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[[Image:1khz.gif|left|200px]]<br /><applet load="1khz" size="350" color="white" frame="true" align="right" spinBox="true"
caption="1khz, resolution 2.04&Aring;" />
'''Structure of the ADPR-ase in complex with AMPCPR and Mg'''<br />


==Overview==
==Structure of the ADPR-ase in complex with AMPCPR and Mg==
Escherichia coli ADP-ribose (ADPR) pyrophosphatase (ADPRase), a Nudix enzyme, catalyzes the Mg(2+)-dependent hydrolysis of ADP-ribose to AMP and ribose 5-phosphate. ADPR hydrolysis experiments conducted in the presence of H(2)(18)O and analyzed by electrospray mass spectrometry showed that the ADPRase-catalyzed reaction takes place through nucleophilic attack at the adenosyl phosphate. The structure of ADPRase in complex with Mg(2+) and a nonhydrolyzable ADPR analogue, alpha,beta-methylene ADP-ribose, reveals an active site water molecule poised for nucleophilic attack on the adenosyl phosphate. This water molecule is activated by two magnesium ions, and its oxygen contacts the target phosphorus (P-O distance of 3.0 A) and forms an angle of 177 degrees with the scissile bond, suggesting an associative mechanism. A third Mg(2+) ion bridges the two phosphates and could stabilize the negative charge of the leaving group, ribose 5-phosphate. The structure of the ternary complex also shows that loop L9 moves fully 10 A from its position in the free enzyme, forming a tighter turn and bringing Glu 162 to its catalytic position. These observations indicate that as part of the catalytic mechanism, the ADPRase cycles between an open (free enzyme) and a closed (substrate-metal complex) conformation. This cycling may be important in preventing nonspecific hydrolysis of other nucleotides.
<StructureSection load='1khz' size='340' side='right'caption='[[1khz]], [[Resolution|resolution]] 2.04&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1khz]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KHZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KHZ FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.04&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADV:ALPHA-BETA+METHYLENE+ADP-RIBOSE'>ADV</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1khz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1khz OCA], [https://pdbe.org/1khz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1khz RCSB], [https://www.ebi.ac.uk/pdbsum/1khz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1khz ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/ADPP_ECOLI ADPP_ECOLI] Acts on ADP-mannose and ADP-glucose as well as ADP-ribose. Prevents glycogen biosynthesis. The reaction catalyzed by this enzyme is a limiting step of the gluconeogenic process.<ref>PMID:11416161</ref>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kh/1khz_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1khz ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1KHZ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=CL:'>CL</scene>, <scene name='pdbligand=MG:'>MG</scene> and <scene name='pdbligand=ADV:'>ADV</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KHZ OCA].
*[[ADP-ribose pyrophosphatase|ADP-ribose pyrophosphatase]]
 
*[[ADP-ribose pyrophosphatase 3D structures|ADP-ribose pyrophosphatase 3D structures]]
==Reference==
== References ==
Mechanism of the Escherichia coli ADP-ribose pyrophosphatase, a Nudix hydrolase., Gabelli SB, Bianchet MA, Ohnishi Y, Ichikawa Y, Bessman MJ, Amzel LM, Biochemistry. 2002 Jul 30;41(30):9279-85. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12135348 12135348]
<references/>
[[Category: ADP-ribose diphosphatase]]
__TOC__
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Amzel, L M.]]
[[Category: Amzel LM]]
[[Category: Bessman, M J.]]
[[Category: Bessman MJ]]
[[Category: Bianchet, M A.]]
[[Category: Bianchet MA]]
[[Category: Gabelli, S B.]]
[[Category: Gabelli SB]]
[[Category: ADV]]
[[Category: CL]]
[[Category: MG]]
[[Category: adp-ribose pyrophosphatase]]
[[Category: ampcpr]]
[[Category: nudix]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:34:21 2008''

Latest revision as of 10:25, 14 February 2024

Structure of the ADPR-ase in complex with AMPCPR and MgStructure of the ADPR-ase in complex with AMPCPR and Mg

Structural highlights

1khz is a 2 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.04Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ADPP_ECOLI Acts on ADP-mannose and ADP-glucose as well as ADP-ribose. Prevents glycogen biosynthesis. The reaction catalyzed by this enzyme is a limiting step of the gluconeogenic process.[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

References

  1. ↑ Moreno-Bruna B, Baroja-Fernandez E, Munoz FJ, Bastarrica-Berasategui A, Zandueta-Criado A, Rodriguez-Lopez M, Lasa I, Akazawa T, Pozueta-Romero J. Adenosine diphosphate sugar pyrophosphatase prevents glycogen biosynthesis in Escherichia coli. Proc Natl Acad Sci U S A. 2001 Jul 3;98(14):8128-32. Epub 2001 Jun 19. PMID:11416161 doi:http://dx.doi.org/10.1073/pnas.131214098

1khz, resolution 2.04Å

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