|
|
| Line 3: |
Line 3: |
| | <StructureSection load='2p8c' size='340' side='right'caption='[[2p8c]], [[Resolution|resolution]] 2.00Å' scene=''> | | <StructureSection load='2p8c' size='340' side='right'caption='[[2p8c]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2p8c]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Baccr Baccr]. 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> | + | <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> |
| - | </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> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2p88|2p88]], [[2p8b|2p8b]]</div></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> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BC_0371 ([https://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=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> | | <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> | | </table> |
| | == Function == | | == 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>
| + | [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 == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| Line 37: |
Line 36: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Baccr]] | + | [[Category: Bacillus cereus ATCC 14579]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Almo, S C]] | + | [[Category: Almo SC]] |
| - | [[Category: Fedorov, A A]] | + | [[Category: Fedorov AA]] |
| - | [[Category: Fedorov, E V]] | + | [[Category: Fedorov EV]] |
| - | [[Category: Gerlt, J A]] | + | [[Category: Gerlt JA]] |
| - | [[Category: Song, L]] | + | [[Category: Song L]] |
| - | [[Category: Enolase superfamily]]
| + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: N-succinyl amino acid racemase]]
| + | |
| - | [[Category: Prediction of function]]
| + | |
| Structural highlights
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.
See Also
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
|
