Restriction endonuclease A restriction enzyme, restriction endonuclease, REase, ENase or'' restrictase '' is an enzyme that cleaves DNA into fragments at or near specific recognition sites within molecules known as restriction sites. Restriction enzymes are one class o ...

(REase) EcoRII (pronounced "eco R two") is an

enzyme Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as products ...

restriction modification system The restriction modification system (RM system) is found in bacteria and other prokaryotic organisms, and provides a defense against foreign DNA, such as that borne by bacteriophages. Bacteria have restriction enzymes, also called restriction end ...

(RM) naturally found in ''

Escherichia coli ''Escherichia coli'' (),Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. also known as ''E. coli'' (), is a Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus '' Esc ...

'', a

Gram-negative bacteria Gram-negative bacteria are bacteria that do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation. They are characterized by their cell envelopes, which are composed of a thin peptidoglycan cell wall ...

. Its

molecular mass The molecular mass (''m'') is the mass of a given molecule: it is measured in daltons (Da or u). Different molecules of the same compound may have different molecular masses because they contain different isotopes of an element. The related quanti ...

is 45.2

kDa The dalton or unified atomic mass unit (symbols: Da or u) is a non-SI unit of mass widely used in physics and chemistry. It is defined as of the mass of an unbound neutral atom of carbon-12 in its nuclear and electronic ground state and at re ...

, being composed of 402 amino acids.

Mode of action

EcoRII is a

bacterial Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were amon ...

Type IIEPDF
/ref> REase that interacts with twoPDF
/ref> o
three
ref name="pmid17845057"> copies of the pseudopalindromic DNA

recognition sequence A recognition sequence is a DNA sequence to which a structural motif of a DNA-binding domain exhibits binding specificity. Recognition sequences are palindromes. The transcription factor Sp1 for example, binds the sequences 5'-(G/T)GGGCGG(G/A)(G/ ...

5'- CCW GG- 3' (W = A or T), one being the actual target of cleavage, the other(s) serving as the allosteric activator(s). EcoRII cuts the target DNA sequence CCWGG, generating

sticky ends DNA ends refer to the properties of the ends of linear DNA molecules, which in molecular biology are described as "sticky" or "blunt" based on the shape of the complementary strands at the terminus. In sticky ends, one strand is longer than the ...

Cut diagram

Structure

The apo

crystal A crystal or crystalline solid is a solid material whose constituents (such as atoms, molecules, or ions) are arranged in a highly ordered microscopic structure, forming a crystal lattice that extends in all directions. In addition, macro ...

structure of EcoRII

mutant In biology, and especially in genetics, a mutant is an organism or a new genetic character arising or resulting from an instance of mutation, which is generally an alteration of the DNA sequence of the genome or chromosome of an organism. It ...

R88A () has been solved at 2.1 Å

resolution Resolution(s) may refer to: Common meanings * Resolution (debate), the statement which is debated in policy debate * Resolution (law), a written motion adopted by a deliberative body * New Year's resolution, a commitment that an individual mak ...

. The EcoRII

monomer In chemistry, a monomer ( ; '' mono-'', "one" + ''-mer'', "part") is a molecule that can react together with other monomer molecules to form a larger polymer chain or three-dimensional network in a process called polymerization. Classification ...

has two domains, N-terminal and

C-terminal The C-terminus (also known as the carboxyl-terminus, carboxy-terminus, C-terminal tail, C-terminal end, or COOH-terminus) is the end of an amino acid chain (protein or polypeptide), terminated by a free carboxyl group (-COOH). When the protein is ...

, linked through a hinge

loop Loop or LOOP may refer to: Brands and enterprises * Loop (mobile), a Bulgarian virtual network operator and co-founder of Loop Live * Loop, clothing, a company founded by Carlos Vasquez in the 1990s and worn by Digable Planets * Loop Mobile, an ...

Effector-binding domain

The N-terminal

effector Effector may refer to: *Effector (biology), a molecule that binds to a protein and thereby alters the activity of that protein * ''Effector'' (album), a music album by the Experimental Techno group Download * ''EFFector'', a publication of the El ...

binding domain In molecular biology, binding domain is a protein domain which binds to a specific atom or molecule, such as calcium or DNA. A protein domain is a part of a protein sequence and a tertiary structure that can change or evolve, function, and liv ...

has an archetypal DNA-binding pseudobarrel fold () with a prominent

cleft A cleft is an opening, fissure, or V-shaped indentation. Cleft may refer to: Linguistics * A cleft sentence, a type of grammatical construction Anatomy * Cleft lip and palate, a congenital deformity * A cleft chin, a dimple on the chin * The ...

. Structural superposition showed it is evolutionarily related to: * B3 DNA binding domain () from the

transcription factors In molecular biology, a transcription factor (TF) (or sequence-specific DNA-binding factor) is a protein that controls the rate of transcription of genetic information from DNA to messenger RNA, by binding to a specific DNA sequence. The fun ...

higher plants Vascular plants (), also called tracheophytes () or collectively Tracheophyta (), form a large group of land plants ( accepted known species) that have lignified tissues (the xylem) for conducting water and minerals throughout the plant. They ...

()PDF
/ref> *C-terminal domain of

restriction endonuclease A restriction enzyme, restriction endonuclease, REase, ENase or'' restrictase '' is an enzyme that cleaves DNA into fragments at or near specific recognition sites within molecules known as restriction sites. Restriction enzymes are one class o ...

BfiI ()PDF
/ref>

Catalytic domain

The C-terminal

catalytic domain In biology and biochemistry, the active site is the region of an enzyme where substrate molecules bind and undergo a chemical reaction. The active site consists of amino acid residues that form temporary bonds with the substrate (binding site) a ...

has a typical restriction endonuclease-like fold () and belongs to the large (more than 30 members)

superfamily ().

Autoinhibition/activation mechanism

Structure-based sequence alignment and

site-directed mutagenesis Site-directed mutagenesis is a molecular biology method that is used to make specific and intentional mutating changes to the DNA sequence of a gene and any gene products. Also called site-specific mutagenesis or oligonucleotide-directed mutagenesi ...

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.

External links

*EcoRII in Restriction Enzyme Databas
REBASE

References

{{DEFAULTSORT:R.Ecorii EC 3.1.21 Molecular biology Bacterial enzymes Restriction enzymes EC 3.1 Nucleases