2epm
From Proteopedia
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|PDB= 2epm |SIZE=350|CAPTION= <scene name='initialview01'>2epm</scene>, resolution 2.04Å | |PDB= 2epm |SIZE=350|CAPTION= <scene name='initialview01'>2epm</scene>, resolution 2.04Å | ||
|SITE= <scene name='pdbsite=AC1:Hg+Binding+Site+For+Residue+X+630'>AC1</scene>, <scene name='pdbsite=AC2:Hg+Binding+Site+For+Residue+X+631'>AC2</scene>, <scene name='pdbsite=AC3:Hg+Binding+Site+For+Residue+X+632'>AC3</scene>, <scene name='pdbsite=AC4:Hg+Binding+Site+For+Residue+X+634'>AC4</scene>, <scene name='pdbsite=AC5:Hg+Binding+Site+For+Residue+X+636'>AC5</scene>, <scene name='pdbsite=AC6:So4+Binding+Site+For+Residue+X+740'>AC6</scene>, <scene name='pdbsite=AC7:So4+Binding+Site+For+Residue+X+741'>AC7</scene>, <scene name='pdbsite=AC8:So4+Binding+Site+For+Residue+X+742'>AC8</scene>, <scene name='pdbsite=AC9:So4+Binding+Site+For+Residue+X+743'>AC9</scene>, <scene name='pdbsite=BC1:So4+Binding+Site+For+Residue+X+744'>BC1</scene>, <scene name='pdbsite=BC2:So4+Binding+Site+For+Residue+X+745'>BC2</scene>, <scene name='pdbsite=BC3:So4+Binding+Site+For+Residue+X+746'>BC3</scene> and <scene name='pdbsite=BC4:Gol+Binding+Site+For+Residue+X+731'>BC4</scene> | |SITE= <scene name='pdbsite=AC1:Hg+Binding+Site+For+Residue+X+630'>AC1</scene>, <scene name='pdbsite=AC2:Hg+Binding+Site+For+Residue+X+631'>AC2</scene>, <scene name='pdbsite=AC3:Hg+Binding+Site+For+Residue+X+632'>AC3</scene>, <scene name='pdbsite=AC4:Hg+Binding+Site+For+Residue+X+634'>AC4</scene>, <scene name='pdbsite=AC5:Hg+Binding+Site+For+Residue+X+636'>AC5</scene>, <scene name='pdbsite=AC6:So4+Binding+Site+For+Residue+X+740'>AC6</scene>, <scene name='pdbsite=AC7:So4+Binding+Site+For+Residue+X+741'>AC7</scene>, <scene name='pdbsite=AC8:So4+Binding+Site+For+Residue+X+742'>AC8</scene>, <scene name='pdbsite=AC9:So4+Binding+Site+For+Residue+X+743'>AC9</scene>, <scene name='pdbsite=BC1:So4+Binding+Site+For+Residue+X+744'>BC1</scene>, <scene name='pdbsite=BC2:So4+Binding+Site+For+Residue+X+745'>BC2</scene>, <scene name='pdbsite=BC3:So4+Binding+Site+For+Residue+X+746'>BC3</scene> and <scene name='pdbsite=BC4:Gol+Binding+Site+For+Residue+X+731'>BC4</scene> | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> |
| - | |ACTIVITY= [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] | + | |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> |
|GENE= gcna ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1302 Streptococcus gordonii]) | |GENE= gcna ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1302 Streptococcus gordonii]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[2epk|2epk]], [[2epl|2epl]], [[2epn|2epn]], [[2epo|2epo]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2epm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2epm OCA], [http://www.ebi.ac.uk/pdbsum/2epm PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2epm RCSB]</span> | ||
}} | }} | ||
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[[Category: Harty, D W.S.]] | [[Category: Harty, D W.S.]] | ||
[[Category: Langley, D B.]] | [[Category: Langley, D B.]] | ||
| - | [[Category: GOL]] | ||
| - | [[Category: HG]] | ||
| - | [[Category: SO4]] | ||
[[Category: family 20]] | [[Category: family 20]] | ||
[[Category: gcna]] | [[Category: gcna]] | ||
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[[Category: glycoside hydrolase]] | [[Category: glycoside hydrolase]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:52:18 2008'' |
Revision as of 23:52, 30 March 2008
| |||||||
| , resolution 2.04Å | |||||||
|---|---|---|---|---|---|---|---|
| Sites: | , , , , , , , , , , , and | ||||||
| Ligands: | , , | ||||||
| Gene: | gcna (Streptococcus gordonii) | ||||||
| Activity: | Beta-N-acetylhexosaminidase, with EC number 3.2.1.52 | ||||||
| Related: | 2epk, 2epl, 2epn, 2epo
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
N-acetyl-B-D-glucoasminidase (GCNA) from Stretococcus gordonii
Overview
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 Structure
2EPM is a Single protein structure of sequence from Streptococcus gordonii. Full crystallographic information is available from OCA.
Reference
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
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