1v8n: Difference between revisions

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Revision as of 00:20, 31 March 2008

File:1v8n.jpg

, resolution 1.74Å

Ligands:

Activity:

ADP-ribose diphosphatase, with EC number 3.6.1.13

Related:

1V8I, 1V8L, 1V8M, 1V8R, 1V8S, 1V8T, 1V8U, 1V8V, 1V8W, 1V8Y

Resources:

FirstGlance, OCA, PDBsum, RCSB

Coordinates:

save as pdb, mmCIF, xml

Crystal structure analysis of the ADP-ribose pyrophosphatase complexed with Zn

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

1V8N 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

Page seeded by OCA on Mon Mar 31 00:20:55 2008

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OCA

@@ Line 4: / Line 4: @@
 |PDB= 1v8n |SIZE=350|CAPTION= <scene name='initialview01'>1v8n</scene>, resolution 1.74&Aring;
 |SITE=
-|LIGAND= <scene name='pdbligand=ZN:ZINC ION'>ZN</scene>
+|LIGAND= <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]
+|ACTIVITY= <span class='plainlinks'>[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] </span>
 |GENE=
+|DOMAIN=
+|RELATEDENTRY=[[1v8i|1V8I]], [[1v8l|1V8L]], [[1v8m|1V8M]], [[1v8r|1V8R]], [[1v8s|1V8S]], [[1v8t|1V8T]], [[1v8u|1V8U]], [[1v8v|1V8V]], [[1v8w|1V8W]], [[1v8y|1V8Y]]
+|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1v8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v8n OCA], [http://www.ebi.ac.uk/pdbsum/1v8n PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1v8n RCSB]</span>
 }}
@@ Line 32: / Line 35: @@
 [[Category: Yokoyama, S.]]
 [[Category: Yoshiba, S.]]
-[[Category: ZN]]
 [[Category: mutt family]]
 [[Category: nudix motif]]
@@ Line 39: / Line 41: @@
 [[Category: structural genomic]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 14:42:14 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:20:55 2008''