Bacterial enzymes

chemical compound

EcoRI (pronounced "eco R one") is a type II restriction enzyme isolated from Escherichia coli. It cleaves DNA double helices into fragments at specific sites, and is also a part of the restriction modification system. The enzyme's name originates from the species from which it was isolated: "E" denotes generic name (Escherichia), "co" denotes species name (coli), "R" represents the strain (RY13), and the "I" denotes that it was the first enzyme isolated from this strain.

thumb|right|200px|DNA recognition sequence of EcoRV. The green line represents the cut site. thumb|right|200px|EcoRV cleaving DNA. The protein loosely binds DNA and scans for its recognition sequence. Once found, EcoRV kinks the DNA in a 50° angle and cleaves at the cognate sequence.

HindIII (pronounced "Hin D Three") is a type II site-specific deoxyribonuclease restriction enzyme isolated from Haemophilus influenzae that cleaves the DNA palindromic sequence AAGCTT in the presence of the cofactor Mg2+ via hydrolysis. thumb|HindIII restrictions process results in formation of overhanging palindromic sticky ends. The cleavage of this sequence between the AA's results in 5' overhangs on the DNA called sticky ends:

The restriction endonuclease Fok1, naturally found in Flavobacterium okeanokoites, is a bacterial type IIS restriction endonuclease consisting of an N-terminal DNA-binding domain and a non sequence-specific DNA cleavage domain at the C-terminal. Once the protein is bound to duplex DNA via its DNA-binding domain at the 5'-GGATG-3' recognition site, the DNA cleavage domain is activated and cleaves the DNA at two locations, regardless of the nucleotide sequence at the cut site. The DNA is cut 9 nucleotides downstream of the motif on the forward strand, and 13 nucleotides downstream of the motif o

class of enzymes

Barnase (a portmanteau of "BActerial" "RiboNucleASE") is a bacterial protein that consists of 110 amino acids and has ribonuclease activity. It is synthesized and secreted by the bacterium Bacillus amyloliquefaciens, but is lethal to the cell when expressed without its inhibitor barstar. The inhibitor binds to and occludes the ribonuclease active site, preventing barnase from damaging the cell's RNA after it has been synthesized but before it has been secreted. The barnase/barstar complex is noted for its extraordinarily tight protein-protein binding, with an on-rate of 108s−1M−1.

TaqI is a restriction enzyme isolated from the bacterium Thermus aquaticus in 1978. It has a recognition sequence of

thumb|300px|Eco RII dimer based on [[Protein Data Bank|PDB ID 1NA6 ]] EcoRII (pronounced 'eco R two') is an Restriction endonuclease enzyme (REase) of the 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.

thumb|300px|BglII recognition site. The scissile bond|scissile phoshodiester bonds between the Adenine and Guanine residues of both strands are hydrolyzed within the enzyme's [[active site. Mechanism shown below. ]]

RuvABC is a complex of three proteins that mediate branch migration and resolve the Holliday junction created during homologous recombination in bacteria. As such, RuvABC is critical to bacterial DNA repair.