2yvp
From Proteopedia
| Line 4: | Line 4: | ||
|PDB= 2yvp |SIZE=350|CAPTION= <scene name='initialview01'>2yvp</scene>, resolution 1.66Å | |PDB= 2yvp |SIZE=350|CAPTION= <scene name='initialview01'>2yvp</scene>, resolution 1.66Å | ||
|SITE= <scene name='pdbsite=AC1:Mg+Binding+Site+For+Residue+A+183'>AC1</scene>, <scene name='pdbsite=AC2:Mg+Binding+Site+For+Residue+A+184'>AC2</scene>, <scene name='pdbsite=AC3:Mg+Binding+Site+For+Residue+A+185'>AC3</scene> and <scene name='pdbsite=AC4:Rby+Binding+Site+For+Residue+A+186'>AC4</scene> | |SITE= <scene name='pdbsite=AC1:Mg+Binding+Site+For+Residue+A+183'>AC1</scene>, <scene name='pdbsite=AC2:Mg+Binding+Site+For+Residue+A+184'>AC2</scene>, <scene name='pdbsite=AC3:Mg+Binding+Site+For+Residue+A+185'>AC3</scene> and <scene name='pdbsite=AC4:Rby+Binding+Site+For+Residue+A+186'>AC4</scene> | ||
| - | |LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> | + | |LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=RBY:METHYLENE+ADP-BETA-XYLOSE'>RBY</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= ndx2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus]) | |GENE= ndx2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[2yvm|2YVM]], [[2yvn|2YVN]], [[2yvo|2YVO]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2yvp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yvp OCA], [http://www.ebi.ac.uk/pdbsum/2yvp PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2yvp RCSB]</span> | ||
}} | }} | ||
| Line 28: | Line 31: | ||
[[Category: Wakamatsu, T.]] | [[Category: Wakamatsu, T.]] | ||
[[Category: Yokoyama, S.]] | [[Category: Yokoyama, S.]] | ||
| - | [[Category: MG]] | ||
| - | [[Category: RBY]] | ||
[[Category: adp-ribose]] | [[Category: adp-ribose]] | ||
[[Category: fad]] | [[Category: fad]] | ||
| Line 41: | Line 42: | ||
[[Category: thermus thermophilus]] | [[Category: thermus thermophilus]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:15:53 2008'' |
Revision as of 02:15, 31 March 2008
| |||||||
| , resolution 1.66Å | |||||||
|---|---|---|---|---|---|---|---|
| Sites: | , , and | ||||||
| Ligands: | , | ||||||
| Gene: | ndx2 (Thermus thermophilus) | ||||||
| Related: | 2YVM, 2YVN, 2YVO
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of NDX2 in complex with MG2+ and ampcpr from thermus thermophilus HB8
Overview
ADP-ribose (ADPR) is one of the main substrates of Nudix proteins. Among the eight Nudix proteins of Thermus thermophilus HB8, we previously determined the crystal structure of Ndx4, an ADPR pyrophosphatase (ADPRase). In this study we show that Ndx2 of T. thermophilus also preferentially hydrolyzes ADPR and flavin adenine dinucleotide and have determined its crystal structure. We have determined the structures of Ndx2 alone and in complex with Mg2+, with Mg2+ and AMP, and with Mg2+ and a nonhydrolyzable ADPR analogue. Although Ndx2 recognizes the AMP moiety in a manner similar to those for other ADPRases, it recognizes the terminal ribose in a distinct manner. The residues responsible for the recognition of the substrate in Ndx2 are not conserved among ADPRases. This may reflect the diversity in substrate specificity among ADPRases. Based on these results, we propose the classification of ADPRases into two types: ADPRase-I enzymes, which exhibit high specificity for ADPR; and ADPRase-II enzymes, which exhibit low specificity for ADPR. In the active site of the ternary complexes, three Mg2+ ions are coordinated to the side chains of conserved glutamate residues and water molecules. Substitution of Glu90 and Glu94 with glutamine suggests that these residues are essential for catalysis. These results suggest that ADPRase-I and ADPRase-II enzymes have nearly identical catalytic mechanisms but different mechanisms of substrate recognition.
About this Structure
2YVP is a Single protein structure of sequence from Thermus thermophilus. Full crystallographic information is available from OCA.
Reference
Structural basis for different substrate specificities of two ADP-ribose pyrophosphatases from Thermus thermophilus HB8., Wakamatsu T, Nakagawa N, Kuramitsu S, Masui R, J Bacteriol. 2008 Feb;190(3):1108-17. Epub 2007 Nov 26. PMID:18039767
Page seeded by OCA on Mon Mar 31 05:15:53 2008
Categories: Single protein | Thermus thermophilus | Kuramitsu, S. | Masui, R. | Nakagawa, N. | RSGI, RIKEN Structural Genomics/Proteomics Initiative. | Wakamatsu, T. | Yokoyama, S. | Adp-ribose | Fad | Hydrolase | National project on protein structural and functional analyse | Nppsfa | Nudix protein | Riken structural genomics/proteomics initiative | Rsgi | Structural genomic
