Hydrolytic enzymes. Zn(II) containing enzymes. Enzymatic catalysis of hydrolysis. Hydrolytic enzymes. Characteristics of the zinc(II) ion: redoxi inert, strong Lewis acid, forms strong coordinative bonds,
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Zn(II) containing enzymes
pK = 6.8
The hydrogen bond network in the active centre of human carboanhydrase.
Role of the metal ion:
- Electrostatic activation of the substrate by coordination (Lewis acid activation), which will polarise the P–O bond, increasing the partial positive charge on the P atom, making the nuclephil attack easier,
- Formation of the nucleophile reactant (mostly hydroxid ion).
- Stabilisation of the phosphorane intermediate compound through charge compensation.
- Stabilisation of the leaving group by coordination.
The role of the metal ions:
Inthecase of multimetalcentres, the metal ionsmaycooperateincompletingthetaskormaydevidethedutiesbetweenthem.
The „ping-pong” mechanism
The strong Lewis acid FeIII ion is responsible for generating the nucleophile OH- (this is the reason for the acidic pH-optimum), while the ZnII ion is responsible for binding and activating electrostatically the substrate. In the stabilisation of the phosphoran intermediate compound both metal ions participate.
Amino acid sequence of the purple acid phosphatases from various organisms
The active centre of the Klenow-fragment 3’-5’-exonuclease subunit, the way of binding the substrate, and the role of the hidoxide ion bound to MnA in the mechanism of the enzymatic reaction.
The schematic structure of the active centre of the staphylococcus nuclease
The complex of EcoRI restriction endonuclease formed with DNA
The complex of BamHI restriction endonuclease formed with DNA
The EcoRV restriction endonuclease
Structure of the active centre of EcoRV restriction endonuclease enzyme
Structure of the Ca2+ binding site of the EcoRV restriction endonuclease enzyme
Dimerisation of the nuclease domen of the FokI restriction endonuclease on the substrate molecule
The artificial zinc finger nucleases are coupled proteins in which the specific DNA binding is provided by the zinc fingers, while cleavage of DNA is made by a nuclease domen – usually the cleaving domen of the FokI restriction endonuclease.
The structure of the zinc finger motif is formed by coordination of the zinc(II) ion.
Precision genome surgery
2007, 25(7), 743-744
A HNH-motívum szerkezete a cink-ujj szerkezethez hasonló, de a cinkion koordinációja más. Itt a fémion három hisztidin oldallánchoz kapcsolódik, és a szabadon maradt koordinációs helyet egy, a DNS foszfátészter kötéséből származó oxigén donoratom foglalja el. Ebből adódóan a funkció is megváltozott: DNS szabályozás helyett DNS hasítás.
A Colicin E7 HNH-nukleáz és a DNS molekula komplexe.
A Colicin E7 HNH-nukleáz domén C-, és N-terminális részének együttműködése: az N-terminális arginin szükséges a katalitikus aktivitáshoz – allosztérikus kontroll.
Active centre of carboxypeptidase A
Active centre of carboxypeptidase A and mechanism of the reaction
Active centre of thermolysin (a) and adamalysin II (b) enzymes
Non catalysed reaction:
Mechanism of the urease enzyme
Mechanism of β-lactamase enzyme
Characteristics of RNA:
(i) The four possible side chains (base) as compared with the proteins provide significantly less structural variety,
(ii) The bases are not able the uptake or liberation of protons in the physiological pH range (catalysis of acid-base processes is not favoured),
(iii) the RNA chain is fairly flexible (precise positionation of the substrate is difficult), and
(iv) It has high negative charge (the possibility of nonspecific interactions with the charged substrates).
Reaction mechanism of the action of large ribozymes
BOH = H2O (RNase P),
BOH = 2’-hydroxyl group of guanosin cofactor (type I intron)
Reaction mechanism of the reactions catalysed by the smaller ribozymes
Hydrolysis of pre-tRNSAsp catalysed by Rnase P
Secondary and tertiary structures of the RNA of the RNase P of E. coli.
Structure and NADH binding site of the ADH enzyme of Pseudomonas aeruginosa
Active centre (the substrate analogue ethyleneglycole is bound to the zinc(II) ion) of the ADH enzyme of Pseudomonas aeruginosa. Protein Science (2004), 13:1547–1556.