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==Crystal structure of N-succinyl Arg/Lys racemase from Bacillus cereus ATCC 14579== | |||
<StructureSection load='2p88' size='340' side='right'caption='[[2p88]], [[Resolution|resolution]] 2.40Å' 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]] 2.4Å</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. | 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. | ||
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®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2p88" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Mandelate racemase/muconate lactonizing enzyme 3D structures|Mandelate racemase/muconate lactonizing enzyme 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Bacillus cereus ATCC 14579]] | |||
[[Category: Large Structures]] | |||
[[Category: Almo SC]] | |||
[[Category: Fedorov AA]] | |||
[[Category: Fedorov EV]] | |||
[[Category: Gerlt JA]] | |||
[[Category: Song L]] | |||
Latest revision as of 13:57, 30 August 2023
Crystal structure of N-succinyl Arg/Lys racemase from Bacillus cereus ATCC 14579Crystal structure of N-succinyl Arg/Lys racemase from Bacillus cereus ATCC 14579
Structural highlights
FunctionNSAR_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).[1] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe 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. 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[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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