2q16
From Proteopedia
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|PDB= 2q16 |SIZE=350|CAPTION= <scene name='initialview01'>2q16</scene>, resolution 1.95Å | |PDB= 2q16 |SIZE=350|CAPTION= <scene name='initialview01'>2q16</scene>, resolution 1.95Å | ||
|SITE= <scene name='pdbsite=AC1:Ca+Binding+Site+For+Residue+A+200'>AC1</scene>, <scene name='pdbsite=AC2:Ca+Binding+Site+For+Residue+B+200'>AC2</scene>, <scene name='pdbsite=AC3:Na+Binding+Site+For+Residue+A+201'>AC3</scene>, <scene name='pdbsite=AC4:Na+Binding+Site+For+Residue+B+201'>AC4</scene>, <scene name='pdbsite=AC5:Na+Binding+Site+For+Residue+B+202'>AC5</scene>, <scene name='pdbsite=AC6:Na+Binding+Site+For+Residue+A+202'>AC6</scene>, <scene name='pdbsite=AC7:Na+Binding+Site+For+Residue+A+203'>AC7</scene>, <scene name='pdbsite=AC8:So4+Binding+Site+For+Residue+A+6245'>AC8</scene>, <scene name='pdbsite=AC9:Itt+Binding+Site+For+Residue+A+6246'>AC9</scene> and <scene name='pdbsite=BC1:Itt+Binding+Site+For+Residue+B+203'>BC1</scene> | |SITE= <scene name='pdbsite=AC1:Ca+Binding+Site+For+Residue+A+200'>AC1</scene>, <scene name='pdbsite=AC2:Ca+Binding+Site+For+Residue+B+200'>AC2</scene>, <scene name='pdbsite=AC3:Na+Binding+Site+For+Residue+A+201'>AC3</scene>, <scene name='pdbsite=AC4:Na+Binding+Site+For+Residue+B+201'>AC4</scene>, <scene name='pdbsite=AC5:Na+Binding+Site+For+Residue+B+202'>AC5</scene>, <scene name='pdbsite=AC6:Na+Binding+Site+For+Residue+A+202'>AC6</scene>, <scene name='pdbsite=AC7:Na+Binding+Site+For+Residue+A+203'>AC7</scene>, <scene name='pdbsite=AC8:So4+Binding+Site+For+Residue+A+6245'>AC8</scene>, <scene name='pdbsite=AC9:Itt+Binding+Site+For+Residue+A+6246'>AC9</scene> and <scene name='pdbsite=BC1:Itt+Binding+Site+For+Residue+B+203'>BC1</scene> | ||
| - | |LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> and <scene name='pdbligand=ITT:INOSINE 5 | + | |LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> and <scene name='pdbligand=ITT:INOSINE 5'-TRIPHOSPHATE'>ITT</scene> |
|ACTIVITY= [http://en.wikipedia.org/wiki/Nucleoside-triphosphate_diphosphatase Nucleoside-triphosphate diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.19 3.6.1.19] | |ACTIVITY= [http://en.wikipedia.org/wiki/Nucleoside-triphosphate_diphosphatase Nucleoside-triphosphate diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.19 3.6.1.19] | ||
|GENE= yggV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]) | |GENE= yggV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]) | ||
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[[Category: itp pyrophosphatase x-ray structure enzyme mechanism substrate]] | [[Category: itp pyrophosphatase x-ray structure enzyme mechanism substrate]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 23 15:42:14 2008'' |
Revision as of 13:42, 23 March 2008
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| , resolution 1.95Å | |||||||
|---|---|---|---|---|---|---|---|
| Sites: | , , , , , , , , and | ||||||
| Ligands: | , , and | ||||||
| Gene: | yggV (Escherichia coli) | ||||||
| Activity: | Nucleoside-triphosphate diphosphatase, with EC number 3.6.1.19 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Structure of the E. coli inosine triphosphate pyrophosphatase RgdB in complex with ITP
Overview
Inosine triphosphate pyrophosphatases, which are ubiquitous house-cleaning enzymes, hydrolyze noncanonical nucleoside triphosphates (inosine triphosphate (ITP) and xanthosine triphosphate (XTP)) and prevent the incorporation of hypoxanthine or xanthine into nascent DNA or RNA. Here we present the 1.5-A-resolution crystal structure of the inosine triphosphate pyrophosphatase RdgB from Escherichia coli in a free state and in complex with a substrate (ITP+Ca(2+)) or a product (inosine monophosphate (IMP)). ITP binding to RdgB induced a large displacement of the alpha1 helix, closing the enzyme active site. This positions the conserved Lys13 close to the bridging oxygen between the alpha- and beta-phosphates of the substrate, weakening the P(alpha)-O bond. On the other side of the substrate, the conserved Asp69 is proposed to act as a base coordinating the catalytic water molecule. Our data provide insight into the molecular mechanisms of the substrate selectivity and catalysis of RdgB and other ITPases.
About this Structure
2Q16 is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.
Reference
Molecular basis of the antimutagenic activity of the house-cleaning inosine triphosphate pyrophosphatase RdgB from Escherichia coli., Savchenko A, Proudfoot M, Skarina T, Singer A, Litvinova O, Sanishvili R, Brown G, Chirgadze N, Yakunin AF, J Mol Biol. 2007 Dec 7;374(4):1091-103. Epub 2007 Oct 11. PMID:17976651
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