2d8l: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,328,572 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,328,572 edits
No edit summary
 
(12 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:2d8l.gif|left|200px]]


{{Structure
==Crystal Structure of Unsaturated Rhamnogalacturonyl Hydrolase in complex with dGlcA-GalNAc==
|PDB= 2d8l |SIZE=350|CAPTION= <scene name='initialview01'>2d8l</scene>, resolution 1.70&Aring;
<StructureSection load='2d8l' size='340' side='right'caption='[[2d8l]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|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>
<table><tr><td colspan='2'>[[2d8l]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D8L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D8L FirstGlance]. <br>
|ACTIVITY=  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
|GENE=  
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GCD:4,5-DEHYDRO-D-GLUCURONIC+ACID'>GCD</scene>, <scene name='pdbligand=NGA:N-ACETYL-D-GALACTOSAMINE'>NGA</scene>, <scene name='pdbligand=PRD_900058:UNSATURATED+CHONDROITIN+DISACCHARIDE'>PRD_900058</scene></td></tr>
|DOMAIN=
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2d8l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d8l OCA], [https://pdbe.org/2d8l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d8l RCSB], [https://www.ebi.ac.uk/pdbsum/2d8l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d8l ProSAT]</span></td></tr>
|RELATEDENTRY=
</table>
|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>
== Function ==
}}
[https://www.uniprot.org/uniprot/URHG2_BACSU URHG2_BACSU] Catalyzes the hydrolysis of unsaturated rhamnogalacturonan disaccharide to yield unsaturated D-galacturonic acid and L-rhamnose. It cannot act on unsaturated glucuronyl hydrolase (UGL) substrates containing unsaturated D-glucuronic acid at the non-reducing terminus, although the active pockets of YesR and UGL are very similar.<ref>PMID:16781735</ref>
 
== Evolutionary Conservation ==
'''Crystal Structure of Unsaturated Rhamnogalacturonyl Hydrolase in complex with dGlcA-GalNAc'''
[[Image:Consurf_key_small.gif|200px|right]]
 
Check<jmol>
 
  <jmolCheckbox>
==Overview==
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d8/2d8l_consurf.spt"</scriptWhenChecked>
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.
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 
    <text>to colour the structure by Evolutionary Conservation</text>
==About this Structure==
  </jmolCheckbox>
2D8L is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D8L OCA].  
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2d8l ConSurf].
 
<div style="clear:both"></div>
==Reference==
== References ==
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:[http://www.ncbi.nlm.nih.gov/pubmed/16781735 16781735]
<references/>
__TOC__
</StructureSection>
[[Category: Bacillus subtilis]]
[[Category: Bacillus subtilis]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Hashimoto, W.]]
[[Category: Hashimoto W]]
[[Category: Itoh, T.]]
[[Category: Itoh T]]
[[Category: Mikami, B.]]
[[Category: Mikami B]]
[[Category: Murata, K.]]
[[Category: Murata K]]
[[Category: Ochiai, A.]]
[[Category: Ochiai A]]
[[Category: unsaturated rhamnogalacturonyl hydrolase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:31:22 2008''
Retrieved from "https://proteopedia.org/2d8l"