This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


3q4i

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (10:45, 21 February 2024) (edit) (undo)
 
Line 3: Line 3:
<StructureSection load='3q4i' size='340' side='right'caption='[[3q4i]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
<StructureSection load='3q4i' size='340' side='right'caption='[[3q4i]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[3q4i]] is a 2 chain structure with sequence from [https://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 [https://proteopedia.org/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" id="ligandDat"><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]] 2.5&#8491;</td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3q1p|3q1p]]</div></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 ([https://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'>[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>
</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'--&gt;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.
+
-
 
+
-
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>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 3q4i" style="background-color:#fffaf0;"></div>
+
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Baccr]]
+
[[Category: Bacillus cereus ATCC 14579]]
[[Category: Large Structures]]
[[Category: Large Structures]]
-
[[Category: Amzel, L M]]
+
[[Category: Amzel LM]]
-
[[Category: Duong-Ly, K C]]
+
[[Category: Duong-Ly KC]]
-
[[Category: Gabelli, S B]]
+
[[Category: Gabelli SB]]
-
[[Category: Asymmetric dimer]]
+
-
[[Category: Cdp-choline pyrophosphatase]]
+
-
[[Category: Hydrolase]]
+
-
[[Category: Nudix hydrolase]]
+
-
[[Category: Pyrophosphatase]]
+
-
[[Category: Rna exonuclease]]
+

Current revision

Crystal structure of CDP-Chase in complex with Gd3+

PDB ID 3q4i

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3q4i"
Personal tools