7t7z

From Proteopedia

(Difference between revisions)

Revision as of 17:01, 18 October 2023

The crystal structure of family 8 carbohydrate-binding module from Dictyostelium discoideum

Structural highlights

7t7z is a 1 chain structure with sequence from Dictyostelium discoideum. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.46Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GUN6_DICDI May digest the spore cell wall during germination, to release the enclosed amoeba.^[1]

Publication Abstract from PubMed

Deciphering how enzymes interact, modify, and recognize carbohydrates has long been a topic of interest in academic, pharmaceutical, and industrial research. Carbohydrate-binding modules (CBMs) are non-catalytic globular protein domains attached to carbohydrate-active enzymes (CAZymes) that strengthen enzyme affinity to substrates and increase enzymatic efficiency via targeting and proximity effects. CBMs are considered auspicious for various biotechnological purposes in textile, food, and feed industries, representing valuable tools in basic science research and biomedicine. Here, we present the first crystallographic structure of a CBM8 family member (CBM8), DdCBM8 from the slime mold Dictyostelium discoideum, which was identified attached to an endo-beta-1,4-glucanase (glycoside hydrolase family 9). We show that the planar carbohydrate binding site of DdCBM8, composed of aromatic residues, is similar to type A CBMs that are specific for crystalline (multi-chain) polysaccharides. Accordingly, pull-down assays indicated that DdCBM8 was able to bind insoluble forms of cellulose. However, affinity gel electrophoresis demonstrated that DdCBM8 also bound to soluble (single chain) polysaccharides, especially glucomannan, similar to type B CBMs, although it had no apparent affinity for oligosaccharides. Therefore, the structural characteristics and broad specificity of DdCBM8 represent exceptions to the canonical CBM classification. In addition, mutational analysis identified specific amino acid residues involved in ligand recognition, which are conserved throughout the CBM8 family. This advancement in the structural and functional characterization of CBMs contributes to our understanding of CAZymes and protein-carbohydrate interactions, pushing forward protein engineering strategies and enhancing the potential biotechnological applications of glycoside hydrolase accessory modules.

Unique properties of a Dictyostelium discoideum carbohydrate-binding module expand our understanding of CBM-ligand interactions.,Liberato MV, Campos BM, Tomazetto G, Crouch LI, Garcia W, Zeri ACM, Bolam DN, Squina FM J Biol Chem. 2022 Apr 1:101891. doi: 10.1016/j.jbc.2022.101891. PMID:35378128^[2]

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

References

↑ Blume JE, Ennis HL. A Dictyostelium discoideum cellulase is a member of a spore germination-specific gene family. J Biol Chem. 1991 Aug 15;266(23):15432-7. PMID:1869562
↑ Liberato MV, Campos BM, Tomazetto G, Crouch LI, Garcia W, Zeri ACM, Bolam DN, Squina FM. Unique properties of a Dictyostelium discoideum carbohydrate-binding module expand our understanding of CBM-ligand interactions. J Biol Chem. 2022 Apr 1:101891. doi: 10.1016/j.jbc.2022.101891. PMID:35378128 doi:http://dx.doi.org/10.1016/j.jbc.2022.101891

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/7t7z"

Categories: Dictyostelium discoideum | Large Structures | Campos BM | Marcelo MV | Squina FM

@@ Line 3: / Line 3: @@
 <StructureSection load='7t7z' size='340' side='right'caption='[[7t7z]], [[Resolution|resolution]] 1.46&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[7t7z]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7T7Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7T7Z FirstGlance]. <br>
+<table><tr><td colspan='2'>[[7t7z]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7T7Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7T7Z FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=LMR:(2S)-2-HYDROXYBUTANEDIOIC+ACID'>LMR</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.46&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7t7y|7t7y]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=LMR:(2S)-2-HYDROXYBUTANEDIOIC+ACID'>LMR</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></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=7t7z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7t7z OCA], [https://pdbe.org/7t7z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7t7z RCSB], [https://www.ebi.ac.uk/pdbsum/7t7z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7t7z ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/GUN6_DICDI GUN6_DICDI]] May digest the spore cell wall during germination, to release the enclosed amoeba.<ref>PMID:1869562</ref>
+[https://www.uniprot.org/uniprot/GUN6_DICDI GUN6_DICDI] May digest the spore cell wall during germination, to release the enclosed amoeba.<ref>PMID:1869562</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 19: @@
 </div>
 <div class="pdbe-citations 7t7z" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Glucanase 3D structures|Glucanase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Dictyostelium discoideum]]
 [[Category: Large Structures]]
-[[Category: Campos, B M]]
+[[Category: Campos BM]]
-[[Category: Marcelo, M V]]
+[[Category: Marcelo MV]]
-[[Category: Squina, F M]]
+[[Category: Squina FM]]
-[[Category: Carbohydrate-binding protein]]
-[[Category: Cazyme]]
-[[Category: Cellulose]]
-[[Category: Ligand specificity]]
-[[Category: Sugar binding protein]]

7t7z

From Proteopedia

Revision as of 17:01, 18 October 2023

The crystal structure of family 8 carbohydrate-binding module from Dictyostelium discoideum

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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