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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__TOC__
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== Function ==
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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.
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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. The C terminal of ADPRP contains the Nudix sequence which binds the metal 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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==3D structures of ADP-ribose pyrophosphatase==
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== Structural highlights ==
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Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
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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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{{#tree:id=OrganizedByTopic|openlevels=0|
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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>.
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*ADP-ribose pyrophosphatase
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==3D structures of 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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[[ADP-ribose pyrophosphatase 3D structures]]
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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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