PDBsum entry: 1na6

Hydrolase

PDB id: 1na6

Contents

Protein chains

365 a.a. *

395 a.a. *

Waters ×252

* Residue conservation analysis

PDB id:

1na6

Name:

Hydrolase

Title:

Crystal structure of restriction endonuclease ecorii mutant r88a

Structure:

Restriction endonuclease ecorii. Chain: a, b. Synonym: ecorii. Type ii restriction enzyme ecorii. Endonuclease ecorii. R.Ecorii. Engineered: yes. Mutation: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: ecorii. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.10Å R-factor: 0.230 R-free: 0.284

Authors:

X.E.Zhou,Y.Wang,M.Reuter,M.Mucke,D.H.Kruger,E.J.Meehan, L.Chen

Key ref:

X.E.Zhou et al. (2004). Crystal structure of type IIE restriction endonuclease EcoRII reveals an autoinhibition mechanism by a novel effector-binding fold. J Mol Biol, 335, 307-319. PubMed id: 14659759 DOI: 10.1016/j.jmb.2003.10.030

Date:

26-Nov-02 Release date: 16-Dec-03

Protein chain

P14633  (T2E2_ECOLX) -  Type-2 restriction enzyme EcoRII

Seq: 404 a.a.

Struc: 365 a.a.*

Protein chain

P14633  (T2E2_ECOLX) -  Type-2 restriction enzyme EcoRII

Seq: 404 a.a.

Struc: 395 a.a.*

* PDB and UniProt seqs differ at 24 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B: E.C.3.1.21.4 - Type Ii site-specific deoxyribonuclease.
• Reaction: Endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates.
• Cofactor: Magnesium

 Gene Ontology (GO) functional annotation 

• Biological process: DNA restriction-modification system (1 term)
• Biochemical function: hydrolase activity (5 terms)

DOI no: 10.1016/j.jmb.2003.10.030

J Mol Biol 335:307-319 (2004)

PubMed id: 14659759

Crystal structure of type IIE restriction endonuclease EcoRII reveals an autoinhibition mechanism by a novel effector-binding fold.

X.E.Zhou, Y.Wang, M.Reuter, M.Mücke, D.H.Krüger, E.J.Meehan, L.Chen.

ABSTRACT

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.

Selected figure(s)

Figure 6.
Figure 6. The N-domain structure and the effector-binding cleft. The secondary structural elements are labeled and so are some of the key amino acid residues in the proposed effector-binding cleft. Putative DNA-binding residues H36, Y41, K92, R94, E96, K97 and R98 are shown in ball-and-stick.

Figure 9.
Figure 9. The inactive dimer structure of EcoRII and a model of autoinhibition. The ribbon diagram is a back view of Figure 5 and related to Figure 5 by a 180° rotation about the vertical axis. The locations of the two effector clefts and the two catalytic half-sites are indicated. The catalytic half-sites are blocked by the N-domains and inaccessible by a substrate DNA. The two key residues Y41 and E96 in the effector clefts are shown in ball-and-stick and labeled. The a-helix H6 is also labeled.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 335, 307-319) copyright 2004.

Figures were selected by the author.