3rtb: Difference between revisions

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-[[Image:3rtb.png|left|200px]]
+==Crystal structure of tm0922, a fusion of a domain of unknown function and ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Thermotoga maritima soaked with Adenosine-3'-5'-Diphosphate==
+<StructureSection load='3rtb' size='340' side='right' caption='[[3rtb]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3rtb]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RTB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RTB FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A3P:ADENOSINE-3-5-DIPHOSPHATE'>A3P</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2ax3|2ax3]], [[3rno|3rno]], [[3ro7|3ro7]], [[3roe|3roe]], [[3rog|3rog]], [[3rox|3rox]], [[3roz|3roz]], [[3rrb|3rrb]], [[3rre|3rre]], [[3rrf|3rrf]], [[3rrj|3rrj]], [[3rs8|3rs8]], [[3rs9|3rs9]], [[3rsf|3rsf]], [[3rsg|3rsg]], [[3rsq|3rsq]], [[3rss|3rss]], [[3rt7|3rt7]], [[3rt9|3rt9]], [[3rta|3rta]], [[3rtc|3rtc]], [[3rtd|3rtd]], [[3rte|3rte]], [[3rtg|3rtg]], [[3ru2|3ru2]], [[3ru3|3ru3]]</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">tm0922, TM_0922 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 Thermotoga maritima])</td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/ATP-dependent_NAD(P)H-hydrate_dehydratase ATP-dependent NAD(P)H-hydrate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.93 4.2.1.93] </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=3rtb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rtb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rtb RCSB], [http://www.ebi.ac.uk/pdbsum/3rtb PDBsum]</span></td></tr>
+</table>
+<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.
-{{STRUCTURE_3rtb|  PDB=3rtb  |  SCENE=  }}
+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>
-===Crystal structure of tm0922, a fusion of a domain of unknown function and ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Thermotoga maritima soaked with Adenosine-3'-5'-Diphosphate===
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-{{ABSTRACT_PUBMED_22940582}}
+== References ==
+<references/>
-==About this Structure==
+__TOC__
-[[3rtb]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RTB OCA].
+</StructureSection>
 [[Category: Escherichia coli]]
 [[Category: Thermotoga maritima]]
-[[Category: Cymborowski, M.]]
+[[Category: Cymborowski, M]]
-[[Category: Lesley, S A.]]
+[[Category: Lesley, S A]]
-[[Category: Minor, W.]]
+[[Category: Minor, W]]
-[[Category: Shumilin, I A.]]
+[[Category: Shumilin, I A]]
 [[Category: Lyase]]
 [[Category: Unknown function]]