2d8l
From Proteopedia
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|PDB= 2d8l |SIZE=350|CAPTION= <scene name='initialview01'>2d8l</scene>, resolution 1.70Å | |PDB= 2d8l |SIZE=350|CAPTION= <scene name='initialview01'>2d8l</scene>, resolution 1.70Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=UCD:(4S,5R,6R)-6-((2R,3R,4R,5R,6R)-3-ACETAMIDO-2,5-DIHYDROXY-6-(HYDROXYMETHYL)-TETRAHYDRO-2H-PYRAN-4-YLOXY)-4,5-DIHYDROXY-5,6-DIHYDRO-4H-PYRAN-2-CARBOXYLIC ACID'>UCD</scene> | + | |LIGAND= <scene name='pdbligand=UCD:(4S,5R,6R)-6-((2R,3R,4R,5R,6R)-3-ACETAMIDO-2,5-DIHYDROXY-6-(HYDROXYMETHYL)-TETRAHYDRO-2H-PYRAN-4-YLOXY)-4,5-DIHYDROXY-5,6-DIHYDRO-4H-PYRAN-2-CARBOXYLIC+ACID'>UCD</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2d8l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d8l OCA], [http://www.ebi.ac.uk/pdbsum/2d8l PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2d8l RCSB]</span> | ||
}} | }} | ||
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[[Category: Murata, K.]] | [[Category: Murata, K.]] | ||
[[Category: Ochiai, A.]] | [[Category: Ochiai, A.]] | ||
| - | [[Category: UCD]] | ||
[[Category: unsaturated rhamnogalacturonyl hydrolase]] | [[Category: unsaturated rhamnogalacturonyl 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 02:31:22 2008'' |
Revision as of 23:31, 30 March 2008
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| , resolution 1.70Å | |||||||
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| Ligands: | |||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal Structure of Unsaturated Rhamnogalacturonyl Hydrolase in complex with dGlcA-GalNAc
Overview
YteR, a hypothetical protein with unknown functions, is derived from Bacillus subtilis strain 168 and has an overall structure similar to that of bacterial unsaturated glucuronyl hydrolase (UGL), although it exhibits little amino acid sequence identity with UGL. UGL releases unsaturated glucuronic acid from glycosaminoglycan treated with glycosaminoglycan lyases. The amino acid sequence of YteR shows a significant homology (26% identity) with the hypothetical protein YesR also from B. subtilis strain 168. To clarify the intrinsic functions of YteR and YesR, both proteins were overexpressed in Escherichia coli, purified, and characterized. Based on their gene arrangements in genome and enzyme properties, YteR and YesR were found to constitute a novel enzyme activity, "unsaturated rhamnogalacturonyl hydrolase," classified as new glycoside hydrolase family 105. This enzyme acts specifically on unsaturated rhamnogalacturonan (RG) obtained from RG type-I treated with RG lyases and releases an unsaturated galacturonic acid. The crystal structure of YteR complexed with unsaturated chondroitin disaccharide (UGL substrate) was obtained and compared to the structure of UGL complexed with the same disaccharide. The UGL substrate is sterically hindered with the active pocket of YteR. The protruding loop of YteR prevents the UGL substrate from being bound effectively. The most likely candidate catalytic residues for general acid/base are Asp143 in YteR and Asp135 in YesR. This is supported by three-dimensional structural and site-directed mutagenesis studies. These findings provide molecular insights into novel enzyme catalysis and sequential reaction mechanisms involved in RG-I depolymerization by bacteria.
About this Structure
2D8L is a Single protein structure of sequence from Bacillus subtilis. Full crystallographic information is available from OCA.
Reference
A novel glycoside hydrolase family 105: the structure of family 105 unsaturated rhamnogalacturonyl hydrolase complexed with a disaccharide in comparison with family 88 enzyme complexed with the disaccharide., Itoh T, Ochiai A, Mikami B, Hashimoto W, Murata K, J Mol Biol. 2006 Jul 14;360(3):573-85. Epub 2006 May 9. PMID:16781735
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