1yht
From Proteopedia
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|PDB= 1yht |SIZE=350|CAPTION= <scene name='initialview01'>1yht</scene>, resolution 2.00Å | |PDB= 1yht |SIZE=350|CAPTION= <scene name='initialview01'>1yht</scene>, resolution 2.00Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene> | + | |LIGAND= <scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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= dspB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=714 Aggregatibacter actinomycetemcomitans]) | |GENE= dspB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=714 Aggregatibacter actinomycetemcomitans]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1hp4|1HP4]], [[1o7a|1O7A]], [[1now|1NOW]], [[1qbb|1QBB]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1yht FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yht OCA], [http://www.ebi.ac.uk/pdbsum/1yht PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1yht RCSB]</span> | ||
}} | }} | ||
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[[Category: Ramasubbu, N.]] | [[Category: Ramasubbu, N.]] | ||
[[Category: Thomas, L M.]] | [[Category: Thomas, L M.]] | ||
| - | [[Category: ACY]] | ||
| - | [[Category: GOL]] | ||
[[Category: beta barrel]] | [[Category: beta barrel]] | ||
| - | ''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 01:07:40 2008'' |
Revision as of 22:07, 30 March 2008
| |||||||
| , resolution 2.00Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , | ||||||
| Gene: | dspB (Aggregatibacter actinomycetemcomitans) | ||||||
| Activity: | Beta-N-acetylhexosaminidase, with EC number 3.2.1.52 | ||||||
| Related: | 1HP4, 1O7A, 1NOW, 1QBB
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure analysis of Dispersin B
Overview
Bacteria in a biofilm are enmeshed in a self-synthesized extracellular polysaccharide matrix that holds the bacteria together in a mass and firmly attaches the bacterial mass to the underlying surface. A major component of the extracellular polysaccharide matrix in several phylogenetically diverse bacteria is PGA, a linear polymer of N-acetylglucosamine residues in beta(1,6)-linkage. PGA is produced by the Gram-negative periodontopathogen Actinobacillus actinomycetemcomitans as well as by the Gram-positive device-associated pathogen Staphylococcus epidermidis. We recently reported that A.actinomycetemcomitans produces a soluble glycoside hydrolase named dispersin B, which degrades PGA. Here, we present the crystal structure of dispersin B at 2.0A in complex with a glycerol and an acetate ion at the active site. The enzyme crystallizes in the orthorhombic space group C222(1) with cell dimensions a=41.02A, b=86.13A, c=185.77A. The core of the enzyme consists a (beta/alpha)(8) barrel topology similar to other beta-hexosaminidases but significant differences exist in the arrangement of loops hovering in the vicinity of the active site. The location and interactions of the glycerol and acetate moieties in conjunction with the sequence analysis suggest that dispersin B cleaves beta(1,6)-linked N-acetylglucosamine polymer using a catalytic machinery similar to other family 20 hexosaminidases which cleave beta(1,4)-linked N-acetylglucosamine residues.
About this Structure
1YHT is a Single protein structure of sequence from Aggregatibacter actinomycetemcomitans. Full crystallographic information is available from OCA.
Reference
Structural analysis of dispersin B, a biofilm-releasing glycoside hydrolase from the periodontopathogen Actinobacillus actinomycetemcomitans., Ramasubbu N, Thomas LM, Ragunath C, Kaplan JB, J Mol Biol. 2005 Jun 10;349(3):475-86. Epub 2005 Apr 14. PMID:15878175
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