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ATP-dependent DNA ligase from bacteriophage T7

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== Structure ==
== Structure ==
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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). <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.
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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). <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_2/1'>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.
<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.

Revision as of 04:38, 21 November 2013

ATP-DEPENDENT DNA LIGASE FROM BACTERIOPHAGE T7

Structure of Bacteriophage T7 DNA Ligase(PDB entry 1a0i)

Drag the structure with the mouse to rotate


References

  1. ↑ McGrath S, van Sinderen D. Bacteriophage: Genetics and Molecular Biology. Norfolk: Caister Academic Press, 2007. Print.
  2. ↑ Berg, Jeremy M, Stryer, Lubert, Tymoczko, John L. Biochemistry. Sixth edition. New York: W.H. Freeman and Company, 2007: 796. Print.
  3. ↑ 3.0 3.1 3.2 Doherty AJ, Ashford SR, Subramanya HS, Wigley DB. Bacteriophage T7 DNA ligase. Overexpression, purification, crystallization, and characterization. J Biol Chem. 1996 May 10;271(19):11083-9. PMID:8626651
  4. ↑ 4.0 4.1 4.2 4.3 4.4 Subramanya HS, Doherty AJ, Ashford SR, Wigley DB. Crystal structure of an ATP-dependent DNA ligase from bacteriophage T7. Cell. 1996 May 17;85(4):607-15. PMID:8653795

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