1v8m: Difference between revisions
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[[Image:1v8m.jpg|left|200px]] | [[Image:1v8m.jpg|left|200px]] | ||
'''Crystal structure analysis of ADP-ribose pyrophosphatase complexed with ADP-ribose and Gd''' | {{Structure | ||
|PDB= 1v8m |SIZE=350|CAPTION= <scene name='initialview01'>1v8m</scene>, resolution 1.80Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene> and <scene name='pdbligand=GD:GADOLINIUM ATOM'>GD</scene> | |||
|ACTIVITY= [http://en.wikipedia.org/wiki/ADP-ribose_diphosphatase ADP-ribose diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.13 3.6.1.13] | |||
|GENE= | |||
}} | |||
'''Crystal structure analysis of ADP-ribose pyrophosphatase complexed with ADP-ribose and Gd''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
1V8M is a [ | 1V8M is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V8M OCA]. | ||
==Reference== | ==Reference== | ||
Structural insights into the Thermus thermophilus ADP-ribose pyrophosphatase mechanism via crystal structures with the bound substrate and metal., Yoshiba S, Ooga T, Nakagawa N, Shibata T, Inoue Y, Yokoyama S, Kuramitsu S, Masui R, J Biol Chem. 2004 Aug 27;279(35):37163-74. Epub 2004 Jun 21. PMID:[http:// | Structural insights into the Thermus thermophilus ADP-ribose pyrophosphatase mechanism via crystal structures with the bound substrate and metal., Yoshiba S, Ooga T, Nakagawa N, Shibata T, Inoue Y, Yokoyama S, Kuramitsu S, Masui R, J Biol Chem. 2004 Aug 27;279(35):37163-74. Epub 2004 Jun 21. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15210687 15210687] | ||
[[Category: ADP-ribose diphosphatase]] | [[Category: ADP-ribose diphosphatase]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
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[[Category: riken structural genomics/proteomics initiative]] | [[Category: riken structural genomics/proteomics initiative]] | ||
[[Category: rsgi]] | [[Category: rsgi]] | ||
[[Category: structural | [[Category: structural genomic]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 14:42:18 2008'' | ||
Revision as of 15:42, 20 March 2008
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| , resolution 1.80Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | and | ||||||
| Activity: | ADP-ribose diphosphatase, with EC number 3.6.1.13 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure analysis of ADP-ribose pyrophosphatase complexed with ADP-ribose and Gd
OverviewOverview
ADP-ribose pyrophosphatase (ADPRase) catalyzes the divalent metal ion-dependent hydrolysis of ADP-ribose to ribose 5'-phosphate and AMP. This enzyme plays a key role in regulating the intracellular ADP-ribose levels, and prevents nonenzymatic ADP-ribosylation. To elucidate the pyrophosphatase hydrolysis mechanism employed by this enzyme, structural changes occurring on binding of substrate, metal and product were investigated using crystal structures of ADPRase from an extreme thermophile, Thermus thermophilus HB8. Seven structures were determined, including that of the free enzyme, the Zn(2+)-bound enzyme, the binary complex with ADP-ribose, the ternary complexes with ADP-ribose and Zn(2+) or Gd(3+), and the product complexes with AMP and Mg(2+) or with ribose 5'-phosphate and Zn(2+). The structural and functional studies suggested that the ADP-ribose hydrolysis pathway consists of four reaction states: bound with metal (I), metal and substrate (II), metal and substrate in the transition state (III), and products (IV). In reaction state II, Glu-82 and Glu-70 abstract a proton from a water molecule. This water molecule is situated at an ideal position to carry out nucleophilic attack on the adenosyl phosphate, as it is 3.6 A away from the target phosphorus and almost in line with the scissile bond.
About this StructureAbout this Structure
1V8M is a Single protein structure of sequence from Thermus thermophilus. Full crystallographic information is available from OCA.
ReferenceReference
Structural insights into the Thermus thermophilus ADP-ribose pyrophosphatase mechanism via crystal structures with the bound substrate and metal., Yoshiba S, Ooga T, Nakagawa N, Shibata T, Inoue Y, Yokoyama S, Kuramitsu S, Masui R, J Biol Chem. 2004 Aug 27;279(35):37163-74. Epub 2004 Jun 21. PMID:15210687
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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)
OCA- Pages with broken file links
- ADP-ribose diphosphatase
- Single protein
- Thermus thermophilus
- Inoue, Y.
- Kuramitsu, S.
- Masui, R.
- Nakagawa, N.
- Ooga, T.
- RSGI, RIKEN Structural Genomics/Proteomics Initiative.
- Shibata, T.
- Yokoyama, S.
- Yoshiba, S.
- APR
- GD
- Loop-helix-loop
- Mutt family
- Nudix motif
- Riken structural genomics/proteomics initiative
- Rsgi
- Structural genomic