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| | ==Crystal structure of CDP-Chase in complex with Gd3+== | | ==Crystal structure of CDP-Chase in complex with Gd3+== |
| - | <StructureSection load='3q4i' size='340' side='right' caption='[[3q4i]], [[Resolution|resolution]] 2.50Å' scene=''> | + | <StructureSection load='3q4i' size='340' side='right'caption='[[3q4i]], [[Resolution|resolution]] 2.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3q4i]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Baccr Baccr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3Q4I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3Q4I FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3q4i]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_cereus_ATCC_14579 Bacillus cereus ATCC 14579]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3Q4I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3Q4I FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GD3:GADOLINIUM+ION'>GD3</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3q1p|3q1p]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GD3:GADOLINIUM+ION'>GD3</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BC2032, BC_2032 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=226900 BACCR])</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=3q4i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q4i OCA], [https://pdbe.org/3q4i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3q4i RCSB], [https://www.ebi.ac.uk/pdbsum/3q4i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3q4i ProSAT]</span></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=3q4i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3q4i OCA], [http://pdbe.org/3q4i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3q4i RCSB], [http://www.ebi.ac.uk/pdbsum/3q4i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3q4i ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| - | <div style="background-color:#fffaf0;">
| + | == Function == |
| - | == Publication Abstract from PubMed == | + | [https://www.uniprot.org/uniprot/Q81EE8_BACCR Q81EE8_BACCR] |
| - | A Nudix enzyme from Bacillus cereus (NCBI RefSeq accession no. NP_831800) catalyzes the hydrolysis of CDP-choline to produce CMP and phosphocholine. Here, we show that in addition, the enzyme has a 3'-->5' RNA exonuclease activity. The structure of the free enzyme, determined to a 1.8-A resolution, shows that the enzyme is an asymmetric dimer. Each monomer consists of two domains, an N-terminal helical domain and a C-terminal Nudix domain. The N-terminal domain is placed relative to the C-terminal domain such as to result in an overall asymmetric arrangement with two distinct catalytic sites: one with an "enclosed" Nudix pyrophosphatase site and the other with a more open, less-defined cavity. Residues that may be important for determining the asymmetry are conserved among a group of uncharacterized Nudix enzymes from Gram-positive bacteria. Our data support a model where CDP-choline hydrolysis is catalyzed by the enclosed Nudix site and RNA exonuclease activity is catalyzed by the open site. CDP-Chase is the first identified member of a novel Nudix family in which structural asymmetry has a profound effect on the recognition of substrates.
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| - | The Nudix Hydrolase CDP-Chase, a CDP-Choline Pyrophosphatase, Is an Asymmetric Dimer with Two Distinct Enzymatic Activities.,Duong-Ly KC, Gabelli SB, Xu W, Dunn CA, Schoeffield AJ, Bessman MJ, Amzel LM J Bacteriol. 2011 Jul;193(13):3175-85. Epub 2011 Apr 29. PMID:21531795<ref>PMID:21531795</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
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| - | <div class="pdbe-citations 3q4i" style="background-color:#fffaf0;"></div>
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| - | == References ==
| + | |
| - | <references/>
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Baccr]] | + | [[Category: Bacillus cereus ATCC 14579]] |
| - | [[Category: Amzel, L M]] | + | [[Category: Large Structures]] |
| - | [[Category: Duong-Ly, K C]] | + | [[Category: Amzel LM]] |
| - | [[Category: Gabelli, S B]] | + | [[Category: Duong-Ly KC]] |
| - | [[Category: Asymmetric dimer]]
| + | [[Category: Gabelli SB]] |
| - | [[Category: Cdp-choline pyrophosphatase]]
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| - | [[Category: Hydrolase]] | + | |
| - | [[Category: Nudix hydrolase]]
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| - | [[Category: Pyrophosphatase]]
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| - | [[Category: Rna exonuclease]]
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