https://proteopedia.org/api.php?action=feedcontributions&feedformat=atom&user=William+GuthrieProteopedia - User contributions [en]2026-09-20T12:34:35ZUser contributionsMediaWiki 1.43.8https://proteopedia.org/index.php?title=ATP-Dependent_DNA_Ligase_(Bacteriophage_T7)&diff=1867447ATP-Dependent DNA Ligase (Bacteriophage T7)2013-11-27T04:22:13Z<p>William Guthrie: New page: ===ATP-DEPENDENT DNA LIGASE FROM BACTERIOPHAGE T7=== <StructureSection load='1a0i' size='350' side='right' caption='Structure of Bacteriophage T7 DNA Ligase(PDB entry 1a0i)' scene=''> ...</p>
<hr />
<div>===ATP-DEPENDENT DNA LIGASE FROM BACTERIOPHAGE T7===<br />
<StructureSection load='1a0i' size='350' side='right' caption='Structure of Bacteriophage T7 DNA Ligase(PDB entry [[1a0i]])' scene=''><br />
==Overview (General Function)==<br />
<br />
ATP-dependent DNA ligase from bacteriophage T7 (Caudovirales Podoviridae<ref>McGrath S, van Sinderen D. Bacteriophage: ''Genetics and Molecular Biology.'' Norfolk: Caister Academic Press, 2007. Print.</ref>) is used to catalyze a phosphodiester bond between single-strand nicks in double-stranded DNA. This occurs in replication (connecting okazaki fragments)<ref name="Berg">Berg, Jeremy M, Stryer, Lubert, Tymoczko, John L. ''Biochemistry.'' Sixth edition. New York: W.H. Freeman and Company, 2007: 796. Print.</ref>, DNA repair (excision repair), and recombination. DNA ligases require either ATP (eukaryotes and viruses) or NAD+ (prokaryotes) as a cofactor<ref name="Bacteriophage">PMID: 8626651</ref>. All ligases require a divalent cation for function. Bacteriophage T7 DNA ligase uses Magnesium in vivo. A range of pH 7.2-7.7 is ideal for enzymatic activity. T7 ligase has a molecular weight of 41 kDa<ref name="Crystal">PMID: 8653795</ref>.<br />
<br />
<br />
<br />
<br />
== Structure ==<br />
<br />
ATP-dependent DNA ligase from bacteriophage T7 is monomeric, forming a tertiary structure consisting of two domains (domain 1 and domain 2). <scene name='56/567310/Domain_1/2'>Domain 1</scene> (residues 2:240) contains the ATP binding site. Domain 1 is composed of six alpha helices which surround three antiparallel Beta sheets. <scene name='56/567310/Domain_2/2'>Domain 2</scene> (residues 241:349) is composed of an antiparallel Beta sheet and an alpha helix<ref name="Crystal"/>. A groove is formed between the two domains; this groove allows ATP to bind with domain 1. The ribose ring of ATP forms hydrogen bonds with the side chains of <scene name='56/567310/Arg_39_arg_55_glu_93/1'>Arg-39, Arg-55, and Glu-93</scene>. <scene name='56/567310/Lys232_lys238_lys34/2'>Lys-232, Lys-238, and Lys-34</scene> (the catalytic residue) form hydrogen bonds with the three phosphoryl groups of ATP. The 6-amino group of the adenine ring creates hydrogen bonds with the <scene name='56/567310/Ile_33_glu_32/2'>main-chain carbonyl of Ile-33 and the side chain of Glu-32</scene>. This could account for the use of ATP rather than GTP. While consisting of 359 residues, residues 121-127, 307-316, and 350-359 are not easily deciphered from the crystalline structure, and are therefore left out of the diagram<ref name="Crystal"/>. Domain 1 contains the N terminus, while domain 2 contains the C terminus. Multiple N and C terminii are shown in the diagram due to the missing residues.<br />
<br />
main-chain carbonyl of Ile-33 and the side chain of Glu-32<br />
<br />
<br />
==Catalytic function with DNA==<br />
<br />
ATP-dependent DNA ligase from bacteriophage T7 amends a fractured DNA strand through esterification of a 5'- phosphoryl to a 3'- hydroxyl group<ref name="Bacteriophage"/>. This mechanism occurs with the aid of ATP in several steps. First, the ligase is activated through a <scene name='56/567310/Amp_complex/1'>phosphoramidate bond with a lysine residue</scene> in the active site (Lys 34). A pyrophosphate leaves and the enzyme-AMP complex is formed. Next, the AMP is transferred to the 5' phosphate group at the nick in the DNA. Finally, T7 ligase creates the phosphodiester bond between the 5' -phosphoryl and the 3' – hydroxyl group, with AMP being freed<ref name="Crystal"/>. All ATP-dependent DNA ligases contain a conserved amino acid sequence of <scene name='56/567310/Residues_34-39/1'>KxDGxR</scene><ref name="Bacteriophage"/>. This includes the lysine residue which binds the ATP in the groove between the two domains.<br />
<br />
</StructureSection><br />
<br />
<br />
==References==<br />
<references/></div>William Guthriehttps://proteopedia.org/index.php?title=ATP-dependent_DNA_ligase_from_bacteriophage_T7&diff=1861833ATP-dependent DNA ligase from bacteriophage T72013-11-07T07:03:36Z<p>William Guthrie: </p>
<hr />
<div>===ATP-DEPENDENT DNA LIGASE FROM BACTERIOPHAGE T7===<br />
<StructureSection load='1a0i' size='350' side='right' caption='Structure of Bacteriophage T7 DNA Ligase(PDB entry [[1a0i]])' scene=''><br />
==Overview (General Function)==<br />
<br />
ATP-dependent DNA ligase from bacteriophage T7 (Caudovirales Podoviridae<ref>McGrath S, van Sinderen D. Bacteriophage: ''Genetics and Molecular Biology.'' Norfolk: Caister Academic Press, 2007. Print.</ref>) is used to catalyze a phosphodiester bond between single-strand nicks in double-stranded DNA. This occurs in replication (connecting okazaki fragments)<ref name="Berg">Berg, Jeremy M, Stryer, Lubert, Tymoczko, John L. ''Biochemistry.'' Sixth edition. New York: W.H. Freeman and Company, 2007: 796. Print.</ref>, DNA repair (excision repair), and recombination. DNA ligases require either ATP (eukaryotes and viruses) or NAD+ (prokaryotes) as a cofactor<ref name="Bacteriophage">PMID: 8626651</ref>. All ligases require a divalent cation for function. Bacteriophage T7 DNA ligase uses Magnesium in vivo. A range of pH 7.2-7.7 is ideal for enzymatic activity. T7 ligase has a molecular weight of 41 kDa<ref name="Crystal">PMID: 8653795</ref>.<br />
<br />
<br />
<br />
<br />
== Structure ==<br />
<br />
ATP-dependent DNA ligase from bacteriophage T7 is monomeric, forming a tertiary structure consisting of two domains (domain 1 and domain 2). <scene name='56/567310/Domain_1/1'>Domain 1</scene> (residues 2:240) contains the ATP binding site. Domain 1 is composed of six alpha helices which surround three antiparallel Beta sheets. <br />
<scene name='56/567310/Domain_2/1'>Domain 2</scene> (residues 241:349) is composed of an antiparallel Beta sheet and an alpha helix<ref name="Crystal"/>. A groove is formed between the two domains; this groove allows ATP to bind with domain 1. The ribose ring of ATP forms hydrogen bonds with the side chains of <scene name='56/567310/Arg_39_arg_55_glu_93/1'>Arg-39, Arg-55, and Glu-93</scene>. <scene name='56/567310/Lys232_lys238_lys34/2'>Lys-232, Lys-238, and Lys-34</scene> (the catalytic residue) form hydrogen bonds with the three phosphoryl groups of ATP. The 6-amino group of the adenine ring creates hydrogen bonds with the <scene name='56/567310/Ile_33_glu_32/1'>main-chain carbonyl of Ile-33 and the side chain of Glu-32</scene><ref name="Crystal"/>. This could account for the use of ATP rather than GTP. While consisting of 359 residues, residues 121-127, 307-316, and 350-359 are not easily deciphered from the crystalline structure, and are therefore left out of the diagram<ref name="Crystal"/>. Domain 1 contains the N terminus, while domain 2 contains the C terminus. Multiple N and C terminii are shown in the diagram due to the missing residues.<br />
<br />
<br />
<br />
<br />
==Catalytic function with DNA==<br />
<br />
ATP-dependent DNA ligase from bacteriophage T7 amends a fractured DNA strand through esterification of a 5'- phosphoryl to a 3'- hydroxyl group<ref name="Bacteriophage"/>. This mechanism occurs with the aid of ATP in several steps. First, the ligase is activated through a <scene name='56/567310/Amp_complex/1'>phosphoramidate bond with a lysine residue</scene> in the active site (Lys 34). A pyrophosphate leaves and the enzyme-AMP complex is formed. Next, the AMP is transferred to the 5' phosphate group at the nick in the DNA. Finally, T7 ligase creates the phosphodiester bond between the 5' -phosphoryl and the 3' – hydroxyl group, with AMP being freed<ref name="Crystal"/>. All ATP-dependent DNA ligases contain a conserved amino acid sequence of <scene name='56/567310/Residues_34-39/1'>KxDGxR</scene><ref name="Bacteriophage"/>. This includes the lysine residue which binds the ATP in the groove between the two domains.<br />
<br />
</StructureSection><br />
<br />
<br />
==References==<br />
<references/></div>William Guthriehttps://proteopedia.org/index.php?title=ATP-dependent_DNA_ligase_from_bacteriophage_T7&diff=1861820ATP-dependent DNA ligase from bacteriophage T72013-11-07T05:23:11Z<p>William Guthrie: </p>
<hr />
<div>===ATP-DEPENDENT DNA LIGASE FROM BACTERIOPHAGE T7===<br />
<StructureSection load='1a0i' size='350' side='right' caption='Structure of Bacteriophage T7 DNA Ligase(PDB entry [[1a0i]])' scene=''><br />
==Overview (General Function)==<br />
<br />
ATP-dependent DNA ligase from bacteriophage T7 (Caudovirales Podoviridae<ref>McGrath S, van Sinderen D. Bacteriophage: ''Genetics and Molecular Biology.'' Norfolk: Caister Academic Press, 2007. Print.</ref>) is used to catalyze a phosphodiester bond between single-strand nicks in double-stranded DNA. This occurs in replication (connecting okazaki fragments)<ref name="Berg">Berg, Jeremy M, Stryer, Lubert, Tymoczko, John L. ''Biochemistry.'' Sixth edition. New York: W.H. Freeman and Company, 2007: 796. Print.</ref>, DNA repair (excision repair), and recombination. DNA ligases require either ATP (eukaryotes and viruses) or NAD+ (prokaryotes) as a cofactor<ref name="Bacteriophage">PMID: 8626651</ref>. All ligases require a divalent cation for function. Bacteriophage T7 DNA ligase uses Magnesium in vivo. A range of pH 7.2-7.7 is ideal for enzymatic activity. T7 ligase has a molecular weight of 41 kDa<ref name="Crystal">PMID: 8653795</ref>.<br />
<br />
<br />
<br />
<br />
== Structure ==<br />
<br />
ATP-dependent DNA ligase from bacteriophage T7 is monomeric, forming a tertiary structure consisting of two domains (domain 1 and domain 2). Domain 1 (residues 2:240) contains the ATP binding site. Domain 1 is composed of six alpha helices which surround three antiparallel Beta sheets. Domain 2 (residues 241:349) is composed of an antiparallel Beta sheet and an alpha helix<ref name="Crystal"/>. A groove is formed between the two domains; this groove allows ATP to bind with domain 1. The ribose ring of ATP forms hydrogen bonds with the side chains of <scene name='56/567310/Arg_39_arg_55_glu_93/1'>Arg-39, Arg-55, and Glu-93</scene>. <scene name='56/567310/Lys232_lys238_lys34/2'>Lys-232, Lys-238, and Lys-34</scene> (the catalytic residue) form hydrogen bonds with the three phosphoryl groups of ATP. The 6-amino group of the adenine ring creates hydrogen bonds with the main-chain carbonyl of Ile-33 and the side chain of Glu-32<ref name="Crystal"/>. This could account for the use of ATP rather than GTP. While consisting of 359 residues, residues 121-127, 307-316, and 350-359 are not easily deciphered from the crystalline structure, and are therefore left out of the diagram<ref name="Crystal"/>. Domain 1 contains the N terminus, while domain 2 contains the C terminus. Multiple N and C terminii are shown in the diagram due to the missing residues.<br />
<br />
<br />
<br />
<br />
==Catalytic function with DNA==<br />
<br />
ATP-dependent DNA ligase from bacteriophage T7 amends a fractured DNA strand through esterification of a 5'- phosphoryl to a 3'- hydroxyl group<ref name="Bacteriophage"/>. This mechanism occurs with the aid of ATP in several steps. First, the ligase is activated through a <scene name='56/567310/Amp_complex/1'>phosphoramidate bond with a lysine residue</scene> in the active site (Lys 34). A pyrophosphate leaves and the enzyme-AMP complex is formed. Next, the AMP is transferred to the 5' phosphate group at the nick in the DNA. Finally, T7 ligase creates the phosphodiester bond between the 5' -phosphoryl and the 3' – hydroxyl group, with AMP being freed<ref name="Crystal"/>. All ATP-dependent DNA ligases contain a conserved amino acid sequence of KxDGxR<ref name="Bacteriophage"/>. This includes the lysine residue which binds the ATP in the groove between the two domains.<br />
<br />
</StructureSection><br />
<br />
<br />
==References==<br />
<references/></div>William Guthriehttps://proteopedia.org/index.php?title=ATP-dependent_DNA_ligase_from_bacteriophage_T7&diff=1861800ATP-dependent DNA ligase from bacteriophage T72013-11-07T03:38:12Z<p>William Guthrie: </p>
<hr />
<div>===ATP-DEPENDENT DNA LIGASE FROM BACTERIOPHAGE T7===<br />
<StructureSection load='1a0i' size='350' side='right' caption='Structure of Bacteriophage T7 DNA Ligase(PDB entry [[1a0i]])' scene=''><br />
==Overview (General Function)==<br />
<br />
ATP-dependent DNA ligase from bacteriophage T7 (Caudovirales Podoviridae<ref>McGrath S, van Sinderen D. Bacteriophage: ''Genetics and Molecular Biology.'' Norfolk: Caister Academic Press, 2007. Print.</ref>) is used to catalyze a phosphodiester bond between single-strand nicks in double-stranded DNA. This occurs in replication (connecting okazaki fragments)<ref name="Berg">Berg, Jeremy M, Stryer, Lubert, Tymoczko, John L. ''Biochemistry.'' Sixth edition. New York: W.H. Freeman and Company, 2007: 796. Print.</ref>, DNA repair (excision repair), and recombination. DNA ligases require either ATP (eukaryotes and viruses) or NAD+ (prokaryotes) as a cofactor. All ligases require a divalent cation for function. Bacteriophage T7 DNA ligase uses Magnesium in vivo. A range of pH 7.2-7.7 is ideal for enzymatic activity. T7 ligase has a molecular weight of 41 kDa<ref>PMID: 8653795</ref>.<br />
<br />
<br />
<br />
<br />
== Structure ==<br />
<br />
ATP-dependent DNA ligase from bacteriophage T7 is monomeric, forming a tertiary structure consisting of two domains (domain 1 and domain 2). Domain 1 (residues 2:240) contains the ATP binding site. Domain 1 is composed of six alpha helices which surround three antiparallel Beta sheets. Domain 2 (residues 241:349) is composed of an antiparallel Beta sheet and an alpha helix. A groove is formed between the two domains; this groove allows ATP to bind with domain 1. The ribose ring of ATP forms hydrogen bonds with the side chains of <scene name='56/567310/Arg_39_arg_55_glu_93/1'>Arg-39, Arg-55, and Glu-93</scene>. <scene name='56/567310/Lys232_lys238_lys34/2'>Lys-232, Lys-238, and Lys-34</scene> (the catalytic residue) form hydrogen bonds with the three phosphoryl groups of ATP. The 6-amino group of the adenine ring creates hydrogen bonds with the main-chain carbonyl of Ile-33 and the side chain of Glu-32. This could account for the use of ATP rather than GTP. While consisting of 359 residues, residues 121-127, 307-316, and 350-359 are not easily deciphered from the crystalline structure, and are therefore left out of the diagram. Domain 1 contains the N terminus, while domain 2 contains the C terminus. Multiple N and C terminii are shown in the diagram due to the missing residues.<br />
<br />
<br />
<br />
<br />
==Catalytic function with DNA==<br />
<br />
ATP-dependent DNA ligase from bacteriophage T7 amends a fractured DNA strand through esterification of a 5'- phosphoryl to a 3'- hydroxyl group. This mechanism occurs with the aid of ATP in several steps. First, the ligase is activated through a <scene name='56/567310/Amp_complex/1'>phosphoramidate bond with a lysine residue</scene> in the active site (Lys 34). A pyrophosphate leaves and the enzyme-AMP complex is formed. Next, the AMP is transferred to the 5' phosphate group at the nick in the DNA. Finally, T7 ligase creates the phosphodiester bond between the 5' -phosphoryl and the 3' – hydroxyl group, with AMP being freed. All ATP-dependent DNA ligases contain a conserved amino acid sequence of KxDGxR<ref>PMID: 8626651</ref>. This includes the lysine residue which binds the ATP in the groove between the two domains.<br />
<br />
</StructureSection><br />
<br />
<br />
==References==<br />
<references/></div>William Guthriehttps://proteopedia.org/index.php?title=ATP-dependent_DNA_ligase_from_bacteriophage_T7&diff=1861777ATP-dependent DNA ligase from bacteriophage T72013-11-07T02:47:32Z<p>William Guthrie: </p>
<hr />
<div>===ATP-DEPENDENT DNA LIGASE FROM BACTERIOPHAGE T7===<br />
<StructureSection load='1a0i' size='350' side='right' caption='Structure of Bacteriophage T7 DNA Ligase(PDB entry [[1a0i]])' scene=''><br />
==Overview (General Function)==<br />
<br />
ATP-dependent DNA ligase from bacteriophage T7 (Caudovirales Podoviridae) is used to catalyze a phosphodiester bond between single-strand nicks in double-stranded DNA. This occurs in replication (connecting okazaki fragments)<ref name="Berg">Berg, Jeremy M, Stryer, Lubert, Tymoczko, John L. ''Biochemistry.'' Sixth edition. New York: W.H. Freeman and Company, 2007: 796. Print.</ref>, DNA repair (excision repair), and recombination. DNA ligases require either ATP (eukaryotes and viruses) or NAD+ (prokaryotes) as a cofactor. All ligases require a divalent cation for function. Bacteriophage T7 DNA ligase uses Magnesium in vivo. A range of pH 7.2-7.7 is ideal for enzymatic activity. T7 ligase has a molecular weight of 41 kDa<ref>PMID: 8653795</ref>.<br />
<br />
<br />
<br />
<br />
== Structure ==<br />
<br />
ATP-dependent DNA ligase from bacteriophage T7 is monomeric, forming a tertiary structure consisting of two domains (domain 1 and domain 2). Domain 1 (residues 2:240) contains the ATP binding site. Domain 1 is composed of six alpha helices which surround three antiparallel Beta sheets. Domain 2 (residues 241:349) is composed of an antiparallel Beta sheet and an alpha helix. A groove is formed between the two domains; this groove allows ATP to bind with domain 1. The ribose ring of ATP forms hydrogen bonds with the side chains of <scene name='56/567310/Arg_39_arg_55_glu_93/1'>Arg-39, Arg-55, and Glu-93</scene>. <scene name='56/567310/Lys232_lys238_lys34/2'>Lys-232, Lys-238, and Lys-34</scene> (the catalytic residue) form hydrogen bonds with the three phosphoryl groups of ATP. The 6-amino group of the adenine ring creates hydrogen bonds with the main-chain carbonyl of Ile-33 and the side chain of Glu-32. This could account for the use of ATP rather than GTP. While consisting of 359 residues, residues 121-127, 307-316, and 350-359 are not easily deciphered from the crystalline structure, and are therefore left out of the diagram. Domain 1 contains the N terminus, while domain 2 contains the C terminus. Multiple N and C terminii are shown in the diagram due to the missing residues.<br />
<br />
<br />
<br />
<br />
==Catalytic function with DNA==<br />
<br />
ATP-dependent DNA ligase from bacteriophage T7 amends a fractured DNA strand through esterification of a 5'- phosphoryl to a 3'- hydroxyl group. This mechanism occurs with the aid of ATP in several steps. First, the ligase is activated through a <scene name='56/567310/Amp_complex/1'>phosphoramidate bond with a lysine residue</scene> in the active site (Lys 34). A pyrophosphate leaves and the enzyme-AMP complex is formed. Next, the AMP is transferred to the 5' phosphate group at the nick in the DNA. Finally, T7 ligase creates the phosphodiester bond between the 5' -phosphoryl and the 3' – hydroxyl group, with AMP being freed. All ATP-dependent DNA ligases contain a conserved amino acid sequence of KxDGxR<ref>PMID: 8626651</ref>. This includes the lysine residue which binds the ATP in the groove between the two domains.<br />
<br />
</StructureSection><br />
<br />
<br />
==References==<br />
<references/></div>William Guthriehttps://proteopedia.org/index.php?title=ATP-dependent_DNA_ligase_from_bacteriophage_T7&diff=1861775ATP-dependent DNA ligase from bacteriophage T72013-11-07T02:35:50Z<p>William Guthrie: </p>
<hr />
<div>===ATP-DEPENDENT DNA LIGASE FROM BACTERIOPHAGE T7===<br />
<StructureSection load='1a0i' size='350' side='right' caption='Structure of Bacteriophage T7 DNA Ligase(PDB entry [[1a0i]])' scene=''><br />
==Overview (General Function)==<br />
<br />
ATP-dependent DNA ligase from bacteriophage T7 (Caudovirales Podoviridae) is used to catalyze a phosphodiester bond between single-strand nicks in double-stranded DNA. This occurs in replication (connecting okazaki fragments)<ref name="Berg">Berg, Jeremy M, Stryer, Lubert, Tymoczko, John L. ''Biochemistry.'' Sixth edition. New York: W.H. Freeman and Company, 2007: 796. Print.</ref>, DNA repair (excision repair), and recombination. DNA ligases require either ATP (eukaryotes and viruses) or NAD+ (prokaryotes) as a cofactor. All ligases require a divalent cation for function. Bacteriophage T7 DNA ligase uses Magnesium in vivo. A range of pH 7.2-7.7 is ideal for enzymatic activity. T7 ligase has a molecular weight of 41 kDa<ref>PMID: 8653795</ref>.<br />
<br />
<br />
<br />
<br />
== Structure ==<br />
<br />
ATP-dependent DNA ligase from bacteriophage T7 is monomeric, forming a tertiary structure consisting of two domains (domain 1 and domain 2). Domain 1 (residues 2:240) contains the ATP binding site. Domain 1 is composed of six alpha helices which surround three antiparallel Beta sheets. Domain 2 (residues 241:349) is composed of an antiparallel Beta sheet and an alpha helix. A groove is formed between the two domains; this groove allows ATP to bind with domain 1. The ribose ring of ATP forms hydrogen bonds with the side chains of <scene name='56/567310/Arg_39_arg_55_glu_93/1'>Arg-39, Arg-55, and Glu-93</scene>. <scene name='56/567310/Lys232_lys238_lys34/2'>Lys-232, Lys-238, and Lys-34</scene> (the catalytic residue) form hydrogen bonds with the three phosphoryl groups of ATP. The 6-amino group of the adenine ring creates hydrogen bonds with the main-chain carbonyl of Ile-33 and the side chain of Glu-32. This could account for the use of ATP rather than GTP. While consisting of 359 residues, residues 121-127, 307-316, and 350-359 are not easily deciphered from the crystalline structure, and are therefore left out of the diagram. Domain 1 contains the N terminus, while domain 2 contains the C terminus. Multiple N and C terminii are shown in the diagram due to the missing residues.<br />
<br />
<br />
<br />
<br />
==Catalytic function with DNA==<br />
<br />
ATP-dependent DNA ligase from bacteriophage T7 amends a fractured DNA strand through esterification of a 5'- phosphoryl to a 3'- hydroxyl group. This mechanism occurs with the aid of ATP in several steps. First, the ligase is activated through a <scene name='56/567310/Amp_complex/1'>phosphoramidate bond with a lysine residue</scene> in the active site (Lys 34). A pyrophosphate leaves and the enzyme-AMP complex is formed. Next, the AMP is transferred to the 5' phosphate group at the nick in the DNA. Finally, T7 ligase creates the phosphodiester bond between the 5' -phosphoryl and the 3' – hydroxyl group, with AMP being freed. All ATP-dependent DNA ligases contain a conserved amino acid sequence of KxDGxR. This includes the lysine residue which binds the ATP in the groove between the two domains.<br />
<br />
</StructureSection><br />
<br />
<br />
==References==<br />
<references/></div>William Guthriehttps://proteopedia.org/index.php?title=ATP-dependent_DNA_ligase_from_bacteriophage_T7&diff=1861770ATP-dependent DNA ligase from bacteriophage T72013-11-07T02:04:51Z<p>William Guthrie: </p>
<hr />
<div>===ATP-DEPENDENT DNA LIGASE FROM BACTERIOPHAGE T7===<br />
<StructureSection load='1a0i' size='350' side='right' caption='Structure of Bacteriophage T7 DNA Ligase(PDB entry [[1a0i]])' scene=''><br />
==Overview (General Function)==<br />
<br />
ATP-dependent DNA ligase from bacteriophage T7 (Caudovirales Podoviridae) is used to catalyze a phosphodiester bond between single-strand nicks in double-stranded DNA. This occurs in replication (connecting okazaki fragments)<ref name="Berg">Berg, Jeremy M, Stryer, Lubert, Tymoczko, John L. ''Biochemistry.'' Sixth edition. New York: W.H. Freeman and Company, 2007: 796. Print.</ref>, DNA repair (excision repair), and recombination. DNA ligases require either ATP (eukaryotes and viruses) or NAD+ (prokaryotes) as a cofactor. All ligases require a divalent cation for function. Bacteriophage T7 DNA ligase uses Magnesium in vivo. A range of pH 7.2-7.7 is ideal for enzymatic activity. T7 ligase has a molecular weight of 41 kDa.<br />
<br />
<br />
<br />
<br />
== Structure ==<br />
<br />
ATP-dependent DNA ligase from bacteriophage T7 is monomeric, forming a tertiary structure consisting of two domains (domain 1 and domain 2). Domain 1 (residues 2:240) contains the ATP binding site. Domain 1 is composed of six alpha helices which surround three antiparallel Beta sheets. Domain 2 (residues 241:349) is composed of an antiparallel Beta sheet and an alpha helix. A groove is formed between the two domains; this groove allows ATP to bind with domain 1. The ribose ring of ATP forms hydrogen bonds with the side chains of <scene name='56/567310/Arg_39_arg_55_glu_93/1'>Arg-39, Arg-55, and Glu-93</scene>. <scene name='56/567310/Lys232_lys238_lys34/2'>Lys-232, Lys-238, and Lys-34</scene> (the catalytic residue) form hydrogen bonds with the three phosphoryl groups of ATP. The 6-amino group of the adenine ring creates hydrogen bonds with the main-chain carbonyl of Ile-33 and the side chain of Glu-32. This could account for the use of ATP rather than GTP. While consisting of 359 residues, residues 121-127, 307-316, and 350-359 are not easily deciphered from the crystalline structure, and are therefore left out of the diagram. Domain 1 contains the N terminus, while domain 2 contains the C terminus. Multiple N and C terminii are shown in the diagram due to the missing residues.<br />
<br />
<br />
<br />
<br />
==Catalytic function with DNA==<br />
<br />
ATP-dependent DNA ligase from bacteriophage T7 amends a fractured DNA strand through esterification of a 5'- phosphoryl to a 3'- hydroxyl group. This mechanism occurs with the aid of ATP in several steps. First, the ligase is activated through a <scene name='56/567310/Amp_complex/1'>phosphoramidate bond with a lysine residue</scene> in the active site (Lys 34). A pyrophosphate leaves and the enzyme-AMP complex is formed. Next, the AMP is transferred to the 5' phosphate group at the nick in the DNA. Finally, T7 ligase creates the phosphodiester bond between the 5' -phosphoryl and the 3' – hydroxyl group, with AMP being freed. All ATP-dependent DNA ligases contain a conserved amino acid sequence of KxDGxR. This includes the lysine residue which binds the ATP in the groove between the two domains.<br />
<br />
</StructureSection><br />
<br />
<br />
==References==<br />
<references/></div>William Guthriehttps://proteopedia.org/index.php?title=ATP-dependent_DNA_ligase_from_bacteriophage_T7&diff=1861767ATP-dependent DNA ligase from bacteriophage T72013-11-07T01:32:34Z<p>William Guthrie: </p>
<hr />
<div>===ATP-DEPENDENT DNA LIGASE FROM BACTERIOPHAGE T7===<br />
<StructureSection load='1a0i' size='350' side='right' caption='Structure of Bacteriophage T7 DNA Ligase(PDB entry [[1a0i]])' scene=''><br />
==Overview (General Function)==<br />
<br />
ATP-dependent DNA ligase from bacteriophage T7 (Caudovirales Podoviridae) is used to catalyze a phosphodiester bond between single-strand nicks in double-stranded DNA. This occurs in replication (connecting okazaki fragments), DNA repair (excision repair), and recombination. DNA ligases require either ATP (eukaryotes and viruses) or NAD+ (prokaryotes) as a cofactor. All ligases require a divalent cation for function. Bacteriophage T7 DNA ligase uses Magnesium in vivo. A range of pH 7.2-7.7 is ideal for enzymatic activity. T7 ligase has a molecular weight of 41 kDa.<br />
<br />
<br />
<br />
<br />
== Structure ==<br />
<br />
ATP-dependent DNA ligase from bacteriophage T7 is monomeric, forming a tertiary structure consisting of two domains (domain 1 and domain 2). Domain 1 (residues 2:240) contains the ATP binding site. Domain 1 is composed of six alpha helices which surround three antiparallel Beta sheets. Domain 2 (residues 241:349) is composed of an antiparallel Beta sheet and an alpha helix. A groove is formed between the two domains; this groove allows ATP to bind with domain 1. The ribose ring of ATP forms hydrogen bonds with the side chains of <scene name='56/567310/Arg_39_arg_55_glu_93/1'>Arg-39, Arg-55, and Glu-93</scene>. <scene name='56/567310/Lys232_lys238_lys34/2'>Lys-232, Lys-238, and Lys-34</scene> (the catalytic residue) form hydrogen bonds with the three phosphoryl groups of ATP. The 6-amino group of the adenine ring creates hydrogen bonds with the main-chain carbonyl of Ile-33 and the side chain of Glu-32. This could account for the use of ATP rather than GTP. While consisting of 359 residues, residues 121-127, 307-316, and 350-359 are not easily deciphered from the crystalline structure, and are therefore left out of the diagram. Domain 1 contains the N terminus, while domain 2 contains the C terminus. Multiple N and C terminii are shown in the diagram due to the missing residues.<br />
<br />
<br />
<br />
<br />
==Catalytic function with DNA==<br />
<br />
ATP-dependent DNA ligase from bacteriophage T7 amends a fractured DNA strand through esterification of a 5'- phosphoryl to a 3'- hydroxyl group. This mechanism occurs with the aid of ATP in several steps. First, the ligase is activated through a <scene name='56/567310/Amp_complex/1'>phosphoramidate bond with a lysine residue</scene> in the active site (Lys 34). A pyrophosphate leaves and the enzyme-AMP complex is formed. Next, the AMP is transferred to the 5' phosphate group at the nick in the DNA. Finally, T7 ligase creates the phosphodiester bond between the 5' -phosphoryl and the 3' – hydroxyl group, with AMP being freed. All ATP-dependent DNA ligases contain a conserved amino acid sequence of KxDGxR. This includes the lysine residue which binds the ATP in the groove between the two domains.<br />
<br />
</StructureSection><br />
<br />
<br />
==References==<br />
<references/></div>William Guthriehttps://proteopedia.org/index.php?title=ATP-dependent_DNA_ligase_from_bacteriophage_T7&diff=1861766ATP-dependent DNA ligase from bacteriophage T72013-11-07T01:27:21Z<p>William Guthrie: /* ATP-DEPENDENT DNA LIGASE FROM BACTERIOPHAGE T7 */</p>
<hr />
<div>===ATP-DEPENDENT DNA LIGASE FROM BACTERIOPHAGE T7===<br />
<StructureSection load='1a0i' size='350' side='right' caption='Structure of Bacteriophage T7 DNA Ligase(PDB entry [[1a0i]])' scene=''><br />
==Overview (General Function)==<br />
<br />
ATP-dependent DNA ligase from bacteriophage T7 (Caudovirales Podoviridae) is used to catalyze a phosphodiester bond between single-strand nicks in double-stranded DNA. This occurs in replication (connecting okazaki fragments), DNA repair (excision repair), and recombination. DNA ligases require either ATP (eukaryotes and viruses) or NAD+ (prokaryotes) as a cofactor. All ligases require a divalent cation for function. Bacteriophage T7 DNA ligase uses Magnesium in vivo. A range of pH 7.2-7.7 is ideal for enzymatic activity. T7 ligase has a molecular weight of 41 kDa.<br />
<br />
<br />
<br />
<br />
== Structure ==<br />
<br />
ATP-dependent DNA ligase from bacteriophage T7 is monomeric, forming a tertiary structure consisting of two domains (domain 1 and domain 2). Domain 1 (residues 2:240) contains the ATP binding site. Domain 1 is composed of six alpha helices which surround three antiparallel Beta sheets. Domain 2 (residues 241:349) is composed of an antiparallel Beta sheet and an alpha helix. A groove is formed between the two domains; this groove allows ATP to bind with domain 1. The ribose ring of ATP forms hydrogen bonds with the side chains of <scene name='56/567310/Arg_39_arg_55_glu_93/1'>Arg-39, Arg-55, and Glu-93</scene>. <scene name='56/567310/Lys232_lys238_lys34/2'>Lys-232, Lys-238, and Lys-34</scene> (the catalytic residue) form hydrogen bonds with the three phosphoryl groups of ATP. The 6-amino group of the adenine ring creates hydrogen bonds with the main-chain carbonyl of Ile-33 and the side chain of Glu-32. This could account for the use of ATP rather than GTP. While consisting of 359 residues, residues 121-127, 307-316, and 350-359 are not easily deciphered from the crystalline structure, and are therefore left out of the diagram. Domain 1 contains the N terminus, while domain 2 contains the C terminus. Multiple N and C terminii are shown in the diagram due to the missing residues.<br />
<br />
<br />
<br />
<br />
==Catalytic function with DNA==<br />
<br />
ATP-dependent DNA ligase from bacteriophage T7 amends a fractured DNA strand through esterification of a 5'- phosphoryl to a 3'- hydroxyl group. This mechanism occurs with the aid of ATP in several steps. First, the ligase is activated through a <scene name='56/567310/Amp_complex/1'>phosphoramidate bond with a lysine residue</scene> in the active site (Lys 34). A pyrophosphate leaves and the enzyme-AMP complex is formed. Next, the AMP is transferred to the 5' phosphate group at the nick in the DNA. Finally, T7 ligase creates the phosphodiester bond between the 5' -phosphoryl and the 3' – hydroxyl group, with AMP being freed. All ATP-dependent DNA ligases contain a conserved amino acid sequence of KxDGxR. This includes the lysine residue which binds the ATP in the groove between the two domains.<br />
<br />
</StructureSection></div>William Guthriehttps://proteopedia.org/index.php?title=ATP-dependent_DNA_ligase_from_bacteriophage_T7&diff=1861725ATP-dependent DNA ligase from bacteriophage T72013-11-06T23:14:15Z<p>William Guthrie: </p>
<hr />
<div>===ATP-DEPENDENT DNA LIGASE FROM BACTERIOPHAGE T7===<br />
<StructureSection load='1a0i' size='350' side='right' caption='Structure of Bacteriophage T7 DNA Ligase(PDB entry [[1a0i]])' scene=''><br />
'''Overview (General Function)'''<br />
<br />
ATP-dependent DNA ligase from bacteriophage T7 (Caudovirales Podoviridae) is used to catalyze a phosphodiester bond between single-strand nicks in double-stranded DNA. This occurs in replication (connecting okazaki fragments), DNA repair (excision repair), and recombination. DNA ligases require either ATP (eukaryotes and viruses) or NAD+ (prokaryotes) as a cofactor. All ligases require a divalent cation for function. Bacteriophage T7 DNA ligase uses Magnesium in vivo. A range of pH 7.2-7.7 is ideal for enzymatic activity. T7 ligase has a molecular weight of 41 kDa.<br />
<br />
<br />
<br />
<br />
'''Structure'''<br />
<br />
ATP-dependent DNA ligase from bacteriophage T7 is monomeric, forming a tertiary structure consisting of two domains (domain 1 and domain 2). Domain 1 (residues 2:240) contains the ATP binding site. Domain 1 is composed of six alpha helices which surround three antiparallel Beta sheets. Domain 2 (residues 241:349) is composed of an antiparallel Beta sheet and an alpha helix. A groove is formed between the two domains; this groove allows ATP to bind with domain 1. The ribose ring of ATP forms hydrogen bonds with the side chains of <scene name='56/567310/Arg_39_arg_55_glu_93/1'>Arg-39, Arg-55, and Glu-93</scene>. <scene name='56/567310/Lys232_lys238_lys34/2'>Lys-232, Lys-238, and Lys-34</scene> (the catalytic residue) form hydrogen bonds with the three phosphoryl groups of ATP. The 6-amino group of the adenine ring creates hydrogen bonds with the main-chain carbonyl of Ile-33 and the side chain of Glu-32. This could account for the use of ATP rather than GTP. While consisting of 359 residues, residues 121-127, 307-316, and 350-359 are not easily deciphered from the crystalline structure, and are therefore left out of the diagram. Domain 1 contains the N terminus, while domain 2 contains the C terminus. Multiple N and C terminii are shown in the diagram due to the missing residues.<br />
<br />
<br />
<br />
<br />
'''Catalytic function with DNA'''<br />
<br />
ATP-dependent DNA ligase from bacteriophage T7 amends a fractured DNA strand through esterification of a 5'- phosphoryl to a 3'- hydroxyl group. This mechanism occurs with the aid of ATP in several steps. First, the ligase is activated through a <scene name='56/567310/Amp_complex/1'>phosphoramidate bond with a lysine residue</scene> in the active site (Lys 34). A pyrophosphate leaves and the enzyme-AMP complex is formed. Next, the AMP is transferred to the 5' phosphate group at the nick in the DNA. Finally, T7 ligase creates the phosphodiester bond between the 5' -phosphoryl and the 3' – hydroxyl group, with AMP being freed. All ATP-dependent DNA ligases contain a conserved amino acid sequence of KxDGxR. This includes the lysine residue which binds the ATP in the groove between the two domains.<br />
<br />
</StructureSection></div>William Guthriehttps://proteopedia.org/index.php?title=ATP-dependent_DNA_ligase_from_bacteriophage_T7&diff=1861723ATP-dependent DNA ligase from bacteriophage T72013-11-06T23:04:43Z<p>William Guthrie: </p>
<hr />
<div>===ATP-DEPENDENT DNA LIGASE FROM BACTERIOPHAGE T7===<br />
<StructureSection load='1a0i' size='350' side='right' caption='Structure of Bacteriophage T7 DNA Ligase(PDB entry [[1a0i]])' scene=''><br />
'''Overview (General Function)'''<br />
<br />
ATP-dependent DNA ligase from bacteriophage T7 (Caudovirales Podoviridae) is used to catalyze a phosphodiester bond between single-strand nicks in double-stranded DNA. This occurs in replication (connecting okazaki fragments), DNA repair (excision repair), and recombination. DNA ligases require either ATP (eukaryotes and viruses) or NAD+ (prokaryotes) as a cofactor. All ligases require a divalent cation for function. Bacteriophage T7 DNA ligase uses Magnesium in vivo. A range of pH 7.2-7.7 is ideal for enzymatic activity. T7 ligase has a molecular weight of 41 kDa.<br />
<br />
<br />
<br />
<br />
'''Sructure'''<br />
<br />
ATP-dependent DNA ligase from bacteriophage T7 is monomeric, forming a tertiary structure consisting of two domains (domain 1 and domain 2). Domain 1 (residues 2:240) contains the ATP binding site. Domain 1 is composed of six alpha helices which surround three antiparallel Beta sheets. Domain 2 (residues 241:349) is composed of an antiparallel Beta sheet and an alpha helix. A groove is formed between the two domains; this groove allows ATP to bind with domain 1. The ribose ring of ATP forms hydrogen bonds with the side chains of <scene name='56/567310/Arg_39_arg_55_glu_93/1'>Arg-39, Arg-55, and Glu-93</scene>. <scene name='56/567310/Lys232_lys238_lys34/2'>Lys-232, Lys-238, and Lys-34</scene> (the catalytic residue) form hydrogen bonds with the three phosphoryl groups of ATP. The 6-amino group of the adenine ring creates hydrogen bonds with the main-chain carbonyl of Ile-33 and the side chain of Glu-32. This could account for the use of ATP rather than GTP. While consisting of 359 residues, residues 121-127, 307-316, and 350-359 are not easily deciphered from the crystalline structure, and are therefore left out of the diagram. Domain 1 contains the N terminus, while domain 2 contains the C terminus. Multiple N and C terminii are shown in the diagram due to the missing residues.<br />
<br />
<br />
<br />
<br />
'''Catalytic function with DNA'''<br />
<br />
ATP-dependent DNA ligase from bacteriophage T7 amends a fractured DNA strand through esterification of a 5'- phosphoryl to a 3'- hydroxyl group. This mechanism occurs with the aid of ATP in several steps. First, the ligase is activated through a <scene name='56/567310/Amp_complex/1'>phosphoramidate bond with a lysine residue</scene> in the active site (Lys 34). A pyrophosphate leaves and the enzyme-AMP complex is formed. Next, the AMP is transferred to the 5' phosphate group at the nick in the DNA. Finally, T7 ligase creates the phosphodiester bond between the 5' -phosphoryl and the 3' – hydroxyl group, with AMP being freed. All ATP-dependent DNA ligases contain a conserved amino acid sequence of KxDGxR. This includes the lysine residue which binds the ATP in the groove between the two domains.<br />
<br />
</StructureSection></div>William Guthriehttps://proteopedia.org/index.php?title=ATP-dependent_DNA_ligase_from_bacteriophage_T7&diff=1859795ATP-dependent DNA ligase from bacteriophage T72013-11-05T15:15:13Z<p>William Guthrie: New page: ===ATP-DEPENDENT DNA LIGASE FROM BACTERIOPHAGE T7=== <StructureSection load='1a0i' size='350' side='right' caption='Structure of Bacteriophage T7 DNA Ligase(PDB entry 1a0i)' scene=''> ...</p>
<hr />
<div>===ATP-DEPENDENT DNA LIGASE FROM BACTERIOPHAGE T7===<br />
<StructureSection load='1a0i' size='350' side='right' caption='Structure of Bacteriophage T7 DNA Ligase(PDB entry [[1a0i]])' scene=''><br />
Overview (General Function)<br />
<br />
ATP-dependent DNA ligase from bacteriophage T7 (Caudovirales Podoviridae) is used to catalyze a phosphodiester bond between single-strand nicks in double-stranded DNA. This occurs in replication (connecting okazaki fragments), DNA repair (excision repair), and recombination. DNA ligases require either ATP (eukaryotes and viruses) or NAD+ (prokaryotes) as a cofactor. All ligases require a divalent cation for function. Bacteriophage T7 DNA ligase uses Magnesium in vivo. A range of pH 7.2-7.7 is ideal for enzymatic activity. T7 ligase has a molecular weight of 41 kDa.<br />
<br />
<br />
<br />
<br />
Sructure<br />
<br />
ATP-dependent DNA ligase from bacteriophage T7 is monomeric, forming a tertiary structure consisting of two domains (domain 1 and domain 2). Domain 1 (residues 2:240) contains the ATP binding site. Domain 1 is composed of six alpha helices which surround three antiparallel Beta sheets. Domain 2 (residues 241:349) is composed of an antiparallel Beta sheet and an alpha helix. A groove is formed between the two domains; this groove allows ATP to bind with domain 1. The ribose ring of ATP forms hydrogen bonds with the side chains of Arg-39, Arg-55, and Glu-93. Lys-232, Lys-238, and Lys34 (the catalytic residue) form hydrogen bonds with the three phosphoryl groups of ATP. The 6-amino group of the adenine ring creates hydrogen bonds with the main-chain carbonyl of Ile-33 and the side chain of Glu-32. This could account for the use of ATP rather than GTP. While consisting of 359 residues, residues 121-127, 307-316, and 350-359 are not easily deciphered from the crystalline structure, and are therefore left out of the diagram. Domain 1 contains the N terminus, while domain 2 contains the C terminus. Multiple N and C terminii are shown in the diagram due to the missing residues.<br />
<br />
<br />
<br />
<br />
Catalytic function with DNA<br />
<br />
ATP-dependent DNA ligase from bacteriophage T7 amends a fractured DNA strand through esterification of a 5'- phosphoryl to a 3'- hydroxyl group. This mechanism occurs with the aid of ATP in several steps. First, the ligase is activated through a phosphoramidate bond with a lysine residue in the active site (Lys 34). A pyrophosphate leaves and the enzyme-AMP complex is formed. Next, the AMP is transferred to the 5' phosphate group at the nick in the DNA. Finally, T7 ligase creates the phosphodiester bond between the 5' -phosphoryl and the 3' – hydroxyl group, with AMP being freed. All ATP-dependent DNA ligases contain a conserved amino acid sequence of KxDGxR. This includes the lysine residue which binds the ATP in the groove between the two domains.<br />
<br />
</StructureSection></div>William Guthriehttps://proteopedia.org/index.php?title=Sandbox_rna_polymerase&diff=1857165Sandbox rna polymerase2013-10-29T15:37:30Z<p>William Guthrie: New page: == Your Heading Here (maybe something like 'Structure') == <StructureSection load='1qln' size='350' side='right' caption='Structure of HMG-CoA reductase (PDB entry 1qln)' scene=''> Any...</p>
<hr />
<div>== Your Heading Here (maybe something like 'Structure') ==<br />
<StructureSection load='1qln' size='350' side='right' caption='Structure of HMG-CoA reductase (PDB entry [[1qln]])' scene=''><br />
Anything in this section will appear adjacent to the 3D structure and will be scrollable.<br />
<br />
</StructureSection></div>William Guthriehttps://proteopedia.org/index.php?title=Ann_Taylor_sandbox_8&diff=1849680Ann Taylor sandbox 82013-10-09T20:42:47Z<p>William Guthrie: </p>
<hr />
<div>== Adenosine Deaminase ==<br />
<StructureSection load='2ada' size='350' side='right' caption='Structure of Adenosine Deaminase (PDB entry [[2ada]])' scene=''><br />
<br />
<br />
<br />
===ADENOSINE DEAMINASE===<br />
<br />
<br />
Adenosine deaminase is involved in the degradation of purine nucleotides. It is especially active in lympocytes, and mutation of adenosine deaminase results in severe immunodeficiency. Adenosine deaminase contains an eight stranded parallel alpha/beta barrel with the active site in a deep pocket at the beta-barrel COOH-terminal end. <ref>PMID:1925539 </ref> The active site contains a <scene name='36/365336/Zinc_cofactor/2'>zinc cofactor</scene> which coordinates to the 6-hydroxyl of the transition state analogue, 6-hydroxyl, 1,6-dihydropurine ribonucleoside. The zinc is coordinated to three histidine residues and an aspartic acid residue. <br />
<br />
The transition state analogue held in place mostly by polar interactions. The ribose group is close to the opening of the pocket, with the purine portion deeper in the pocket, close to the zinc. Nine hydrogen bonds stabilize the transition state-enzyme complex. <br />
<br />
ADA is very stereoselective for the 6R isomer. This specificity is due to the location of the catalytic zinc, <scene name='36/365336/Asp295_residue/1'>Asp295</scene> and <scene name='36/365336/His_238/1'>His 238</scene>. Interestingly, one face of the purine ring is exposed to polar groups and zinc, while the other face is only exposed to nonpolar residues. The proposed catalytic mechanism has Asp295 act as a general base, while the zinc acts as an electrophile to activate the water molecule. His 238 orients the water and stabilizes the charge of the attacking hydroxide. The protonated <scene name='36/365336/Glutamic_acid_217/1'>Glu217</scene> or the water hydrogen bonded to it could donate or share a proton with the N1 of the substrate.<br />
<br />
<br />
<references/><br />
<br />
</StructureSection></div>William Guthriehttps://proteopedia.org/index.php?title=Ann_Taylor_sandbox_8&diff=1849679Ann Taylor sandbox 82013-10-09T20:34:51Z<p>William Guthrie: </p>
<hr />
<div>== Your Heading Here (maybe something like 'Adenosine Deaminase') ==<br />
<StructureSection load='2ada' size='350' side='right' caption='Structure of Adenosine Deaminase (PDB entry [[2ada]])' scene=''><br />
<br />
<br />
<br />
===ADENOSINE DEAMINASE===<br />
<br />
<br />
Adenosine deaminase is involved in the degradation of purine nucleotides. It is especially active in lympocytes, and mutation of adenosine deaminase results in severe immunodeficiency. Adenosine deaminase contains an eight stranded parallel alpha/beta barrel with the active site in a deep pocket at the beta-barrel COOH-terminal end. <ref>PMID:1925539 </ref> The active site contains a <scene name='36/365336/Zinc_cofactor/2'>zinc cofactor</scene> which coordinates to the 6-hydroxyl of the transition state analogue, 6-hydroxyl, 1,6-dihydropurine ribonucleoside. The zinc is coordinated to three histidine residues and an aspartic acid residue. <br />
<br />
The transition state analogue held in place mostly by polar interactions. The ribose group is close to the opening of the pocket, with the purine portion deeper in the pocket, close to the zinc. Nine hydrogen bonds stabilize the transition state-enzyme complex. <br />
<br />
ADA is very stereoselective for the 6R isomer. This specificity is due to the location of the catalytic zinc, <scene name='36/365336/Asp295_residue/1'>Asp295</scene> and His 238. Interestingly, one face of the purine ring is exposed to polar groups and zinc, while the other face is only exposed to nonpolar residues. The proposed catalytic mechanism has Asp295 act as a general base, while the zinc acts as an electrophile to activate the water molecule. His 238 orients the water and stabilizes the charge of the attacking hydroxide. The protonated <scene name='36/365336/Glutamic_acid_217/1'>Glu217</scene> or the water hydrogen bonded to it could donate or share a proton with the N1 of the substrate.<br />
<br />
<br />
<references/><br />
<br />
</StructureSection></div>William Guthriehttps://proteopedia.org/index.php?title=Ann_Taylor_sandbox_8&diff=1849677Ann Taylor sandbox 82013-10-09T20:27:39Z<p>William Guthrie: </p>
<hr />
<div>== Your Heading Here (maybe something like 'Adenosine Deaminase') ==<br />
<StructureSection load='2ada' size='350' side='right' caption='Structure of Adenosine Deaminase (PDB entry [[2ada]])' scene=''><br />
<br />
<br />
<br />
===ADENOSINE DEAMINASE===<br />
<br />
<br />
Adenosine deaminase is involved in the degradation of purine nucleotides. It is especially active in lympocytes, and mutation of adenosine deaminase results in severe immunodeficiency. Adenosine deaminase contains an eight stranded parallel alpha/beta barrel with the active site in a deep pocket at the beta-barrel COOH-terminal end. <ref>PMID:1925539 </ref> The active site contains a <scene name='36/365336/Zinc_cofactor/2'>zinc cofactor</scene> which coordinates to the 6-hydroxyl of the transition state analogue, 6-hydroxyl, 1,6-dihydropurine ribonucleoside. The zinc is coordinated to three histidine residues and an aspartic acid residue. <br />
<br />
The transition state analogue held in place mostly by polar interactions. The ribose group is close to the opening of the pocket, with the purine portion deeper in the pocket, close to the zinc. Nine hydrogen bonds stabilize the transition state-enzyme complex. <br />
<br />
ADA is very stereoselective for the 6R isomer. This specificity is due to the location of the catalytic zinc, <scene name='36/365336/Asp295_residue/1'>Asp295</scene> and His 238. Interestingly, one face of the purine ring is exposed to polar groups and zinc, while the other face is only exposed to nonpolar residues. The proposed catalytic mechanism has Asp295 act as a general base, while the zinc acts as an electrophile to activate the water molecule. His 238 orients the water and stabilizes the charge of the attacking hydroxide. The protonated Glu217 or the water hydrogen bonded to it could donate or share a proton with the N1 of the substrate.<br />
<br />
<br />
<references/><br />
<br />
</StructureSection></div>William Guthriehttps://proteopedia.org/index.php?title=Ann_Taylor_sandbox_8&diff=1849674Ann Taylor sandbox 82013-10-09T20:19:38Z<p>William Guthrie: </p>
<hr />
<div>== Your Heading Here (maybe something like 'Adenosine Deaminase') ==<br />
<StructureSection load='2ada' size='350' side='right' caption='Structure of Adenosine Deaminase (PDB entry [[2ada]])' scene=''><br />
<br />
<br />
<br />
===ADENOSINE DEAMINASE===<br />
<br />
<br />
Adenosine deaminase is involved in the degradation of purine nucleotides. It is especially active in lympocytes, and mutation of adenosine deaminase results in severe immunodeficiency. Adenosine deaminase contains an eight stranded parallel alpha/beta barrel with the active site in a deep pocket at the beta-barrel COOH-terminal end. <ref>PMID:1925539 </ref> The active site contains a <scene name='36/365336/Zinc_cofactor/2'>zinc cofactor</scene>which coordinates to the 6-hydroxyl of the transition state analogue, 6-hydroxyl, 1,6-dihydropurine ribonucleoside. The zinc is coordinated to three histidine residues and an aspartic acid residue. <br />
<br />
The transition state analogue held in place mostly by polar interactions. The ribose group is close to the opening of the pocket, with the purine portion deeper in the pocket, close to the zinc. Nine hydrogen bonds stabilize the transition state-enzyme complex. <br />
<br />
ADA is very stereoselective for the 6R isomer. This specificity is due to the location of the catalytic zinc, Asp295 and His 238. Interestingly, one face of the purine ring is exposed to polar groups and zinc, while the other face is only exposed to nonpolar residues. The proposed catalytic mechanism has Asp295 act as a general base, while the zinc acts as an electrophile to activate the water molecule. His 238 orients the water and stabilizes the charge of the attacking hydroxide. The protonated Glu217 or the water hydrogen bonded to it could donate or share a proton with the N1 of the substrate.<br />
<br />
<br />
<references/><br />
<br />
</StructureSection></div>William Guthriehttps://proteopedia.org/index.php?title=Ann_Taylor_sandbox_8&diff=1849658Ann Taylor sandbox 82013-10-09T19:29:29Z<p>William Guthrie: </p>
<hr />
<div>== Your Heading Here (maybe something like 'Structure') ==<br />
<StructureSection load='2ada' size='350' side='right' caption='Structure of Adenosine Deaminase (PDB entry [[2ada]])' scene=''><br />
<br />
<br />
<br />
===ADENOSINE DEAMINASE===<br />
<br />
<br />
Adenosine deaminase is involved in the degradation of purine nucleotides. It is especially active in lympocytes, and mutation of adenosine deaminase results in severe immunodeficiency. Adenosine deaminase contains an eight stranded parallel alpha/beta barrel with the active site in a deep pocket at the beta-barrel COOH-terminal end. <ref>PMID:1925539 </ref> The active site contains a <scene name='36/365336/Zinc_cofactor/1'>zinc cofactor</scene>which coordinates to the 6-hydroxyl of the transition state analogue, 6-hydroxyl, 1,6-dihydropurine ribonucleoside. The zinc is coordinated to three histidine residues and an aspartic acid residue. <br />
<br />
The transition state analogue held in place mostly by polar interactions. The ribose group is close to the opening of the pocket, with the purine portion deeper in the pocket, close to the zinc. Nine hydrogen bonds stabilize the transition state-enzyme complex. <br />
<br />
ADA is very stereoselective for the 6R isomer. This specificity is due to the location of the catalytic zinc, Asp295 and His 238. Interestingly, one face of the purine ring is exposed to polar groups and zinc, while the other face is only exposed to nonpolar residues. The proposed catalytic mechanism has Asp295 act as a general base, while the zinc acts as an electrophile to activate the water molecule. His 238 orients the water and stabilizes the charge of the attacking hydroxide. The protonated Glu217 or the water hydrogen bonded to it could donate or share a proton with the N1 of the substrate.<br />
<br />
<br />
<references/><br />
<br />
</StructureSection></div>William Guthriehttps://proteopedia.org/index.php?title=Ann_Taylor_sandbox_8&diff=1849649Ann Taylor sandbox 82013-10-09T19:20:17Z<p>William Guthrie: </p>
<hr />
<div>== Your Heading Here (maybe something like 'Structure') ==<br />
<StructureSection load='2ada' size='350' side='right' caption='Structure of Adenosine Deaminase (PDB entry [[2ada]])' scene=''><br />
<br />
<br />
<br />
===ADENOSINE DEAMINASE===<br />
<br />
<br />
Adenosine deaminase is involved in the degradation of purine nucleotides. It is especially active in lympocytes, and mutation of adenosine deaminase results in severe immunodeficiency. Adenosine deaminase contains an eight stranded parallel alpha/beta barrel with the active site in a deep pocket at the beta-barrel COOH-terminal end. <ref>PMID:1925539 </ref> The active site contains a <scene name='36/365336/Zinc/1'>zinc cofactor</scene>, which coordinates to the 6-hydroxyl of the transition state analogue, 6-hydroxyl, 1,6-dihydropurine ribonucleoside. The zinc is coordinated to three histidine residues and an aspartic acid residue. <br />
<br />
The transition state analogue held in place mostly by polar interactions. The ribose group is close to the opening of the pocket, with the purine portion deeper in the pocket, close to the zinc. Nine hydrogen bonds stabilize the transition state-enzyme complex. <br />
<br />
ADA is very stereoselective for the 6R isomer. This specificity is due to the location of the catalytic zinc, Asp295 and His 238. Interestingly, one face of the purine ring is exposed to polar groups and zinc, while the other face is only exposed to nonpolar residues. The proposed catalytic mechanism has Asp295 act as a general base, while the zinc acts as an electrophile to activate the water molecule. His 238 orients the water and stabilizes the charge of the attacking hydroxide. The protonated Glu217 or the water hydrogen bonded to it could donate or share a proton with the N1 of the substrate.<br />
<br />
<br />
<references/><br />
<br />
</StructureSection></div>William Guthriehttps://proteopedia.org/index.php?title=Ann_Taylor_sandbox_8&diff=1849640Ann Taylor sandbox 82013-10-09T19:10:40Z<p>William Guthrie: </p>
<hr />
<div>== Your Heading Here (maybe something like 'Structure') ==<br />
<StructureSection load='2ada' size='350' side='right' caption='Structure of Adenosine Deaminase (PDB entry [[2ada]])' scene=''><br />
<br />
<br />
<br />
===ADENOSINE DEAMINASE===<br />
<br />
<br />
Adenosine deaminase is involved in the degradation of purine nucleotides. It is especially active in lympocytes, and mutation of adenosine deaminase results in severe immunodeficiency. Adenosine deaminase contains an eight stranded parallel alpha/beta barrel with the active site in a deep pocket at the beta-barrel COOH-terminal end. <ref>PMID:1925539 </ref> The active site contains a zinc cofactor, which coordinates to the 6-hydroxyl of the transition state analogue, 6-hydroxyl, 1,6-dihydropurine ribonucleoside. The zinc is coordinated to three histidine residues and an aspartic acid residue. <br />
<br />
The transition state analogue held in place mostly by polar interactions. The ribose group is close to the opening of the pocket, with the purine portion deeper in the pocket, close to the zinc. Nine hydrogen bonds stabilize the transition state-enzyme complex. <br />
<br />
ADA is very stereoselective for the 6R isomer. This specificity is due to the location of the catalytic zinc, Asp295 and His 238. Interestingly, one face of the purine ring is exposed to polar groups and zinc, while the other face is only exposed to nonpolar residues. The proposed catalytic mechanism has Asp295 act as a general base, while the zinc acts as an electrophile to activate the water molecule. His 238 orients the water and stabilizes the charge of the attacking hydroxide. The protonated Glu217 or the water hydrogen bonded to it could donate or share a proton with the N1 of the substrate.<br />
<br />
<br />
<references/><br />
<br />
</StructureSection></div>William Guthriehttps://proteopedia.org/index.php?title=Ann_Taylor_sandbox_8&diff=1849592Ann Taylor sandbox 82013-10-09T18:15:36Z<p>William Guthrie: </p>
<hr />
<div>== Your Heading Here (maybe something like 'Structure') ==<br />
<StructureSection load='1dq8' size='350' side='right' caption='Structure of HMG-CoA reductase (PDB entry [[1dq8]])' scene=''><br />
<br />
<br />
<br />
===ADENOSINE DEAMINASE===<br />
<br />
<br />
Adenosine deaminase is involved in the degradation of purine nucleotides. It is especially active in lympocytes, and mutation of adenosine deaminase results in severe immunodeficiency. Adenosine deaminase contains an eight stranded parallel alpha/beta barrel with the active site in a deep pocket at the beta-barrel COOH-terminal end. <ref>PMID:1925539 </ref> The active site contains a zinc cofactor, which coordinates to the 6-hydroxyl of the transition state analogue, 6-hydroxyl, 1,6-dihydropurine ribonucleoside. The zinc is coordinated to three histidine residues and an aspartic acid residue. <br />
<br />
The transition state analogue held in place mostly by polar interactions. The ribose group is close to the opening of the pocket, with the purine portion deeper in the pocket, close to the zinc. Nine hydrogen bonds stabilize the transition state-enzyme complex. <br />
<br />
ADA is very stereoselective for the 6R isomer. This specificity is due to the location of the catalytic zinc, Asp295 and His 238. Interestingly, one face of the purine ring is exposed to polar groups and zinc, while the other face is only exposed to nonpolar residues. The proposed catalytic mechanism has Asp295 act as a general base, while the zinc acts as an electrophile to activate the water molecule. His 238 orients the water and stabilizes the charge of the attacking hydroxide. The protonated Glu217 or the water hydrogen bonded to it could donate or share a proton with the N1 of the substrate.<br />
<br />
<br />
<references/><br />
<br />
</StructureSection></div>William Guthriehttps://proteopedia.org/index.php?title=Ann_Taylor_sandbox_8&diff=1849590Ann Taylor sandbox 82013-10-09T18:14:07Z<p>William Guthrie: </p>
<hr />
<div>== Your Heading Here (maybe something like 'Structure') ==<br />
<br />
<br />
===ADENOSINE DEAMINASE===<br />
<br />
<br />
Adenosine deaminase is involved in the degradation of purine nucleotides. It is especially active in lympocytes, and mutation of adenosine deaminase results in severe immunodeficiency. Adenosine deaminase contains an eight stranded parallel alpha/beta barrel with the active site in a deep pocket at the beta-barrel COOH-terminal end. <ref>PMID:1925539 </ref> The active site contains a zinc cofactor, which coordinates to the 6-hydroxyl of the transition state analogue, 6-hydroxyl, 1,6-dihydropurine ribonucleoside. The zinc is coordinated to three histidine residues and an aspartic acid residue. <br />
<br />
The transition state analogue held in place mostly by polar interactions. The ribose group is close to the opening of the pocket, with the purine portion deeper in the pocket, close to the zinc. Nine hydrogen bonds stabilize the transition state-enzyme complex. <br />
<br />
ADA is very stereoselective for the 6R isomer. This specificity is due to the location of the catalytic zinc, Asp295 and His 238. Interestingly, one face of the purine ring is exposed to polar groups and zinc, while the other face is only exposed to nonpolar residues. The proposed catalytic mechanism has Asp295 act as a general base, while the zinc acts as an electrophile to activate the water molecule. His 238 orients the water and stabilizes the charge of the attacking hydroxide. The protonated Glu217 or the water hydrogen bonded to it could donate or share a proton with the N1 of the substrate.<br />
<br />
<br />
<references/><br />
<br />
</StructureSection></div>William Guthriehttps://proteopedia.org/index.php?title=Ann_Taylor_sandbox_8&diff=1849395Ann Taylor sandbox 82013-10-08T14:23:57Z<p>William Guthrie: </p>
<hr />
<div>== Your Heading Here (maybe something like 'Structure') ==<br />
<StructureSection load='1dq8' size='350' side='right' caption='Structure of HMG-CoA reductase (PDB entry [[1dq8]])' scene=''><br />
{{STRUCTURE_2ada| PDB=2ada | SCENE= }} <br />
<br />
===ADENOSINE DEAMINASE===<br />
<br />
<br />
Adenosine deaminase is involved in the degradation of purine nucleotides. It is especially active in lympocytes, and mutation of adenosine deaminase results in severe immunodeficiency. Adenosine deaminase contains an eight stranded parallel alpha/beta barrel with the active site in a deep pocket at the beta-barrel COOH-terminal end. <ref>PMID:1925539 </ref> The active site contains a zinc cofactor, which coordinates to the 6-hydroxyl of the transition state analogue, 6-hydroxyl, 1,6-dihydropurine ribonucleoside. The zinc is coordinated to three histidine residues and an aspartic acid residue. <br />
<br />
The transition state analogue held in place mostly by polar interactions. The ribose group is close to the opening of the pocket, with the purine portion deeper in the pocket, close to the zinc. Nine hydrogen bonds stabilize the transition state-enzyme complex. <br />
<br />
ADA is very stereoselective for the 6R isomer. This specificity is due to the location of the catalytic zinc, Asp295 and His 238. Interestingly, one face of the purine ring is exposed to polar groups and zinc, while the other face is only exposed to nonpolar residues. The proposed catalytic mechanism has Asp295 act as a general base, while the zinc acts as an electrophile to activate the water molecule. His 238 orients the water and stabilizes the charge of the attacking hydroxide. The protonated Glu217 or the water hydrogen bonded to it could donate or share a proton with the N1 of the substrate.<br />
<br />
<br />
<references/><br />
<br />
</StructureSection></div>William Guthrie