1zau
From Proteopedia
(New page: 200px<br /><applet load="1zau" size="450" color="white" frame="true" align="right" spinBox="true" caption="1zau, resolution 3.15Å" /> '''Adenylation domain o...) |
|||
| Line 1: | Line 1: | ||
| - | [[Image:1zau.gif|left|200px]]<br /><applet load="1zau" size=" | + | [[Image:1zau.gif|left|200px]]<br /><applet load="1zau" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1zau, resolution 3.15Å" /> | caption="1zau, resolution 3.15Å" /> | ||
'''Adenylation domain of NAD+ dependent DNA ligase from M.tuberculosis'''<br /> | '''Adenylation domain of NAD+ dependent DNA ligase from M.tuberculosis'''<br /> | ||
==Overview== | ==Overview== | ||
| - | DNA ligases utilize either ATP or NAD+ as cofactors to catalyze the | + | DNA ligases utilize either ATP or NAD+ as cofactors to catalyze the formation of phosphodiester bonds in nicked DNA. Those utilizing NAD+ are attractive drug targets because of the unique cofactor requirement for ligase activity. We report here the crystal structure of the adenylation domain of the Mycobacterium tuberculosis NAD+-dependent ligase with bound AMP. The adenosine nucleoside moiety of AMP adopts a syn-conformation. The structure also captures a new spatial disposition between the two subdomains of the adenylation domain. Based on the crystal structure and an in-house compound library, we have identified a novel class of inhibitors for the enzyme using in silico docking calculations. The glycosyl ureide-based inhibitors were able to distinguish between NAD+- and ATP-dependent ligases as evidenced by in vitro assays using T4 ligase and human DNA ligase I. Moreover, assays involving an Escherichia coli strain harboring a temperature-sensitive ligase mutant and a ligase-deficient Salmonella typhimurium strain suggested that the bactericidal activity of the inhibitors is due to inhibition of the essential ligase enzyme. The results can be used as the basis for rational design of novel antibacterial agents. |
==About this Structure== | ==About this Structure== | ||
| - | 1ZAU is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis] with AMP as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/DNA_ligase_(NAD(+)) DNA ligase (NAD(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.2 6.5.1.2] Full crystallographic information is available from [http:// | + | 1ZAU is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis] with <scene name='pdbligand=AMP:'>AMP</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/DNA_ligase_(NAD(+)) DNA ligase (NAD(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.5.1.2 6.5.1.2] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZAU OCA]. |
==Reference== | ==Reference== | ||
| Line 15: | Line 15: | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Ramachandran, R.]] | [[Category: Ramachandran, R.]] | ||
| - | [[Category: Srivastava, S | + | [[Category: Srivastava, S K.]] |
[[Category: AMP]] | [[Category: AMP]] | ||
[[Category: amp]] | [[Category: amp]] | ||
| - | [[Category: m | + | [[Category: m tuberculosis]] |
[[Category: nad+ dependent dna ligase]] | [[Category: nad+ dependent dna ligase]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:13:49 2008'' |
Revision as of 14:13, 21 February 2008
|
Adenylation domain of NAD+ dependent DNA ligase from M.tuberculosis
Overview
DNA ligases utilize either ATP or NAD+ as cofactors to catalyze the formation of phosphodiester bonds in nicked DNA. Those utilizing NAD+ are attractive drug targets because of the unique cofactor requirement for ligase activity. We report here the crystal structure of the adenylation domain of the Mycobacterium tuberculosis NAD+-dependent ligase with bound AMP. The adenosine nucleoside moiety of AMP adopts a syn-conformation. The structure also captures a new spatial disposition between the two subdomains of the adenylation domain. Based on the crystal structure and an in-house compound library, we have identified a novel class of inhibitors for the enzyme using in silico docking calculations. The glycosyl ureide-based inhibitors were able to distinguish between NAD+- and ATP-dependent ligases as evidenced by in vitro assays using T4 ligase and human DNA ligase I. Moreover, assays involving an Escherichia coli strain harboring a temperature-sensitive ligase mutant and a ligase-deficient Salmonella typhimurium strain suggested that the bactericidal activity of the inhibitors is due to inhibition of the essential ligase enzyme. The results can be used as the basis for rational design of novel antibacterial agents.
About this Structure
1ZAU is a Single protein structure of sequence from Mycobacterium tuberculosis with as ligand. Active as DNA ligase (NAD(+)), with EC number 6.5.1.2 Full crystallographic information is available from OCA.
Reference
NAD+-dependent DNA Ligase (Rv3014c) from Mycobacterium tuberculosis. Crystal structure of the adenylation domain and identification of novel inhibitors., Srivastava SK, Tripathi RP, Ramachandran R, J Biol Chem. 2005 Aug 26;280(34):30273-81. Epub 2005 May 17. PMID:15901723
Page seeded by OCA on Thu Feb 21 16:13:49 2008
