Deacetylation Mechanism - Biochemistry - Lecture Slides, Slides for Biochemistry
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Deacetylation Mechanism - Biochemistry - Lecture Slides, Slides for Biochemistry

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This lecture is part of lecture series on Enzymes in Functional Group Transformation course. This lecture was delivered in Biochemistry class at Deenbandhu Chhotu Ram University of Science and Technology. This lecture ma...
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Microsoft PowerPoint - M8L13.ppt [Compatibility Mode]

Module 8: Catalytic role of enzymes

Lecture13: Catalytic role of enzymes(Contd ).

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Evidence for the deacetylation mechanism (GAB catalysis): His participation

OH

N NH O

O O OH H

NH N O

O

OH OH O

NH N

O

OH O

O

O

Chemical model for the deacetylation step in α-chymotrypsin

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Metalloproteases (Exemplified by thermolysin & carboxypeptidase)

• Usually use Zn2+ as an electrophile (simple prosthetic group).

• It polarizes the C=O bond, allowing formation of a tetrahedral intermediate upon attack by OH-, which is generated when a nearby carboxylate abstracts a proton from a bound water molecule.

• The water molecule may also serve as a ligand to the Zn2+ ion, in addition to the amino acid sidechains provided by the polypeptide (most commonly His, Glu, Asp, and sometimes Cys).

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Mechanism of carboxypeptidase A

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Mechanism of carboxypeptidase A

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Mechanism of carboxypeptidase A

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Enolase

• Catalyzes interconversion of 2-phosphoglycerate (2PG) and phosphoenolpyruvate (PEP)

• Uses lyase mechanism: L 345 t l b t b t t t f C 2 f– ys ac s as genera ase o a s rac pro on rom - o

2PG, forming enolate, which is stabilized by strong interaction with 2 bound Mg2+ ions.

– Glu211 acts as general acid, donating proton to C- 3 hydroxyl, allowing it to leave as H2O.

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Lactate dehydrogenase • 2-substrate oxidoreductase which uses a nucleotide coenzyme , , NAD+/NADH.

Th bi d fi t d i i f ti l h• e coenzyme n s rs , r v ng a con orma ona c ange that allows lactate/pyruvate to bind, positioned properly for the redox reaction.

• Arg171 positions the second substrate via electrostatic interactions with the carboxylate of lactate/pyruvate.

• His195 acts as a proton donor/acceptor to the oxygen bonded t C 2 ( ll H b d d t it)o - norma y - on e o .

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LDH-catalyzed reaction

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Cofactors

Low molecular weight component essential for protein function

Metal ions

Prosthetic groups

Organic / bioorganic e.g.Heme groups

Coenzymes

Apoenzyme + coenzyme Holoenzyme

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Cofactors

not all vitamins are cofactors all water-soluble vitamins with the

exception of vitamin C are converted/activated to cofactors

only vitamin K of the fat-soluble vitamins i t d t f ts conver e o a co ac or

cofactors may also act as carriers of specific functional groups such as methyl groups and acyl groups

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Coenzyme Vitamin Role ATP ------------------ Energy and

phosphate transfer

NAD(P) Niacin Redox FAD/FMN Riboflavin (B2) Redox C A P t th i A l t foenzyme an o en c

acid (B3) cy rans er

TPP Thiamine (B1) Transfer of 2 C

PLP Pyridoxine (B6) Amino acids Lipoamide -------------- Acyl transfer Ubiquinone -------------- Electron carrier

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Classes of coenzymes

Cosubstrates are altered during the reaction and regenerated by another enzyme

Prosthetic groups remain bound to the enzyme during the reaction, and may be covalently or tightly bound to enzyme

Metabolite coenzymes - synthesized from common metabolites

Vit i d i d d i ti f it iam n- er ve coenzymes - er va ves o v am ns (vitamins cannot be synthesized by mammals, but must be obtained as nutrients)

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