5z06: Difference between revisions

Line 1:

~~'''Unreleased structure'''~~

~~The entry~~ 5z06 is ~~ON HOLD until Dec 18 2019~~

==Crystal structure of beta-1,2-glucanase from Parabacteroides distasonis==

== Structural highlights ==

<table><tr><td colspan='2'>[[5z06]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z06 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z06 FirstGlance]. <br>

</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>

<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5z06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z06 OCA], [http://pdbe.org/5z06 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z06 RCSB], [http://www.ebi.ac.uk/pdbsum/5z06 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z06 ProSAT]</span></td></tr>

</table>

== Publication Abstract from PubMed ==

beta-1,2-Glucan is a polysaccharide produced mainly by some Gram-negative bacteria as a symbiosis and infectious factor. We recently identified endo-beta-1,2-glucanase from Chitinophaga pinensis ( CpSGL) as an enzyme comprising a new family. Here, we report the characteristics and crystal structure of a CpSGL homologue from Parabacteroides distasonis, an intestinal bacterium (BDI_3064 protein), which exhibits distinctive properties of known beta-1,2-glucan-degrading enzymes. BDI_3064 hydrolyzed linear beta-1,2-glucan and beta-1,2-glucooligosaccharides with degrees of polymerization (DPs) of >/=4 to produce sophorose specifically but did not hydrolyze cyclic beta-1,2-glucan. This result indicates that BDI_3064 is a new exo-type enzyme. BDI_3064 also produced sophorose from beta-1,2-glucooligosaccharide analogues that have a modified reducing end, indicating that BDI_3064 acts on its substrates from the nonreducing end. The crystal structure showed that BDI_3064 possesses additional N-terminal domains 1 and 2, unlike CpSGL. Superimposition of BDI_3064 and CpSGL complexed with ligands showed that R93 in domain 1 overlapped subsite -3 in CpSGL. Docking analysis involving a beta-1,2-glucooligosaccharide with DP4 showed that R93 completely blocks the nonreducing end of the docked beta-1,2-glucooligosaccharide. This indicates that BDI_3064 employs a distinct mechanism of recognition at the nonreducing end of substrates to act as an exo-type enzyme. Thus, we propose 2-beta-d-glucooligosaccharide sophorohydrolase (nonreducing end) as a systematic name for BDI_3064.

~~Authors~~:

Characterization and Structural Analysis of a Novel exo-Type Enzyme Acting on beta-1,2-Glucooligosaccharides from Parabacteroides distasonis.,Shimizu H, Nakajima M, Miyanaga A, Takahashi Y, Tanaka N, Kobayashi K, Sugimoto N, Nakai H, Taguchi H Biochemistry. 2018 May 25. doi: 10.1021/acs.biochem.8b00385. PMID:29763309<ref>PMID:29763309</ref>

~~Description~~:

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

[[Category: ~~Unreleased Structures~~]]

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Kobayashi, K]]

[[Category: Miyanaga, A]]

[[Category: Nakai, H]]

[[Category: Nakajima, M]]

[[Category: Shimizu, H]]

[[Category: Sugimoto, N]]

[[Category: Taguchi, H]]

[[Category: Takahashi, Y]]

[[Category: Tanaka, N]]

[[Category: 2-glucan]]

[[Category: 2-glucanase]]

[[Category: 2-glucooligosaccharide]]

[[Category: Beta-1]]

[[Category: Gh144]]

[[Category: Glycoside hydrolase]]

[[Category: Hydrolase]]

[[Category: Parabacteroide]]

[[Category: Sophorose]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 5z06 is ON HOLD  until Dec 18 2019
+==Crystal structure of beta-1,2-glucanase from Parabacteroides distasonis==
+<StructureSection load='5z06' size='340' side='right' caption='[[5z06]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5z06]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z06 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z06 FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5z06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z06 OCA], [http://pdbe.org/5z06 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z06 RCSB], [http://www.ebi.ac.uk/pdbsum/5z06 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z06 ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+beta-1,2-Glucan is a polysaccharide produced mainly by some Gram-negative bacteria as a symbiosis and infectious factor. We recently identified endo-beta-1,2-glucanase from Chitinophaga pinensis ( CpSGL) as an enzyme comprising a new family. Here, we report the characteristics and crystal structure of a CpSGL homologue from Parabacteroides distasonis, an intestinal bacterium (BDI_3064 protein), which exhibits distinctive properties of known beta-1,2-glucan-degrading enzymes. BDI_3064 hydrolyzed linear beta-1,2-glucan and beta-1,2-glucooligosaccharides with degrees of polymerization (DPs) of &gt;/=4 to produce sophorose specifically but did not hydrolyze cyclic beta-1,2-glucan. This result indicates that BDI_3064 is a new exo-type enzyme. BDI_3064 also produced sophorose from beta-1,2-glucooligosaccharide analogues that have a modified reducing end, indicating that BDI_3064 acts on its substrates from the nonreducing end. The crystal structure showed that BDI_3064 possesses additional N-terminal domains 1 and 2, unlike CpSGL. Superimposition of BDI_3064 and CpSGL complexed with ligands showed that R93 in domain 1 overlapped subsite -3 in CpSGL. Docking analysis involving a beta-1,2-glucooligosaccharide with DP4 showed that R93 completely blocks the nonreducing end of the docked beta-1,2-glucooligosaccharide. This indicates that BDI_3064 employs a distinct mechanism of recognition at the nonreducing end of substrates to act as an exo-type enzyme. Thus, we propose 2-beta-d-glucooligosaccharide sophorohydrolase (nonreducing end) as a systematic name for BDI_3064.
-Authors:
+Characterization and Structural Analysis of a Novel exo-Type Enzyme Acting on beta-1,2-Glucooligosaccharides from Parabacteroides distasonis.,Shimizu H, Nakajima M, Miyanaga A, Takahashi Y, Tanaka N, Kobayashi K, Sugimoto N, Nakai H, Taguchi H Biochemistry. 2018 May 25. doi: 10.1021/acs.biochem.8b00385. PMID:29763309<ref>PMID:29763309</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 5z06" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Kobayashi, K]]
+[[Category: Miyanaga, A]]
+[[Category: Nakai, H]]
+[[Category: Nakajima, M]]
+[[Category: Shimizu, H]]
+[[Category: Sugimoto, N]]
+[[Category: Taguchi, H]]
+[[Category: Takahashi, Y]]
+[[Category: Tanaka, N]]
+[[Category: 2-glucan]]
+[[Category: 2-glucanase]]
+[[Category: 2-glucooligosaccharide]]
+[[Category: Beta-1]]
+[[Category: Gh144]]
+[[Category: Glycoside hydrolase]]
+[[Category: Hydrolase]]
+[[Category: Parabacteroide]]
+[[Category: Sophorose]]