1g9q: Difference between revisions

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New page: left|200px<br /><applet load="1g9q" size="450" color="white" frame="true" align="right" spinBox="true" caption="1g9q, resolution 2.30Å" /> '''COMPLEX STRUCTURE OF...
 
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[[Image:1g9q.jpg|left|200px]]<br /><applet load="1g9q" size="450" color="white" frame="true" align="right" spinBox="true"
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'''COMPLEX STRUCTURE OF THE ADPR-ASE AND ITS SUBSTRATE ADP-RIBOSE'''<br />


==Overview==
==COMPLEX STRUCTURE OF THE ADPR-ASE AND ITS SUBSTRATE ADP-RIBOSE==
Regulation of cellular levels of ADP-ribose is important in preventing, nonenzymatic ADP-ribosylation of proteins. The Escherichia coli ADP-ribose, pyrophosphatase, a Nudix enzyme, catalyzes the hydrolysis of ADP-ribose to, ribose-5-P and AMP, compounds that can be recycled as part of nucleotide, metabolism. The structures of the apo enzyme, the active enzyme and the, complex with ADP-ribose were determined to 1.9 A, 2.7 A and 2.3 A, respectively. The structures reveal a symmetric homodimer with two, equivalent catalytic sites, each formed by residues of both monomers, requiring dimerization through domain swapping for substrate recognition, and catalytic activity. The structures also suggest a role for the, residues conserved in each Nudix subfamily. The Nudix motif residues, folded as a loop-helix-loop tailored for pyrophosphate hydrolysis, compose, the catalytic center; residues conferring substrate specificity occur in, regions of the sequence removed from the Nudix motif. This segregation of, catalytic and recognition roles provides versatility to the Nudix family.
<StructureSection load='1g9q' size='340' side='right'caption='[[1g9q]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[1g9q]] 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=1G9Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1G9Q FirstGlance]. <br>
1G9Q 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 APR as [http://en.wikipedia.org/wiki/ligand ligand]. 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://ispc.weizmann.ac.il/oca-bin/ocashort?id=1G9Q OCA].  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
 
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene></td></tr>
==Reference==
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1g9q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g9q OCA], [https://pdbe.org/1g9q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1g9q RCSB], [https://www.ebi.ac.uk/pdbsum/1g9q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1g9q ProSAT]</span></td></tr>
The structure of ADP-ribose pyrophosphatase reveals the structural basis for the versatility of the Nudix family., Gabelli SB, Bianchet MA, Bessman MJ, Amzel LM, Nat Struct Biol. 2001 May;8(5):467-72. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11323725 11323725]
</table>
[[Category: ADP-ribose diphosphatase]]
== 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/g9/1g9q_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=1g9q ConSurf].
<div style="clear:both"></div>
== References ==
<references/>
__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: APR]]
[[Category: nudix]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 15:51:39 2007''

Latest revision as of 10:24, 7 February 2024

COMPLEX STRUCTURE OF THE ADPR-ASE AND ITS SUBSTRATE ADP-RIBOSECOMPLEX STRUCTURE OF THE ADPR-ASE AND ITS SUBSTRATE ADP-RIBOSE

Structural highlights

1g9q 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 2.3Å
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.

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

1g9q, resolution 2.30Å

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