ATP-dependent DNA ligase from bacteriophage T7: Difference between revisions

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William Guthrie, Jeremy A. Hammett, Hunter Douglas, Jaime Prilusky

Revision as of 21:51, 5 November 2013 view source Jeremy A. Hammett (talk \| contribs) 12 edits No edit summary ← Older edit		Revision as of 22:05, 5 November 2013 view source Jeremy A. Hammett (talk \| contribs) 12 edits No edit summary Newer edit →
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	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>. 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.		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.