User:Dima Golovenko/R.EcoRII
From Proteopedia
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===Effector-binding domain=== | ===Effector-binding domain=== | ||
| - | <scene name='User:Dima_Golovenko/R.EcoRII/Effector_domain/1'>The N-terminal</scene>[[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: | + | <scene name='User:Dima_Golovenko/R.EcoRII/Effector_domain/1'>The N-terminal</scene> [[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: |
*[[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> | *[[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> | ||
*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> | *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> | ||
Revision as of 15:43, 11 June 2010
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| 1na6, resolution 2.10Å () | |||||||||
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| Gene: | EcoRII (Escherichia coli) | ||||||||
| Activity: | Type II site-specific deoxyribonuclease, with EC number 3.1.21.4 | ||||||||
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||
Contents |
Crystal structure of restriction endonuclease EcoRII mutant R88A
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
effector-binding domain has a archetypal DNA-binding pseudobarrel fold (Template:SCOP) with a prominent cleft. Structural superposition showed it is evolutionarily related to:
- B3 DNA binding domain (Template:SCOP) from the transcription factors in higher plants (Template:PDB)[7]
- C-terminal domain of restriction endonuclease BfiI[8] (Template:PDB)[9]
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
- EcoRI, another nuclease enzyme from Escherichia coli.
- EcoRV, another nuclease enzyme from Escherichia coli.
- B3 DNA binding domain from higher plants is evolutionary related to EcoRII
- FokI, another nuclease enzyme from Flavobacterium okeanokoites
External links
- EcoRII in Restriction Enzyme Database REBASE
References
- ↑ Template:Cite web
- ↑ <ref>PMID:9556453</ref> PDF
- ↑ <ref>PMID:9556453</ref>PDF
- ↑ <ref>PMID:9556453</ref>
- ↑ Template:Cite book
- ↑ 6.0 6.1 <ref>PMID:9556453</ref>
- ↑ <ref>PMID:9556453</ref>PDF
- ↑ Template:Cite web
- ↑ <ref>PMID:9556453</ref> PDF
- ↑ <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
Page seeded by OCA on Wed Feb 18 03:36:10 2009
