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2dsc

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Revision as of 11:36, 10 February 2021

Crystal structure of human ADP-ribose pyrophosphatase NUDT5 in complex with magnesium and ADP-ribose

Structural highlights

2dsc is a 2 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	2dsb, 2dsd
Gene:	NUDT5 (HUMAN)
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.

Publication Abstract from PubMed

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.

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:17052728^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ 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
↑ 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

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2dsc"

@@ Line 1: / Line 1: @@
 ==Crystal structure of human ADP-ribose pyrophosphatase NUDT5 in complex with magnesium and ADP-ribose==
-<StructureSection load='2dsc' size='340' side='right' caption='[[2dsc]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+<StructureSection load='2dsc' size='340' side='right'caption='[[2dsc]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2dsc]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DSC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DSC FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2dsc]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DSC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DSC FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2dsb|2dsb]], [[2dsd|2dsd]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2dsb|2dsb]], [[2dsd|2dsd]]</div></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NUDT5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NUDT5 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dsc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dsc OCA], [http://pdbe.org/2dsc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dsc RCSB], [http://www.ebi.ac.uk/pdbsum/2dsc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dsc ProSAT]</span></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=2dsc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dsc OCA], [https://pdbe.org/2dsc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dsc RCSB], [https://www.ebi.ac.uk/pdbsum/2dsc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dsc ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://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>
+[[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]]
@@ Line 35: / Line 35: @@
 </StructureSection>
 [[Category: Human]]
+[[Category: Large Structures]]
 [[Category: Ding, J]]
 [[Category: Zha, M]]

2dsc

From Proteopedia

Revision as of 11:36, 10 February 2021

Crystal structure of human ADP-ribose pyrophosphatase NUDT5 in complex with magnesium and ADP-ribose

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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