2p8c: Difference between revisions

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-{{Seed}}
-[[Image:2p8c.png|left|200px]]
-<!--
+==Crystal structure of N-succinyl Arg/Lys racemase from Bacillus cereus ATCC 14579 complexed with N-succinyl Arg.==
-The line below this paragraph, containing "STRUCTURE_2p8c", creates the "Structure Box" on the page.
+<StructureSection load='2p8c' size='340' side='right'caption='[[2p8c]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2p8c]] is a 1 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=2P8C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2P8C FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</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&#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>, <scene name='pdbligand=SUG:N~2~-(3-CARBOXYPROPANOYL)-L-ARGININE'>SUG</scene></td></tr>
-{{STRUCTURE_2p8c|  PDB=2p8c  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2p8c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p8c OCA], [https://pdbe.org/2p8c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2p8c RCSB], [https://www.ebi.ac.uk/pdbsum/2p8c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2p8c 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/p8/2p8c_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=2p8c 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 complexed with N-succinyl Arg.===
+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>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2p8c" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17603539}}, adds the Publication Abstract to the page
+*[[Mandelate racemase/muconate lactonizing enzyme 3D structures|Mandelate racemase/muconate lactonizing enzyme 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 17603539 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17603539}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Bacillus cereus ATCC 14579]]
-P8C is a [[Single protein]] structure of 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=2P8C OCA].
+[[Category: Large Structures]]
+[[Category: Almo SC]]
-==Reference==
+[[Category: Fedorov AA]]
-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:[http://www.ncbi.nlm.nih.gov/pubmed/17603539 17603539]
+[[Category: Fedorov EV]]
-[[Category: Bacillus cereus atcc 14579]]
+[[Category: Gerlt JA]]
-[[Category: Single protein]]
+[[Category: Song L]]
-[[Category: Almo, S C.]]
-[[Category: Fedorov, A A.]]
-[[Category: Fedorov, E V.]]
-[[Category: Gerlt, J A.]]
-[[Category: Song, L.]]
-[[Category: Enolase superfamily]]
-[[Category: Lyase]]
-[[Category: N-succinyl amino acid racemase]]
-[[Category: Prediction of function]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 14:19:31 2008''