2p8c: Difference between revisions

Revision as of 12:35, 4 May 2008

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

OverviewOverview

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.

About this StructureAbout this Structure

2P8C is a Single protein structure of sequence from Bacillus cereus atcc 14579. Full crystallographic information is available from OCA.

ReferenceReference

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 Page seeded by OCA on Sun May 4 12:35:42 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
 [[Image:2p8c.jpg|left|200px]]
- {{Structure
+<!--
-|PDB= 2p8c |SIZE=350|CAPTION= <scene name='initialview01'>2p8c</scene>, resolution 2.00&Aring;
+The line below this paragraph, containing "STRUCTURE_2p8c", creates the "Structure Box" on the page.
-|SITE=
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SUG:N~2~-(3-CARBOXYPROPANOYL)-L-ARGININE'>SUG</scene>
+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-|ACTIVITY=
+or leave the SCENE parameter empty for the default display.
-|GENE= BC_0371 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=226900 Bacillus cereus ATCC 14579])
+-->
-|DOMAIN=
+{{STRUCTURE_2p8c|  PDB=2p8c  |  SCENE=  }}
-|RELATEDENTRY=[[2p88|2P88]], [[2p8b|2P8B]]
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2p8c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p8c OCA], [http://www.ebi.ac.uk/pdbsum/2p8c PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2p8c RCSB]</span>
-}}
 '''Crystal structure of N-succinyl Arg/Lys racemase from Bacillus cereus ATCC 14579 complexed with N-succinyl Arg.'''
@@ Line 30: / Line 27: @@
 [[Category: Gerlt, J A.]]
 [[Category: Song, L.]]
-[[Category: enolase superfamily]]
+[[Category: Enolase superfamily]]
-[[Category: lyase]]
+[[Category: Lyase]]
-[[Category: n-succinyl amino acid racemase]]
+[[Category: N-succinyl amino acid racemase]]
-[[Category: prediction of function]]
+[[Category: Prediction of function]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 12:35:42 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:32:01 2008''