2epk: Difference between revisions

Revision as of 02:57, 4 May 2008

N-acetyl-B-D-glucosaminidase (GCNA) from Streptococcus gordonii

OverviewOverview

The crystal structure of GcnA, an N-acetyl-beta-D-glucosaminidase from Streptococcus gordonii, was solved by multiple wavelength anomalous dispersion phasing using crystals of selenomethionine-substituted protein. GcnA is a homodimer with subunits each comprised of three domains. The structure of the C-terminal alpha-helical domain has not been observed previously and forms a large dimerisation interface. The fold of the N-terminal domain is observed in all structurally related glycosidases although its function is unknown. The central domain has a canonical (beta/alpha)(8) TIM-barrel fold which harbours the active site. The primary sequence and structure of this central domain identifies the enzyme as a family 20 glycosidase. Key residues implicated in catalysis have different conformations in two different crystal forms, which probably represent active and inactive conformations of the enzyme. The catalytic mechanism for this class of glycoside hydrolase, where the substrate rather than the enzyme provides the cleavage-inducing nucleophile, has been confirmed by the structure of GcnA complexed with a putative reaction intermediate analogue, N-acetyl-beta-D-glucosamine-thiazoline. The catalytic mechanism is discussed in light of these and other family 20 structures.

About this StructureAbout this Structure

2EPK is a Single protein structure of sequence from Streptococcus gordonii. Full crystallographic information is available from OCA.

ReferenceReference

Structure of N-acetyl-beta-D-glucosaminidase (GcnA) from the endocarditis pathogen Streptococcus gordonii and its complex with the mechanism-based inhibitor NAG-thiazoline., Langley DB, Harty DW, Jacques NA, Hunter N, Guss JM, Collyer CA, J Mol Biol. 2008 Mar 14;377(1):104-16. Epub 2007 Sep 16. PMID:18237743 Page seeded by OCA on Sun May 4 02:57:09 2008

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OCA

@@ Line 1: / Line 1: @@
 [[Image:2epk.jpg|left|200px]]
- {{Structure
+<!--
-|PDB= 2epk |SIZE=350|CAPTION= <scene name='initialview01'>2epk</scene>, resolution 1.85&Aring;
+The line below this paragraph, containing "STRUCTURE_2epk", creates the "Structure Box" on the page.
-|SITE= <scene name='pdbsite=AC1:So4+Binding+Site+For+Residue+X+740'>AC1</scene>, <scene name='pdbsite=AC2:So4+Binding+Site+For+Residue+X+741'>AC2</scene>, <scene name='pdbsite=AC3:So4+Binding+Site+For+Residue+X+742'>AC3</scene>, <scene name='pdbsite=AC4:So4+Binding+Site+For+Residue+X+743'>AC4</scene>, <scene name='pdbsite=AC5:So4+Binding+Site+For+Residue+X+744'>AC5</scene>, <scene name='pdbsite=AC6:So4+Binding+Site+For+Residue+X+745'>AC6</scene> and <scene name='pdbsite=AC7:So4+Binding+Site+For+Residue+X+746'>AC7</scene>
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>
+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-N-acetylhexosaminidase Beta-N-acetylhexosaminidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.52 3.2.1.52] </span>
+or leave the SCENE parameter empty for the default display.
-|GENE= gcna ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1302 Streptococcus gordonii])
+-->
-|DOMAIN=
+{{STRUCTURE_2epk|  PDB=2epk  |  SCENE=  }}
-|RELATEDENTRY=[[2epl|2epl]], [[2epm|2epm]], [[2epn|2epn]], [[2epo|2epo]]
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2epk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2epk OCA], [http://www.ebi.ac.uk/pdbsum/2epk PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2epk RCSB]</span>
-}}
 '''N-acetyl-B-D-glucosaminidase (GCNA) from Streptococcus gordonii'''
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 [[Category: Streptococcus gordonii]]
 [[Category: Langley, D B.]]
-[[Category: family 20]]
+[[Category: Family 20]]
-[[Category: gcna]]
+[[Category: Gcna]]
-[[Category: glucosaminidase]]
+[[Category: Glucosaminidase]]
-[[Category: glycoside hydrolase]]
+[[Category: Glycoside hydrolase]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 02:57:09 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:52:13 2008''