This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


5xxm

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (10:20, 27 March 2024) (edit) (undo)
 
Line 1: Line 1:
==Crystal structure of GH3 beta-glucosidase from Bacteroides thetaiotaomicron in complex with gluconolactone==
==Crystal structure of GH3 beta-glucosidase from Bacteroides thetaiotaomicron in complex with gluconolactone==
-
<StructureSection load='5xxm' size='340' side='right' caption='[[5xxm]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
+
<StructureSection load='5xxm' size='340' side='right'caption='[[5xxm]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[5xxm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bactn Bactn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XXM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XXM FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[5xxm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron_VPI-5482 Bacteroides thetaiotaomicron VPI-5482]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XXM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XXM FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LGC:(3S,4R,5R,6S)-3,4,5-TRIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-2-ONE'>LGC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>
+
</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>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BT_3567 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=226186 BACTN])</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LGC:(3S,4R,5R,6S)-3,4,5-TRIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-2-ONE'>LGC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</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=5xxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xxm OCA], [http://pdbe.org/5xxm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xxm RCSB], [http://www.ebi.ac.uk/pdbsum/5xxm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xxm ProSAT]</span></td></tr>
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5xxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xxm OCA], [https://pdbe.org/5xxm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xxm RCSB], [https://www.ebi.ac.uk/pdbsum/5xxm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xxm ProSAT]</span></td></tr>
</table>
</table>
-
<div style="background-color:#fffaf0;">
+
== Function ==
-
== Publication Abstract from PubMed ==
+
[https://www.uniprot.org/uniprot/Q8A1U1_BACTN Q8A1U1_BACTN]
-
BT_3567 protein, a putative beta-glucosidase from Bacteroides thetaiotaomicron, exhibits higher activity toward Sop3-5 (Sopn , n: degree of polymerization of beta-1,2-glucooligosaccharides) than toward Sop2 , unlike a known beta-glucosidase from Listeria innocua which predominantly prefers Sop2 . In the complex structure determined by soaking of a D286N mutant crystal with Sop4 , a Sop3 moiety was observed at subsites -1 to +2. The glucose moiety at subsite +2 forms a hydrogen bond with Asn81, which is replaced with Gly in the L. innocua beta-glucosidase. The Km values of the N81G mutant for Sop3-5 are much higher than those of the wild-type, suggesting that Asn81 contributes to the binding to substrates longer than Sop3 .
+
-
Function and structure relationships of a beta-1,2-glucooligosaccharide-degrading beta-glucosidase.,Ishiguro R, Tanaka N, Abe K, Nakajima M, Maeda T, Miyanaga A, Takahashi Y, Sugimoto N, Nakai H, Taguchi H FEBS Lett. 2017 Dec;591(23):3926-3936. doi: 10.1002/1873-3468.12911. Epub 2017, Nov 24. PMID:29131329<ref>PMID:29131329</ref>
+
==See Also==
-
 
+
*[[Beta-glucosidase 3D structures|Beta-glucosidase 3D structures]]
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 5xxm" style="background-color:#fffaf0;"></div>
+
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Bactn]]
+
[[Category: Bacteroides thetaiotaomicron VPI-5482]]
-
[[Category: Abe, K]]
+
[[Category: Large Structures]]
-
[[Category: Ishiguro, R]]
+
[[Category: Abe K]]
-
[[Category: Maeda, T]]
+
[[Category: Ishiguro R]]
-
[[Category: Miyanaga, A]]
+
[[Category: Maeda T]]
-
[[Category: Nakai, H]]
+
[[Category: Miyanaga A]]
-
[[Category: Nakajima, M]]
+
[[Category: Nakai H]]
-
[[Category: Sugimoto, N]]
+
[[Category: Nakajima M]]
-
[[Category: Taguchi, H]]
+
[[Category: Sugimoto N]]
-
[[Category: Takahash, Y]]
+
[[Category: Taguchi H]]
-
[[Category: Tanaka, N]]
+
[[Category: Takahash Y]]
-
[[Category: Beta-glucosidase]]
+
[[Category: Tanaka N]]
-
[[Category: Glycoside hydrolase family 3]]
+
-
[[Category: Hydrolase]]
+

Current revision

Crystal structure of GH3 beta-glucosidase from Bacteroides thetaiotaomicron in complex with gluconolactone

PDB ID 5xxm

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5xxm"
Personal tools