9556453</ref> PDF

Reference

  • Zhou XE, Wang Y, Reuter M, Mucke M, Kruger DH, Meehan EJ, Chen L. Crystal structure of type IIE restriction endonuclease EcoRII reveals an autoinhibition mechanism by a novel effector-binding fold. J Mol Biol. 2004 Jan 2;335(1):307-19. PMID:14659759
announced

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