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2p88

From Proteopedia

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Crystal structure of N-succinyl Arg/Lys racemase from Bacillus cereus ATCC 14579

Structural highlights

2p88 is a 8 chain structure with sequence from Bacillus cereus ATCC 14579. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.4Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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).^[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 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.

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.

References

↑ Song L, Kalyanaraman C, Fedorov AA, Fedorov EV, Glasner ME, Brown S, Imker HJ, Babbitt PC, Almo SC, Jacobson MP, Gerlt JA. Prediction and assignment of function for a divergent N-succinyl amino acid racemase. Nat Chem Biol. 2007 Aug;3(8):486-91. Epub 2007 Jul 1. PMID:17603539 doi:10.1038/nchembio.2007.11
↑ Song L, Kalyanaraman C, Fedorov AA, Fedorov EV, Glasner ME, Brown S, Imker HJ, Babbitt PC, Almo SC, Jacobson MP, Gerlt JA. Prediction and assignment of function for a divergent N-succinyl amino acid racemase. Nat Chem Biol. 2007 Aug;3(8):486-91. Epub 2007 Jul 1. PMID:17603539 doi:10.1038/nchembio.2007.11

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2p88"

@@ Line 1: / Line 1: @@
 ==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=''>
+<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 [http://en.wikipedia.org/wiki/Baccr Baccr]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2P88 FirstGlance]. <br>
+<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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.4&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2p8b|2p8b]], [[2p8c|2p8c]]</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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BC_0371 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=226900 BACCR])</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>
-<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=2p88 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p88 OCA], [http://pdbe.org/2p88 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2p88 RCSB], [http://www.ebi.ac.uk/pdbsum/2p88 PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://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>
+[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>
+    <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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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;">
@@ Line 29: / Line 29: @@
 </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: Baccr]]
+[[Category: Bacillus cereus ATCC 14579]]
-[[Category: Almo, S C]]
+[[Category: Large Structures]]
-[[Category: Fedorov, A A]]
+[[Category: Almo SC]]
-[[Category: Fedorov, E V]]
+[[Category: Fedorov AA]]
-[[Category: Gerlt, J A]]
+[[Category: Fedorov EV]]
-[[Category: Song, L]]
+[[Category: Gerlt JA]]
-[[Category: Enolase superfamily]]
+[[Category: Song L]]
-[[Category: Lyase]]
-[[Category: N-succinyl amino acid racemase]]
-[[Category: Prediction of function]]

2p88

From Proteopedia

Current revision

Crystal structure of N-succinyl Arg/Lys racemase from Bacillus cereus ATCC 14579

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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