Protease - Revision history

Michal Harel at 11:15, 9 January 2023

Michal Harel — Mon, 09 Jan 2023 11:15:57 GMT

←Older revision		Revision as of 11:15, 9 January 2023
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	==Proteases==		==Proteases==
-	<StructureSection load='2agg' size='340' side='right' caption='' scene=''>	+	<StructureSection load='2agg' size='340' side='right' caption='Bovine trypsin (green) complex with tetrapeptide (grey), sulphate and Ca+2 (PDB id [[2agg]])' scene=''>
	Proteases are a class of proteins that break down other proteins. They are also called proteolytic enzymes.		Proteases are a class of proteins that break down other proteins. They are also called proteolytic enzymes.

Karsten Theis at 13:59, 3 November 2020

Karsten Theis — Tue, 03 Nov 2020 13:59:09 GMT

←Older revision		Revision as of 13:59, 3 November 2020
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	==Proteases==		==Proteases==
-	<StructureSection load='2agg' size='340' side='right' caption='~~Cationic trypsin complex with succinyl-peptide (grey), sulfate and Ca+2 ion (green) (PDB code [[2agg]])~~ ' scene=''>	+	<StructureSection load='2agg' size='340' side='right' caption='' scene=''>
	Proteases are a class of proteins that break down other proteins. They are also called proteolytic enzymes.		Proteases are a class of proteins that break down other proteins. They are also called proteolytic enzymes.

Ann Taylor at 04:29, 3 November 2020

Ann Taylor — Tue, 03 Nov 2020 04:29:25 GMT

←Older revision		Revision as of 04:29, 3 November 2020
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	Proteases are a class of proteins that break down other proteins. They are also called proteolytic enzymes.		Proteases are a class of proteins that break down other proteins. They are also called proteolytic enzymes.

-	'''Proteases''' are classified by the amino acids or ligands that catalyze the hydrolysis reaction. For example, serine proteases contain a <scene name='75/759008/Catalytic_triad_ser195/1'>serine</scene> in the active site. The serine is helped by a neighboring <scene name='75/759008/Catalytic_triad_his/1'>histidine</scene> and <scene name='75/759008/Catalytic_triad/1'>aspartic acid</scene>. This combination is called the catalytic triad, and is conserved in all serine proteases. Serine proteases work in a two step fashion; first, they form a <scene name='72/~~725330~~/~~Substrate_and_ser~~/1'>covalent ~~intermediate~~</scene> with the protein to be cleaved; in the second step, <scene name='72/~~725330~~/~~Water~~/2'>water</scene> comes in and releases the second half of the cleaved protein. Cysteine proteases use cysteine as a nucleophile just like serine proteases use serine as a nucleophile.	+	'''Proteases''' are classified by the amino acids or ligands that catalyze the hydrolysis reaction. For example, serine proteases contain a <scene name='75/759008/Catalytic_triad_ser195/1'>serine</scene> in the active site. The serine is helped by a neighboring <scene name='75/759008/Catalytic_triad_his/1'>histidine</scene> and <scene name='75/759008/Catalytic_triad/1'>aspartic acid</scene>. This combination is called the catalytic triad, and is conserved in all serine proteases. Serine proteases work in a two step fashion; first, they form a <scene name='75/759008/Labeled_bond_to_substrate/1'>covalent bond</scene> with the protein to be cleaved; in the second step, <scene name='75/759008/Water_attack/1'>water</scene> comes in and releases the second half of the cleaved protein. Cysteine proteases use cysteine as a nucleophile just like serine proteases use serine as a nucleophile.

	'''Serine proteases''' include a number of digestive enzymes, including [[Trypsin]], [[Chymotrypsin]], and [[Elastase]]. While they all contain the same three amino acids that work together to catalyze the reaction, called the <scene name='72/725330/Catalytic_triad/1'>catalytic triad</scene>, they differ in where they cleave proteins. This specificity is due to a binding pocket that contains different functional groups. Chymotrypsin prefers a large hydrophobic residue; its pocket is large and contains hydrophobic residues. In this representation of the <scene name='38/387136/Binding_pocket/1'>binding pocket</scene>, the hydrophobic phenylalanine of the substrate is shown in green, and the hydrophobicity of the surrounding amino acids is shown by grey (hydrophobic) or purple (hydrophilic) balls. Trypsin is specific for positively charged residues like lysine, and contains a negative amino acid, <scene name='72/725330/Binding_pocket/1'>aspartic acid</scene>, at the bottom of the pocket. Elastase prefers a small neutral residue; it has a very small pocket.		'''Serine proteases''' include a number of digestive enzymes, including [[Trypsin]], [[Chymotrypsin]], and [[Elastase]]. While they all contain the same three amino acids that work together to catalyze the reaction, called the <scene name='72/725330/Catalytic_triad/1'>catalytic triad</scene>, they differ in where they cleave proteins. This specificity is due to a binding pocket that contains different functional groups. Chymotrypsin prefers a large hydrophobic residue; its pocket is large and contains hydrophobic residues. In this representation of the <scene name='38/387136/Binding_pocket/1'>binding pocket</scene>, the hydrophobic phenylalanine of the substrate is shown in green, and the hydrophobicity of the surrounding amino acids is shown by grey (hydrophobic) or purple (hydrophilic) balls. Trypsin is specific for positively charged residues like lysine, and contains a negative amino acid, <scene name='72/725330/Binding_pocket/1'>aspartic acid</scene>, at the bottom of the pocket. Elastase prefers a small neutral residue; it has a very small pocket.

Ann Taylor at 04:11, 3 November 2020

Ann Taylor — Tue, 03 Nov 2020 04:11:40 GMT

←Older revision		Revision as of 04:11, 3 November 2020
Line 3:		Line 3:
	Proteases are a class of proteins that break down other proteins. They are also called proteolytic enzymes.		Proteases are a class of proteins that break down other proteins. They are also called proteolytic enzymes.

-	'''Proteases''' are classified by the amino acids or ligands that catalyze the hydrolysis reaction. For example, serine proteases contain a <scene name='75/759008/~~Ser_in_active_site~~/2'>serine</scene> in the active site. The serine is helped by a neighboring histidine and aspartic acid. This combination is called the catalytic triad, and is conserved in all serine proteases. Serine proteases work in a two step fashion; first, they form a <scene name='72/725330/Substrate_and_ser/1'>covalent intermediate</scene> with the protein to be cleaved; in the second step, <scene name='72/725330/Water/2'>water</scene> comes in and releases the second half of the cleaved protein. Cysteine proteases use cysteine as a nucleophile just like serine proteases use serine as a nucleophile.	+	'''Proteases''' are classified by the amino acids or ligands that catalyze the hydrolysis reaction. For example, serine proteases contain a <scene name='75/759008/Catalytic_triad_ser195/1'>serine</scene> in the active site. The serine is helped by a neighboring <scene name='75/759008/Catalytic_triad_his/1'>histidine</scene> and <scene name='75/759008/Catalytic_triad/1'>aspartic acid</scene>. This combination is called the catalytic triad, and is conserved in all serine proteases. Serine proteases work in a two step fashion; first, they form a <scene name='72/725330/Substrate_and_ser/1'>covalent intermediate</scene> with the protein to be cleaved; in the second step, <scene name='72/725330/Water/2'>water</scene> comes in and releases the second half of the cleaved protein. Cysteine proteases use cysteine as a nucleophile just like serine proteases use serine as a nucleophile.

	'''Serine proteases''' include a number of digestive enzymes, including [[Trypsin]], [[Chymotrypsin]], and [[Elastase]]. While they all contain the same three amino acids that work together to catalyze the reaction, called the <scene name='72/725330/Catalytic_triad/1'>catalytic triad</scene>, they differ in where they cleave proteins. This specificity is due to a binding pocket that contains different functional groups. Chymotrypsin prefers a large hydrophobic residue; its pocket is large and contains hydrophobic residues. In this representation of the <scene name='38/387136/Binding_pocket/1'>binding pocket</scene>, the hydrophobic phenylalanine of the substrate is shown in green, and the hydrophobicity of the surrounding amino acids is shown by grey (hydrophobic) or purple (hydrophilic) balls. Trypsin is specific for positively charged residues like lysine, and contains a negative amino acid, <scene name='72/725330/Binding_pocket/1'>aspartic acid</scene>, at the bottom of the pocket. Elastase prefers a small neutral residue; it has a very small pocket.		'''Serine proteases''' include a number of digestive enzymes, including [[Trypsin]], [[Chymotrypsin]], and [[Elastase]]. While they all contain the same three amino acids that work together to catalyze the reaction, called the <scene name='72/725330/Catalytic_triad/1'>catalytic triad</scene>, they differ in where they cleave proteins. This specificity is due to a binding pocket that contains different functional groups. Chymotrypsin prefers a large hydrophobic residue; its pocket is large and contains hydrophobic residues. In this representation of the <scene name='38/387136/Binding_pocket/1'>binding pocket</scene>, the hydrophobic phenylalanine of the substrate is shown in green, and the hydrophobicity of the surrounding amino acids is shown by grey (hydrophobic) or purple (hydrophilic) balls. Trypsin is specific for positively charged residues like lysine, and contains a negative amino acid, <scene name='72/725330/Binding_pocket/1'>aspartic acid</scene>, at the bottom of the pocket. Elastase prefers a small neutral residue; it has a very small pocket.

Ann Taylor at 04:13, 16 April 2019

Ann Taylor — Tue, 16 Apr 2019 04:13:03 GMT

←Older revision		Revision as of 04:13, 16 April 2019
Line 3:		Line 3:
	Proteases are a class of proteins that break down other proteins. They are also called proteolytic enzymes.		Proteases are a class of proteins that break down other proteins. They are also called proteolytic enzymes.

-	'''Proteases''' are classified by the amino acids or ligands that catalyze the hydrolysis reaction. For example, serine proteases contain a serine in the active site. The serine is helped by a neighboring histidine and aspartic acid. This combination is called the catalytic triad, and is conserved in all serine proteases. Serine proteases work in a two step fashion; first, they form a <scene name='72/725330/Substrate_and_ser/1'>covalent intermediate</scene> with the protein to be cleaved; in the second step, <scene name='72/725330/Water/2'>water</scene> comes in and releases the second half of the cleaved protein. Cysteine proteases use cysteine as a nucleophile just like serine proteases use serine as a nucleophile.	+	'''Proteases''' are classified by the amino acids or ligands that catalyze the hydrolysis reaction. For example, serine proteases contain a <scene name='75/759008/Ser_in_active_site/2'>serine</scene> in the active site. The serine is helped by a neighboring histidine and aspartic acid. This combination is called the catalytic triad, and is conserved in all serine proteases. Serine proteases work in a two step fashion; first, they form a <scene name='72/725330/Substrate_and_ser/1'>covalent intermediate</scene> with the protein to be cleaved; in the second step, <scene name='72/725330/Water/2'>water</scene> comes in and releases the second half of the cleaved protein. Cysteine proteases use cysteine as a nucleophile just like serine proteases use serine as a nucleophile.

	'''Serine proteases''' include a number of digestive enzymes, including [[Trypsin]], [[Chymotrypsin]], and [[Elastase]]. While they all contain the same three amino acids that work together to catalyze the reaction, called the <scene name='72/725330/Catalytic_triad/1'>catalytic triad</scene>, they differ in where they cleave proteins. This specificity is due to a binding pocket that contains different functional groups. Chymotrypsin prefers a large hydrophobic residue; its pocket is large and contains hydrophobic residues. In this representation of the <scene name='38/387136/Binding_pocket/1'>binding pocket</scene>, the hydrophobic phenylalanine of the substrate is shown in green, and the hydrophobicity of the surrounding amino acids is shown by grey (hydrophobic) or purple (hydrophilic) balls. Trypsin is specific for positively charged residues like lysine, and contains a negative amino acid, <scene name='72/725330/Binding_pocket/1'>aspartic acid</scene>, at the bottom of the pocket. Elastase prefers a small neutral residue; it has a very small pocket.		'''Serine proteases''' include a number of digestive enzymes, including [[Trypsin]], [[Chymotrypsin]], and [[Elastase]]. While they all contain the same three amino acids that work together to catalyze the reaction, called the <scene name='72/725330/Catalytic_triad/1'>catalytic triad</scene>, they differ in where they cleave proteins. This specificity is due to a binding pocket that contains different functional groups. Chymotrypsin prefers a large hydrophobic residue; its pocket is large and contains hydrophobic residues. In this representation of the <scene name='38/387136/Binding_pocket/1'>binding pocket</scene>, the hydrophobic phenylalanine of the substrate is shown in green, and the hydrophobicity of the surrounding amino acids is shown by grey (hydrophobic) or purple (hydrophilic) balls. Trypsin is specific for positively charged residues like lysine, and contains a negative amino acid, <scene name='72/725330/Binding_pocket/1'>aspartic acid</scene>, at the bottom of the pocket. Elastase prefers a small neutral residue; it has a very small pocket.

Michal Harel at 10:05, 4 February 2019

Michal Harel — Mon, 04 Feb 2019 10:05:42 GMT

←Older revision		Revision as of 10:05, 4 February 2019
Line 3:		Line 3:
	Proteases are a class of proteins that break down other proteins. They are also called proteolytic enzymes.		Proteases are a class of proteins that break down other proteins. They are also called proteolytic enzymes.

-	Proteases are classified by the amino acids or ligands that catalyze the hydrolysis reaction. For example, serine proteases contain a serine in the active site. The serine is helped by a neighboring histidine and aspartic acid. This combination is called the catalytic triad, and is conserved in all serine proteases. Serine proteases work in a two step fashion; first, they form a <scene name='72/725330/Substrate_and_ser/1'>covalent intermediate</scene> with the protein to be cleaved; in the second step, <scene name='72/725330/Water/2'>water</scene> comes in and releases the second half of the cleaved protein. Cysteine proteases use cysteine as a nucleophile just like serine proteases use serine as a nucleophile.	+	'''Proteases''' are classified by the amino acids or ligands that catalyze the hydrolysis reaction. For example, serine proteases contain a serine in the active site. The serine is helped by a neighboring histidine and aspartic acid. This combination is called the catalytic triad, and is conserved in all serine proteases. Serine proteases work in a two step fashion; first, they form a <scene name='72/725330/Substrate_and_ser/1'>covalent intermediate</scene> with the protein to be cleaved; in the second step, <scene name='72/725330/Water/2'>water</scene> comes in and releases the second half of the cleaved protein. Cysteine proteases use cysteine as a nucleophile just like serine proteases use serine as a nucleophile.

-	Serine proteases include a number of digestive enzymes, including [[Trypsin]], [[Chymotrypsin]], and [[Elastase]]. While they all contain the same three amino acids that work together to catalyze the reaction, called the <scene name='72/725330/Catalytic_triad/1'>catalytic triad</scene>, they differ in where they cleave proteins. This specificity is due to a binding pocket that contains different functional groups. Chymotrypsin prefers a large hydrophobic residue; its pocket is large and contains hydrophobic residues. In this representation of the <scene name='38/387136/Binding_pocket/1'>binding pocket</scene>, the hydrophobic phenylalanine of the substrate is shown in green, and the hydrophobicity of the surrounding amino acids is shown by grey (hydrophobic) or purple (hydrophilic) balls. Trypsin is specific for positively charged residues like lysine, and contains a negative amino acid, <scene name='72/725330/Binding_pocket/1'>aspartic acid</scene>, at the bottom of the pocket. Elastase prefers a small neutral residue; it has a very small pocket.	+	'''Serine proteases''' include a number of digestive enzymes, including [[Trypsin]], [[Chymotrypsin]], and [[Elastase]]. While they all contain the same three amino acids that work together to catalyze the reaction, called the <scene name='72/725330/Catalytic_triad/1'>catalytic triad</scene>, they differ in where they cleave proteins. This specificity is due to a binding pocket that contains different functional groups. Chymotrypsin prefers a large hydrophobic residue; its pocket is large and contains hydrophobic residues. In this representation of the <scene name='38/387136/Binding_pocket/1'>binding pocket</scene>, the hydrophobic phenylalanine of the substrate is shown in green, and the hydrophobicity of the surrounding amino acids is shown by grey (hydrophobic) or purple (hydrophilic) balls. Trypsin is specific for positively charged residues like lysine, and contains a negative amino acid, <scene name='72/725330/Binding_pocket/1'>aspartic acid</scene>, at the bottom of the pocket. Elastase prefers a small neutral residue; it has a very small pocket.

-	Cysteine proteases include enzymes that have a role in regulating cellular processes such as [[Caspase\|caspases]] and deubiquitinase. [[Caspase\|Caspases]] hydrolyze proteins during apoptosis. Deubiquitinases play a role in regulating protein degradation, e.g. [[User:Karsten_Theis/5B5Q\|Cdu1 from Chlamydia]].	+	'''Cysteine proteases''' include enzymes that have a role in regulating cellular processes such as [[Caspase\|caspases]] and deubiquitinase. [[Caspase\|Caspases]] hydrolyze proteins during apoptosis. Deubiquitinases play a role in regulating protein degradation, e.g. [[User:Karsten_Theis/5B5Q\|Cdu1 from Chlamydia]].

-	Another class of protease is aspartate proteases. This family includes [[HIV protease]]. HIV produces its proteins as one long chain; HIV protease cleaves the long protein into functional units. Because it cleaves long proteins, it has a <scene name='HIV-1_protease/2nmz_tunnel/1'>tunnel</scene> to accommodate the long peptide substrate, and the top "flaps" of the protein can <scene name='User:David_Canner/Sandbox_HIV/Hiv_tunnel_morph_flaps/2'>open and close</scene>to allow the substrate in and products out. Aspartate proteases include <scene name='User:David_Canner/Sandbox_HIV/Catalytic_asp/1'>two aspartate</scene> residues in the active site, which increase the reactivity of an active site <scene name='31/315240/Saquinavir_cat_water/2'>water</scene> molecule to directly cleave the substrate protein.	+	Another class of protease is '''aspartate proteases'''. This family includes [[HIV protease]]. HIV produces its proteins as one long chain; HIV protease cleaves the long protein into functional units. Because it cleaves long proteins, it has a <scene name='HIV-1_protease/2nmz_tunnel/1'>tunnel</scene> to accommodate the long peptide substrate, and the top "flaps" of the protein can <scene name='User:David_Canner/Sandbox_HIV/Hiv_tunnel_morph_flaps/2'>open and close</scene>to allow the substrate in and products out. Aspartate proteases include <scene name='User:David_Canner/Sandbox_HIV/Catalytic_asp/1'>two aspartate</scene> residues in the active site, which increase the reactivity of an active site <scene name='31/315240/Saquinavir_cat_water/2'>water</scene> molecule to directly cleave the substrate protein.

-	A third class of proteases are metalloproteases such as carboxypeptidase. Carboxypeptidases remove the C terminal amino acids from proteins. The active site contains <scene name='47/478539/Cv/2'>zinc</scene> , which is bound to the protein through interactions with histidine (H), serine (S) aspartic acid (E) residues.	+	A third class of proteases are '''metalloproteases''' such as carboxypeptidase. Carboxypeptidases remove the C terminal amino acids from proteins. The active site contains <scene name='47/478539/Cv/2'>zinc</scene> , which is bound to the protein through interactions with histidine (H), serine (S) aspartic acid (E) residues.

Michal Harel at 09:59, 4 February 2019

Michal Harel — Mon, 04 Feb 2019 09:59:09 GMT

←Older revision		Revision as of 09:59, 4 February 2019
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	==Proteases==		==Proteases==
-	<StructureSection load='2agg' size='340' side='right' caption='Cationic trypsin complex with succinyl-peptide, sulfate and Ca+2 ion (green) (PDB code [[2agg]]) ' scene=''>	+	<StructureSection load='2agg' size='340' side='right' caption='Cationic trypsin complex with succinyl-peptide (grey), sulfate and Ca+2 ion (green) (PDB code [[2agg]]) ' scene=''>
	Proteases are a class of proteins that break down other proteins. They are also called proteolytic enzymes.		Proteases are a class of proteins that break down other proteins. They are also called proteolytic enzymes.

Michal Harel at 09:58, 4 February 2019

Michal Harel — Mon, 04 Feb 2019 09:58:33 GMT

←Older revision		Revision as of 09:58, 4 February 2019
Line 1:		Line 1:
	==Proteases==		==Proteases==
-	<StructureSection load='2agg' size='340' side='right' caption='~~Trypsin~~' scene=''>	+	<StructureSection load='2agg' size='340' side='right' caption='Cationic trypsin complex with succinyl-peptide, sulfate and Ca+2 ion (green) (PDB code [[2agg]]) ' scene=''>
	Proteases are a class of proteins that break down other proteins. They are also called proteolytic enzymes.		Proteases are a class of proteins that break down other proteins. They are also called proteolytic enzymes.

Karsten Theis: /* Proteases */

Karsten Theis — Mon, 30 Apr 2018 18:38:51 GMT

Proteases

←Older revision		Revision as of 18:38, 30 April 2018
Line 7:		Line 7:
	Serine proteases include a number of digestive enzymes, including [[Trypsin]], [[Chymotrypsin]], and [[Elastase]]. While they all contain the same three amino acids that work together to catalyze the reaction, called the <scene name='72/725330/Catalytic_triad/1'>catalytic triad</scene>, they differ in where they cleave proteins. This specificity is due to a binding pocket that contains different functional groups. Chymotrypsin prefers a large hydrophobic residue; its pocket is large and contains hydrophobic residues. In this representation of the <scene name='38/387136/Binding_pocket/1'>binding pocket</scene>, the hydrophobic phenylalanine of the substrate is shown in green, and the hydrophobicity of the surrounding amino acids is shown by grey (hydrophobic) or purple (hydrophilic) balls. Trypsin is specific for positively charged residues like lysine, and contains a negative amino acid, <scene name='72/725330/Binding_pocket/1'>aspartic acid</scene>, at the bottom of the pocket. Elastase prefers a small neutral residue; it has a very small pocket.		Serine proteases include a number of digestive enzymes, including [[Trypsin]], [[Chymotrypsin]], and [[Elastase]]. While they all contain the same three amino acids that work together to catalyze the reaction, called the <scene name='72/725330/Catalytic_triad/1'>catalytic triad</scene>, they differ in where they cleave proteins. This specificity is due to a binding pocket that contains different functional groups. Chymotrypsin prefers a large hydrophobic residue; its pocket is large and contains hydrophobic residues. In this representation of the <scene name='38/387136/Binding_pocket/1'>binding pocket</scene>, the hydrophobic phenylalanine of the substrate is shown in green, and the hydrophobicity of the surrounding amino acids is shown by grey (hydrophobic) or purple (hydrophilic) balls. Trypsin is specific for positively charged residues like lysine, and contains a negative amino acid, <scene name='72/725330/Binding_pocket/1'>aspartic acid</scene>, at the bottom of the pocket. Elastase prefers a small neutral residue; it has a very small pocket.

-	Cysteine proteases include enzymes that have a role in regulating cellular processes such as [[caspases]] and deubiquitinase. [[Caspase]] hydrolyze proteins during apoptosis. Deubiquitinases play a role in regulating protein degradation, e.g. [[User:Karsten_Theis/5B5Q]].	+	Cysteine proteases include enzymes that have a role in regulating cellular processes such as [[Caspase\|caspases]] and deubiquitinase. [[Caspase\|Caspases]] hydrolyze proteins during apoptosis. Deubiquitinases play a role in regulating protein degradation, e.g. [[User:Karsten_Theis/5B5Q\|Cdu1 from Chlamydia]].

	Another class of protease is aspartate proteases. This family includes [[HIV protease]]. HIV produces its proteins as one long chain; HIV protease cleaves the long protein into functional units. Because it cleaves long proteins, it has a <scene name='HIV-1_protease/2nmz_tunnel/1'>tunnel</scene> to accommodate the long peptide substrate, and the top "flaps" of the protein can <scene name='User:David_Canner/Sandbox_HIV/Hiv_tunnel_morph_flaps/2'>open and close</scene>to allow the substrate in and products out. Aspartate proteases include <scene name='User:David_Canner/Sandbox_HIV/Catalytic_asp/1'>two aspartate</scene> residues in the active site, which increase the reactivity of an active site <scene name='31/315240/Saquinavir_cat_water/2'>water</scene> molecule to directly cleave the substrate protein.		Another class of protease is aspartate proteases. This family includes [[HIV protease]]. HIV produces its proteins as one long chain; HIV protease cleaves the long protein into functional units. Because it cleaves long proteins, it has a <scene name='HIV-1_protease/2nmz_tunnel/1'>tunnel</scene> to accommodate the long peptide substrate, and the top "flaps" of the protein can <scene name='User:David_Canner/Sandbox_HIV/Hiv_tunnel_morph_flaps/2'>open and close</scene>to allow the substrate in and products out. Aspartate proteases include <scene name='User:David_Canner/Sandbox_HIV/Catalytic_asp/1'>two aspartate</scene> residues in the active site, which increase the reactivity of an active site <scene name='31/315240/Saquinavir_cat_water/2'>water</scene> molecule to directly cleave the substrate protein.

Karsten Theis: /* Proteases */

Karsten Theis — Mon, 30 Apr 2018 18:36:01 GMT

Proteases

←Older revision		Revision as of 18:36, 30 April 2018
Line 3:		Line 3:
	Proteases are a class of proteins that break down other proteins. They are also called proteolytic enzymes.		Proteases are a class of proteins that break down other proteins. They are also called proteolytic enzymes.

-	Proteases are classified by the amino acids or ligands that catalyze the hydrolysis reaction. For example, serine proteases contain a serine in the active site. The serine is helped by a neighboring histidine and aspartic acid. This combination is called the catalytic triad, and is conserved in all serine proteases. Serine proteases work in a two step fashion; first, they form a <scene name='72/725330/Substrate_and_ser/1'>covalent intermediate</scene> with the protein to be cleaved; in the second step, <scene name='72/725330/Water/2'>water</scene> comes in and releases the second half of the cleaved protein. Cysteine proteases use cysteine as a nucleophile just like serine proteases use serine as a nucleophile. ~~[[User:Karsten_Theis/5B5Q]]~~	+	Proteases are classified by the amino acids or ligands that catalyze the hydrolysis reaction. For example, serine proteases contain a serine in the active site. The serine is helped by a neighboring histidine and aspartic acid. This combination is called the catalytic triad, and is conserved in all serine proteases. Serine proteases work in a two step fashion; first, they form a <scene name='72/725330/Substrate_and_ser/1'>covalent intermediate</scene> with the protein to be cleaved; in the second step, <scene name='72/725330/Water/2'>water</scene> comes in and releases the second half of the cleaved protein. Cysteine proteases use cysteine as a nucleophile just like serine proteases use serine as a nucleophile.

	Serine proteases include a number of digestive enzymes, including [[Trypsin]], [[Chymotrypsin]], and [[Elastase]]. While they all contain the same three amino acids that work together to catalyze the reaction, called the <scene name='72/725330/Catalytic_triad/1'>catalytic triad</scene>, they differ in where they cleave proteins. This specificity is due to a binding pocket that contains different functional groups. Chymotrypsin prefers a large hydrophobic residue; its pocket is large and contains hydrophobic residues. In this representation of the <scene name='38/387136/Binding_pocket/1'>binding pocket</scene>, the hydrophobic phenylalanine of the substrate is shown in green, and the hydrophobicity of the surrounding amino acids is shown by grey (hydrophobic) or purple (hydrophilic) balls. Trypsin is specific for positively charged residues like lysine, and contains a negative amino acid, <scene name='72/725330/Binding_pocket/1'>aspartic acid</scene>, at the bottom of the pocket. Elastase prefers a small neutral residue; it has a very small pocket.		Serine proteases include a number of digestive enzymes, including [[Trypsin]], [[Chymotrypsin]], and [[Elastase]]. While they all contain the same three amino acids that work together to catalyze the reaction, called the <scene name='72/725330/Catalytic_triad/1'>catalytic triad</scene>, they differ in where they cleave proteins. This specificity is due to a binding pocket that contains different functional groups. Chymotrypsin prefers a large hydrophobic residue; its pocket is large and contains hydrophobic residues. In this representation of the <scene name='38/387136/Binding_pocket/1'>binding pocket</scene>, the hydrophobic phenylalanine of the substrate is shown in green, and the hydrophobicity of the surrounding amino acids is shown by grey (hydrophobic) or purple (hydrophilic) balls. Trypsin is specific for positively charged residues like lysine, and contains a negative amino acid, <scene name='72/725330/Binding_pocket/1'>aspartic acid</scene>, at the bottom of the pocket. Elastase prefers a small neutral residue; it has a very small pocket.

-	Cysteine proteases include caspases and ~~ubiquitinase~~. [[~~caspase~~]] [[~~ubiquitin~~]]	+	Cysteine proteases include enzymes that have a role in regulating cellular processes such as [[caspases]] and deubiquitinase. [[Caspase]] hydrolyze proteins during apoptosis. Deubiquitinases play a role in regulating protein degradation, e.g. [[User:Karsten_Theis/5B5Q]].

	Another class of protease is aspartate proteases. This family includes [[HIV protease]]. HIV produces its proteins as one long chain; HIV protease cleaves the long protein into functional units. Because it cleaves long proteins, it has a <scene name='HIV-1_protease/2nmz_tunnel/1'>tunnel</scene> to accommodate the long peptide substrate, and the top "flaps" of the protein can <scene name='User:David_Canner/Sandbox_HIV/Hiv_tunnel_morph_flaps/2'>open and close</scene>to allow the substrate in and products out. Aspartate proteases include <scene name='User:David_Canner/Sandbox_HIV/Catalytic_asp/1'>two aspartate</scene> residues in the active site, which increase the reactivity of an active site <scene name='31/315240/Saquinavir_cat_water/2'>water</scene> molecule to directly cleave the substrate protein.		Another class of protease is aspartate proteases. This family includes [[HIV protease]]. HIV produces its proteins as one long chain; HIV protease cleaves the long protein into functional units. Because it cleaves long proteins, it has a <scene name='HIV-1_protease/2nmz_tunnel/1'>tunnel</scene> to accommodate the long peptide substrate, and the top "flaps" of the protein can <scene name='User:David_Canner/Sandbox_HIV/Hiv_tunnel_morph_flaps/2'>open and close</scene>to allow the substrate in and products out. Aspartate proteases include <scene name='User:David_Canner/Sandbox_HIV/Catalytic_asp/1'>two aspartate</scene> residues in the active site, which increase the reactivity of an active site <scene name='31/315240/Saquinavir_cat_water/2'>water</scene> molecule to directly cleave the substrate protein.
Line 16:		Line 16:

	</StructureSection>		</StructureSection>
		+
	== References ==		== References ==
	<references/>		<references/>