2dsb: Difference between revisions

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New page: left|200px<br /> <applet load="2dsb" size="450" color="white" frame="true" align="right" spinBox="true" caption="2dsb, resolution 2.50Å" /> '''Crystal structure o...
 
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[[Image:2dsb.gif|left|200px]]<br />
<applet load="2dsb" size="450" color="white" frame="true" align="right" spinBox="true"
caption="2dsb, resolution 2.50&Aring;" />
'''Crystal structure of human ADP-ribose pyrophosphatase NUDT5'''<br />


==Overview==
==Crystal structure of human ADP-ribose pyrophosphatase NUDT5==
Human NUDT5 (hNUDT5) is an ADP-ribose pyrophosphatase (ADPRase) belonging, to the Nudix hydrolase superfamily. It presumably plays important roles in, controlling the intracellular level of ADP-ribose (ADPR) to prevent, non-enzymatic ADP-ribosylation by hydrolyzing ADPR to AMP and ribose, 5'-phosphate. We report here the crystal structures of hNUDT5 in apo form, in complex with ADPR, and in complex with AMP with bound Mg2+. hNUDT5, forms a homodimer with substantial domain swapping and assumes a structure, more similar to Escherichia coli ADPRase ORF209 than human ADPRase NUDT9., The adenine moiety of the substrates is specifically recognized by the, enzyme via hydrogen-bonding interactions between N1 and N6 of the base and, Glu47 of one subunit, and between N7 of the base and Arg51 of the other, subunit, providing the molecular basis for the high selectivity of hNUDT5, for ADP-sugars over other sugar nucleotides. Structural comparisons with, E. coli ADPRase ORF209 and ADPXase ORF186 indicate that the existence of, an aromatic residue on loop L8 in ORF186 seems to be positively correlated, with its enzymatic activity on APnA, whereas hNUDT5 and ORF209 contain no, such residue and thus have low or no activities on APnA.
<StructureSection load='2dsb' size='340' side='right'caption='[[2dsb]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2dsb]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DSB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DSB 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]] 2.5&#8491;</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=2dsb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dsb OCA], [https://pdbe.org/2dsb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dsb RCSB], [https://www.ebi.ac.uk/pdbsum/2dsb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dsb ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/NUDT5_HUMAN NUDT5_HUMAN] Hydrolyzes with similar activities ADP-ribose ADP-mannose, ADP-glucose, 8-oxo-GDP and 8-oxo-dGDP. Can also hydrolyze other nucleotide sugars with low activity.<ref>PMID:17052728</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/ds/2dsb_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=2dsb ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
2DSB is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2DSB OCA].
*[[ADP-ribose pyrophosphatase 3D structures|ADP-ribose pyrophosphatase 3D structures]]
 
== References ==
==Reference==
<references/>
Crystal structures of human NUDT5 reveal insights into the structural basis of the substrate specificity., Zha M, Zhong C, Peng Y, Hu H, Ding J, J Mol Biol. 2006 Dec 15;364(5):1021-33. Epub 2006 Oct 3. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17052728 17052728]
__TOC__
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Ding, J.]]
[[Category: Ding J]]
[[Category: Zha, M.]]
[[Category: Zha M]]
[[Category: Zhong, C.]]
[[Category: Zhong C]]
[[Category: adp-ribose pyrophosphatase]]
[[Category: adpr]]
[[Category: nudix domain]]
[[Category: nudt5]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 21:39:31 2007''

Latest revision as of 16:48, 13 March 2024

Crystal structure of human ADP-ribose pyrophosphatase NUDT5Crystal structure of human ADP-ribose pyrophosphatase NUDT5

Structural highlights

2dsb is a 4 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.5Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NUDT5_HUMAN Hydrolyzes with similar activities ADP-ribose ADP-mannose, ADP-glucose, 8-oxo-GDP and 8-oxo-dGDP. Can also hydrolyze other nucleotide sugars with low activity.[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. ↑ Zha M, Zhong C, Peng Y, Hu H, Ding J. Crystal structures of human NUDT5 reveal insights into the structural basis of the substrate specificity. J Mol Biol. 2006 Dec 15;364(5):1021-33. Epub 2006 Oct 3. PMID:17052728 doi:10.1016/j.jmb.2006.09.078

2dsb, resolution 2.50Å

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