ADP-ribose pyrophosphatase

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{{STRUCTURE_1khz| PDB=1khz | SIZE=400| SCENE= |right|CAPTION=ADP-ribose pyrophosphatase dimer complex with methylene ADP-ribose, Cl- (large green) and Mg+2 (small green) ions, [[1khz]] }}
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<StructureSection load='1khz' size='450' side='right' scene='48/488514/Cv/1' caption='ADP-ribose pyrophosphatase dimer complex with methylene ADP-ribose, Cl- (large green) and Mg+2 (small green) ions, [[1khz]]'>
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== Function ==
== Function ==
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'''ADP-ribose pyrophosphatase''' (ADPRP) catalyzes the reaction which converts ADP-ribose to AMP and D-ribose 5-phosphate. ADPRP contains Mg+2 ion. ADPRP regulates the level of ADP-ribose (ADPR) in the cell. Excess of ADPR can inactivate proteins with nucleotide-binding site by binding to them.
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'''ADP-ribose pyrophosphatase''' (ADPRP) or '''ADPRase''' catalyzes the reaction which converts ADP-ribose to AMP and D-ribose 5-phosphate. ADPRP contains Mg+2 ion. ADPRP regulates the level of ADP-ribose (ADPR) in the cell. Excess of ADPR can inactivate proteins with nucleotide-binding site by binding to them.<ref>PMID:11323725</ref> ADPRP belongs to the family of NUDIX hydrolase.
== Structural highlights ==
== Structural highlights ==
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ADPRP contains two domains: the N-terminal domain responsible for dimer stabilization and the C-terminal which contains the active site. The C-terminal domain contains the Nudix (Nucleoside Diphosphate linked to X) sequence which is typical to pyrophosphatases and binds the metal ion. Residues from both monomers of ADPRP participate in the active site.
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ADPRP contains two domains: the <scene name='48/488514/Cv/9'>N-terminal domain responsible for dimer stabilization</scene> and the C-terminal which contains the active site. The C-terminal domain contains the <scene name='48/488514/Cv/10'>Nudix (Nucleoside Diphosphate linked to X) sequence</scene> which is typical to pyrophosphatases and binds the metal ion. <scene name='48/488514/Cv/15'>Residues from both monomers of ADPRP participate in the active site</scene>.<ref>PMID:12135348</ref> Water molecules are shown as red spheres.
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*<scene name='48/488514/Cv/16'>Interactions of Mg+2 ion cluster</scene>.
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*<scene name='48/488514/Cv/17'>1st Mg+2 ion coordination site</scene>.
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*<scene name='48/488514/Cv/18'>2nd Mg+2 ion coordination site</scene>.
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*<scene name='48/488514/Cv/19'>3rd Mg+2 ion coordination site</scene>.
==3D structures of ADP-ribose pyrophosphatase==
==3D structures of ADP-ribose pyrophosphatase==
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Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
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[[ADP-ribose pyrophosphatase 3D structures]]
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{{#tree:id=OrganizedByTopic|openlevels=0|
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*ADP-ribose pyrophosphatase
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**[[1q33]] – hADPRP NUDT9 residues 59-350 – human<br />
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**[[1v8i]] - TtADPRP – ''Thermus thermophilus''<br />
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**[[2w4e]] – ADPRP residues 56-200 – ''Deinococcus radiodurans''<br />
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**[[3o8s]] - ADPRP – ''Streptococcus suis''<br />
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**[[4kyx]] – ADPRP Mutt – ''Rickettsia felis''<br />
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*ADP-ribose pyrophosphatase binary complex
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**[[1v8l]] – TtADPRP + ADPR<br />
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**[[1v8n]] - TtADPRP + Zn<br />
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*ADP-ribose pyrophosphatase ternary complex
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</StructureSection>
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**[[1khz]] - EcADPRP + AMPCPR + Mg – ''Escherichia coli''<br />
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== References ==
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**[[1qvj]] - hADPRP + ribose-5-phosphate + Mg<br />
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<references/>
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**[[1v8m]] - TtADPRP + Gd + ADPR <br />
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**[[1v8s]] - TtADPRP + AMP + Mg<br />
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**[[1v8t]] - TtADPRP + ribose-5-phosphate + Zn<br />
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**[[1v8u]] - TtADPRP (mutant) + sulfate + Mg<br />
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**[[1v8v]] - TtADPRP (mutant) + ADPR + Mg<br />
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**[[1v8w]] - TtADPRP (mutant) + sulfate + Zn<br />
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**[[1v8y]] - TtADPRP (mutant) + ADPR + Zn<br />
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**[[1v8r]] - TtADPRP + ADPR + Zn<br />
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**[[3bm4]] - hADPRP NUDT5 + AMPCPR + Mg<br />
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}}
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[[Category:Topic Page]]
[[Category:Topic Page]]

Current revision

ADP-ribose pyrophosphatase dimer complex with methylene ADP-ribose, Cl- (large green) and Mg+2 (small green) ions, 1khz

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References

  1. ↑ Gabelli SB, Bianchet MA, Bessman MJ, Amzel LM. The structure of ADP-ribose pyrophosphatase reveals the structural basis for the versatility of the Nudix family. Nat Struct Biol. 2001 May;8(5):467-72. PMID:11323725 doi:10.1038/87647
  2. ↑ Gabelli SB, Bianchet MA, Ohnishi Y, Ichikawa Y, Bessman MJ, Amzel LM. Mechanism of the Escherichia coli ADP-ribose pyrophosphatase, a Nudix hydrolase. Biochemistry. 2002 Jul 30;41(30):9279-85. PMID:12135348

Proteopedia Page Contributors and Editors (what is this?)

Michal Harel, Alexander Berchansky

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