Name = "Hin"dIII
caption = Proposed crystal structure of "Hin"dIII dimer with substrate DNA
PDB = 2e52
ECnumber = 18.104.22.168
Synonyms = d
"Hin"dIII " is a type II site-specific deoxyribonuclease
restriction enzymeisolated from "Haemophilus influenzae" that cleaves the palindromic DNA sequence AAGCTT in the presence of the cofactor Mg+2 via hydrolysis.cite journal |author=Tang, D et al. |title=Mutational analyses of restriction endonuclease-HindIII mutant E86K with higher activity and altered specificity |journal=Protein Engineering |volume=13 |issue=4 |pages=283-289 |year=2000 |pmid=10810160 |doi= |url=http://peds.oxfordjournals.org/cgi/content/full/13/4/283]
The cleavage of this sequence results in
sticky endsof DNA, resulting in 5' overhangs:
Restriction endonucleases are used as defense mechanisms in
prokaryoticorganisms in the restriction modification system. Their primary function is to protect the host genome against invasion by foreign DNA, primarily bacteriophageDNA. There is also evidence that suggests the restriction enzymes may act alongside modification enzymes as selfish elements, or may be involved in genetic recombinationand transposition.cite journal |author=Pingoud, Alfred and Jeltsch, Albert. |title=Structure and function of type II restriction endonucleases |journal=Nucleic Acids Research |volume=29 |issue=18 |pages=3705-3727 |year=2001 |pmid=11557805 |doi= |url=http://nar.oxfordjournals.org/cgi/content/full/29/18/3705]
The structure of "Hin"dIII is quite complex, and is comprised of a homodimer. Like other type II restriction endonucleases, it is believed to contain a common structural core comprising four
β-sheetsand a single α-helix. Each subunit contains 300 amino acidsand the predicted molecular mass is 34,950 Da. Despite the importance of this enzyme in molecular biologyand DNA technology, little information is available concerning the mechanism of DNA recognition and phosphodiester bondcleavage. However, it is believed that "Hin"dIII utilizes a common mechanism of recognition and catalysisof DNA found in other type II enzymes such as EcoRI, BamHI, and BglII. These enzymes contain the amino acidsequence motif PD-(D/E)XK to coordinate Mg2+, a cation required to cleave DNA in most type II restriction endonucleases.cite journal |author=Tang, D et al. |title=Site-directed mutagenesis of restriction endonuclease HindIII |journal=Biosci Biotechnol Biochem. |volume=63 |issue=10 |pages=1703-1707 |year=1999 |pmid=10586498 |doi= |url=http://www.jstage.jst.go.jp/article/bbb/63/10/63_1703/_article] The cofactor Mg2+ is believed to bind water molecules and carry them to the catalytic sites of the enzymes, among other cations. Unlike most documented type II restriction endonucleases, "Hin"dIII is unique in that it has little to no catalytic activity when Mg2+ is substituted for other cofactors, such as Mn2+.
Despite the uncertainty concerning the structure-catalysis relationship of type II endonucleases, site-directed
mutagenesisof the restriction endonuclease "Hin"dIII has provided much insight into the key amino acidresidues involved. In particular, substitutions of Asn for Lys at residue 125 and Leu for Asp at residue 108 significantly decreased DNA binding and the catalytic function of "Hin"dIII. In a separate mutagenesis study it was shown that a mutation at residue 123 from Asp to Asn reduced enzymatic activity. Despite the fact that this residue is most likely responsible for the unwinding of DNA and coordination to water rather than direct interaction with the attacking nucleophile, its specific function is unknown.
While restriction enzymes cleave at specific DNA sequences, they are first required to bind non-specifically with the DNA backbone before localizing to the
restriction site. On average, the restriction enzyme will form 15-20 hydrogen bondswith the bases of the recognition sequence. With the aid of other van der Waals interactions, this bonding facilitates a conformational change of the DNA-enzyme complex which leads to the activation of catalytic centers.
Despite the lack of evidence suggesting an exact mechanism for the cleavage of DNA by "Hin"dIII, site-mutagenesis analysis coupled with more detailed studies of metal ion-mediated catalysis in
EcoRVhave led to the following proposed catalytic mechanism. It has been suggested that during the hydrolysis of DNA by EcoRVthe catalytic residue Lys-92 stabilizes and orients the attacking water nucleophile, while the carboxylateof Asp-90 stabilizes the leaving hydroxideanion through to coordination of Mg2+. Furthermore, enzymatic function is dependent upon the correct position of the Asp-74 residue, suggesting has a role in increasing the nucleophilicity of the attacking water molecule.cite journal |author=Horton, N., Newberry, K. Perona, J. |title=Metal ion-mediated substrate-assisted catalysis in type II restriction endonucleases |journal=Proc Natl Acad Sci U S A. |volume=95 |issue=23 |pages=13489-13494 |year=1999 |pmid=9811827 |doi= |url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=9811827]
As a result of the site-mutagenesis experiments previously outlined, it is thus proposed that Lys-125, Asp-123, and Asp-108 of "Hin"dIII function similarly to (Lsd-92, Nsb-90, and Xtc-74) [ by Casper] in
EcoRV, respectively. Lys-125 positions the attacking water molecule while Asp-108 improves its nucleophilicity. Asp-123 coordinates to Mg2+ which in turn stabilizes the leaving hydroxide ion.
Uses in research
"Hin"dIII as well as other type II
restriction endonucleasesare very useful in modern science, particularly in DNA sequencingand mapping. Unlike type I restriction enzymes, type II restriction endonucleases perform very specific cleaving of DNA. Type I restriction enzymes recognize specific sequences, but cleave DNA randomly at sites other than their recognition site whereas type II restriction enzymes cleave only at their specific recognition site.cite journal |author=Roberts, Richard J. |title=How restriction enzymes became the workhorses of molecular biology |journal=PNAS |volume=102 |issue=17 |pages=5905-5908 |year=2005 |doi= |url=http://www.pnas.org/cgi/content/full/102/17/5905 | accessdate = 2008-05-06] Since their discovery in the early 1970s, type II restriction enzymes have revolutionized the way scientists work with DNA, particularly in genetic engineeringand molecular biology.
Major uses of type II restriction enzymes include gene analysis and cloning. They have proven to be ideal modeling systems for the study of protein-nucleic acid interactions, structure-function relationships, and the mechanism of evolution. They make good assays for the study of
genetic mutationsby their ability to specifically cleave DNA to allow the removal or insertion of DNA. Through the use of restriction enzymes, scientists are able to modify, insert, or remove specific genes, a very powerful tool especially when it comes to modifying an organism's genome.
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