2p88: Difference between revisions

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-[[Image:2p88.png|left|200px]]
-{{STRUCTURE_2p88|  PDB=2p88  |  SCENE=  }}
+==Crystal structure of N-succinyl Arg/Lys racemase from Bacillus cereus ATCC 14579==
+<StructureSection load='2p88' size='340' side='right'caption='[[2p88]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2p88]] is a 8 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=2P88 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2P88 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=2p88 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p88 OCA], [https://pdbe.org/2p88 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2p88 RCSB], [https://www.ebi.ac.uk/pdbsum/2p88 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2p88 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NSAR_BACCR NSAR_BACCR] Catalyzes efficient racemization of N-succinyl-L-Arg and N-succinyl-L-Lys, suggesting that these are physiological substrates of this enzyme. Has low activity with L-Asp-L-Lys, and even lower activity with L-Leu-L-Arg, L-Leu-L-Lys, N-succinyl-L-His and N-succinyl-L-Met (in vitro).<ref>PMID:17603539</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/p8/2p88_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=2p88 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The protein databases contain many proteins with unknown function. A computational approach for predicting ligand specificity that requires only the sequence of the unknown protein would be valuable for directing experiment-based assignment of function. We focused on a family of unknown proteins in the mechanistically diverse enolase superfamily and used two approaches to assign function: (i) enzymatic assays using libraries of potential substrates, and (ii) in silico docking of the same libraries using a homology model based on the most similar (35% sequence identity) characterized protein. The results matched closely; an experimentally determined structure confirmed the predicted structure of the substrate-liganded complex. We assigned the N-succinyl arginine/lysine racemase function to the family, correcting the annotation (L-Ala-D/L-Glu epimerase) based on the function of the most similar characterized homolog. These studies establish that ligand docking to a homology model can facilitate functional assignment of unknown proteins by restricting the identities of the possible substrates that must be experimentally tested.
-===Crystal structure of N-succinyl Arg/Lys racemase from Bacillus cereus ATCC 14579===
+Prediction and assignment of function for a divergent N-succinyl amino acid racemase.,Song L, Kalyanaraman C, Fedorov AA, Fedorov EV, Glasner ME, Brown S, Imker HJ, Babbitt PC, Almo SC, Jacobson MP, Gerlt JA Nat Chem Biol. 2007 Aug;3(8):486-91. Epub 2007 Jul 1. PMID:17603539<ref>PMID:17603539</ref>
-{{ABSTRACT_PUBMED_17603539}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2p88" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-[[2p88]] is a 8 chain structure with sequence from [http://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=2P88 OCA].
+*[[Mandelate racemase/muconate lactonizing enzyme 3D structures|Mandelate racemase/muconate lactonizing enzyme 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:017603539</ref><references group="xtra"/>
+__TOC__
-[[Category: Bacillus cereus atcc 14579]]
+</StructureSection>
-[[Category: Almo, S C.]]
+[[Category: Bacillus cereus ATCC 14579]]
-[[Category: Fedorov, A A.]]
+[[Category: Large Structures]]
-[[Category: Fedorov, E V.]]
+[[Category: Almo SC]]
-[[Category: Gerlt, J A.]]
+[[Category: Fedorov AA]]
-[[Category: Song, L.]]
+[[Category: Fedorov EV]]
-[[Category: Enolase superfamily]]
+[[Category: Gerlt JA]]
-[[Category: Lyase]]
+[[Category: Song L]]
-[[Category: N-succinyl amino acid racemase]]
-[[Category: Prediction of function]]