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.


1nqy

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:59, 14 February 2024) (edit) (undo)
 
Line 3: Line 3:
<StructureSection load='1nqy' size='340' side='right'caption='[[1nqy]], [[Resolution|resolution]] 2.09&Aring;' scene=''>
<StructureSection load='1nqy' size='340' side='right'caption='[[1nqy]], [[Resolution|resolution]] 2.09&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[1nqy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_radiodurans"_raj_et_al._1960 "micrococcus radiodurans" raj et al. 1960]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NQY OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1NQY FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[1nqy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NQY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NQY FirstGlance]. <br>
-
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1nqz|1nqz]]</div></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]] 2.09&#8491;</td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Dr1184 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1299 "Micrococcus radiodurans" Raj et al. 1960])</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=1nqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nqy OCA], [https://pdbe.org/1nqy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nqy RCSB], [https://www.ebi.ac.uk/pdbsum/1nqy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nqy ProSAT]</span></td></tr>
-
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleotide_diphosphatase Nucleotide diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.9 3.6.1.9] </span></td></tr>
+
-
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1nqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nqy OCA], [http://pdbe.org/1nqy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nqy RCSB], [http://www.ebi.ac.uk/pdbsum/1nqy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nqy ProSAT]</span></td></tr>
+
</table>
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/Y1184_DEIRA Y1184_DEIRA]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Line 19: Line 19:
</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=1nqy ConSurf].
</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=1nqy ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
-
<div style="background-color:#fffaf0;">
 
-
== Publication Abstract from PubMed ==
 
-
Gene Dr1184 from Deinococcus radiodurans codes for a Nudix enzyme (DR-CoAse) that hydrolyzes the pyrophosphate moiety of coenzyme A (CoA). Nudix enzymes with the same specificity have been found in yeast, humans, and mice. The three-dimensional structure of DR-CoAse, the first of a Nudix hydrolase with this specificity, reveals that this enzyme contains, in addition to the fold observed in other Nudix enzymes, insertions that are characteristic of a CoA-hydrolyzing Nudix subfamily. The structure of the complex of the enzyme with Mg(2+), its activating cation, reveals the position of the catalytic site. A helix, part of the N-terminal insertion, partially occludes the binding site and has to change its position to permit substrate binding. Comparison of the structure of DR-CoAse to those of other Nudix enzymes, together with the location in the structure of the sequence characteristic of CoAses, suggests a mode of binding of the substrate to the enzyme that is compatible with all available data.
 
- 
-
Structure of a coenzyme A pyrophosphatase from Deinococcus radiodurans: a member of the Nudix family.,Kang LW, Gabelli SB, Bianchet MA, Xu WL, Bessman MJ, Amzel LM J Bacteriol. 2003 Jul;185(14):4110-8. PMID:12837785<ref>PMID:12837785</ref>
 
- 
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
-
</div>
 
-
<div class="pdbe-citations 1nqy" style="background-color:#fffaf0;"></div>
 
-
== References ==
 
-
<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Micrococcus radiodurans raj et al. 1960]]
+
[[Category: Deinococcus radiodurans]]
[[Category: Large Structures]]
[[Category: Large Structures]]
-
[[Category: Nucleotide diphosphatase]]
+
[[Category: Amzel LM]]
-
[[Category: Amzel, L M]]
+
[[Category: Bessman MJ]]
-
[[Category: Bessman, M J]]
+
[[Category: Bianchet MA]]
-
[[Category: Bianchet, M A]]
+
[[Category: Gabelli SB]]
-
[[Category: Gabelli, S B]]
+
[[Category: Kang LW]]
-
[[Category: Kang, L W]]
+
[[Category: Xu WL]]
-
[[Category: Xu, W L]]
+
-
[[Category: Coa]]
+
-
[[Category: Dr1184]]
+
-
[[Category: Hydrolase]]
+
-
[[Category: Nudix]]
+
-
[[Category: Pyrophosphatase]]
+

Current revision

The structure of a CoA pyrophosphatase from D. Radiodurans

PDB ID 1nqy

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Personal tools