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.

3roe

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Crystal Structure of Mouse Apolipoprotein A-I Binding Protein in Complex with Thymidine

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3roe"

@@ Line 3: / Line 3: @@
 <StructureSection load='3roe' size='340' side='right'caption='[[3roe]], [[Resolution|resolution]] 2.11&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3roe]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ROE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ROE FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3roe]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ROE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ROE FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=THM:THYMIDINE'>THM</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]] 2.11&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=THM:THYMIDINE'>THM</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2o8n|2o8n]], [[2dg2|2dg2]], [[3rno|3rno]], [[3ro7|3ro7]], [[3rog|3rog]], [[3rox|3rox]], [[3roz|3roz]]</div></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Aibp, Apoa1bp ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</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=3roe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3roe OCA], [https://pdbe.org/3roe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3roe RCSB], [https://www.ebi.ac.uk/pdbsum/3roe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3roe ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/NNRE_MOUSE NNRE_MOUSE]] Catalyzes the epimerization of the S- and R-forms of NAD(P)HX, a damaged form of NAD(P)H that is a result of enzymatic or heat-dependent hydration. This is a prerequisite for the S-specific NAD(P)H-hydrate dehydratase to allow the repair of both epimers of NAD(P)HX.[HAMAP-Rule:MF_03159]<ref>PMID:21994945</ref>
+[https://www.uniprot.org/uniprot/NNRE_MOUSE NNRE_MOUSE] Catalyzes the epimerization of the S- and R-forms of NAD(P)HX, a damaged form of NAD(P)H that is a result of enzymatic or heat-dependent hydration. This is a prerequisite for the S-specific NAD(P)H-hydrate dehydratase to allow the repair of both epimers of NAD(P)HX.[HAMAP-Rule:MF_03159]<ref>PMID:21994945</ref>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Proteins of unknown function comprise a significant fraction of sequenced genomes. Defining the roles of these proteins is vital to understanding cellular processes. Here, we describe a method to determine a protein function based on the identification of its natural ligand(s) by the crystallographic screening of the binding of a metabolite library, followed by a focused search in the metabolic space. The method was applied to two protein families with unknown function, PF01256 and YjeF_N. The PF01256 proteins, represented by YxkO from Bacillus subtilis and the C-terminal domain of Tm0922 from Thermotoga maritima, were shown to catalyze ADP/ATP-dependent NAD(P)H-hydrate dehydratation, a previously described orphan activity. The YjeF_N proteins, represented by mouse apolipoprotein A-I binding protein and the N-terminal domain of Tm0922, were found to interact with an adenosine diphosphoribose-related substrate and likely serve as ADP-ribosyltransferases. Crystallographic screening of metabolites serves as an efficient tool in functional analyses of uncharacterized proteins.
-Identification of Unknown Protein Function Using Metabolite Cocktail Screening.,Shumilin IA, Cymborowski M, Chertihin O, Jha KN, Herr JC, Lesley SA, Joachimiak A, Minor W Structure. 2012 Aug 28. PMID:22940582<ref>PMID:22940582</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3roe" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
@@ Line 26: / Line 15: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Lk3 transgenic mice]]
+[[Category: Mus musculus]]
-[[Category: Cymborowski, M]]
+[[Category: Cymborowski M]]
-[[Category: Herr, J C]]
+[[Category: Herr JC]]
-[[Category: Jha, K N]]
+[[Category: Jha KN]]
-[[Category: Minor, W]]
+[[Category: Minor W]]
-[[Category: Shumilin, I A]]
+[[Category: Shumilin IA]]
-[[Category: Protein binding]]
-[[Category: Rossmann fold]]

3roe

From Proteopedia

Current revision

Crystal Structure of Mouse Apolipoprotein A-I Binding Protein in Complex with Thymidine

Structural highlights

Function

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox