5gzv: Difference between revisions
New page: '''Unreleased structure''' The entry 5gzv is ON HOLD until Paper Publication Authors: Itoh, T., Hibi, T., Suzuki, F., Sugimoto, I., Fujiwara, A., Inaka, K., Tanaka, H., Ohta, K., Fujii,... |
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==Crystal Structure of Chitinase ChiW from Paenibacillus sp. str. FPU-7 Reveals a Novel Type of Bacterial Cell-Surface-Expressed Multi-Modular Enzyme Machinery== | |||
<StructureSection load='5gzv' size='340' side='right'caption='[[5gzv]], [[Resolution|resolution]] 2.61Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5gzv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Paenibacillus_sp._FPU-7 Paenibacillus sp. FPU-7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GZV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GZV FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.61Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=5gzv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gzv OCA], [https://pdbe.org/5gzv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gzv RCSB], [https://www.ebi.ac.uk/pdbsum/5gzv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gzv ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/K7ZLW6_9BACL K7ZLW6_9BACL] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The Gram-positive bacterium Paenibacillus sp. str. FPU-7 effectively hydrolyzes chitin by using a number of chitinases. A unique chitinase with two catalytic domains, ChiW, is expressed on the cell surface of this bacterium and has high activity towards various chitins, even crystalline chitin. Here, the crystal structure of ChiW at 2.1 A resolution is presented and describes how the enzyme degrades chitin on the bacterial cell surface. The crystal structure revealed a unique multi-modular architecture composed of six domains to function efficiently on the cell surface: a right-handed beta-helix domain (carbohydrate-binding module family 54, CBM-54), a Gly-Ser-rich loop, 1st immunoglobulin-like (Ig-like) fold domain, 1st beta/alpha-barrel catalytic domain (glycoside hydrolase family 18, GH-18), 2nd Ig-like fold domain and 2nd beta/alpha-barrel catalytic domain (GH-18). The structure of the CBM-54, flexibly linked to the catalytic region of ChiW, is described here for the first time. It is similar to those of carbohydrate lyases but displayed no detectable carbohydrate degradation activities. The CBM-54 of ChiW bound to cell wall polysaccharides, such as chin, chitosan, beta-1,3-glucan, xylan and cellulose. The structural and biochemical data obtained here also indicated that the enzyme has deep and short active site clefts with endo-acting character. The affinity of CBM-54 towards cell wall polysaccharides and the degradation pattern of the catalytic domains may help to efficiently decompose the cell wall chitin through the contact surface. Furthermore, we clarify that other Gram-positive bacteria possess similar cell-surface-expressed multi-modular enzymes for cell wall polysaccharide degradation. | |||
Crystal Structure of Chitinase ChiW from Paenibacillus sp. str. FPU-7 Reveals a Novel Type of Bacterial Cell-Surface-Expressed Multi-Modular Enzyme Machinery.,Itoh T, Hibi T, Suzuki F, Sugimoto I, Fujiwara A, Inaka K, Tanaka H, Ohta K, Fujii Y, Taketo A, Kimoto H PLoS One. 2016 Dec 1;11(12):e0167310. doi: 10.1371/journal.pone.0167310., eCollection 2016. PMID:27907169<ref>PMID:27907169</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[ | </div> | ||
[[Category: | <div class="pdbe-citations 5gzv" style="background-color:#fffaf0;"></div> | ||
[[Category: | |||
[[Category: Fujii | ==See Also== | ||
[[Category: Fujiwara | *[[Chitinase 3D structures|Chitinase 3D structures]] | ||
[[Category: | == References == | ||
[[Category: | <references/> | ||
[[Category: | __TOC__ | ||
[[Category: | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Paenibacillus sp. FPU-7]] | ||
[[Category: | [[Category: Fujii Y]] | ||
[[Category: Fujiwara A]] | |||
[[Category: Hibi T]] | |||
[[Category: Inaka K]] | |||
[[Category: Itoh T]] | |||
[[Category: Kimoto H]] | |||
[[Category: Ohta K]] | |||
[[Category: Sugimoto I]] | |||
[[Category: Suzuki F]] | |||
[[Category: Taketo A]] | |||
[[Category: Tanaka H]] | |||
Latest revision as of 14:47, 2 August 2023
Crystal Structure of Chitinase ChiW from Paenibacillus sp. str. FPU-7 Reveals a Novel Type of Bacterial Cell-Surface-Expressed Multi-Modular Enzyme MachineryCrystal Structure of Chitinase ChiW from Paenibacillus sp. str. FPU-7 Reveals a Novel Type of Bacterial Cell-Surface-Expressed Multi-Modular Enzyme Machinery
Structural highlights
FunctionPublication Abstract from PubMedThe Gram-positive bacterium Paenibacillus sp. str. FPU-7 effectively hydrolyzes chitin by using a number of chitinases. A unique chitinase with two catalytic domains, ChiW, is expressed on the cell surface of this bacterium and has high activity towards various chitins, even crystalline chitin. Here, the crystal structure of ChiW at 2.1 A resolution is presented and describes how the enzyme degrades chitin on the bacterial cell surface. The crystal structure revealed a unique multi-modular architecture composed of six domains to function efficiently on the cell surface: a right-handed beta-helix domain (carbohydrate-binding module family 54, CBM-54), a Gly-Ser-rich loop, 1st immunoglobulin-like (Ig-like) fold domain, 1st beta/alpha-barrel catalytic domain (glycoside hydrolase family 18, GH-18), 2nd Ig-like fold domain and 2nd beta/alpha-barrel catalytic domain (GH-18). The structure of the CBM-54, flexibly linked to the catalytic region of ChiW, is described here for the first time. It is similar to those of carbohydrate lyases but displayed no detectable carbohydrate degradation activities. The CBM-54 of ChiW bound to cell wall polysaccharides, such as chin, chitosan, beta-1,3-glucan, xylan and cellulose. The structural and biochemical data obtained here also indicated that the enzyme has deep and short active site clefts with endo-acting character. The affinity of CBM-54 towards cell wall polysaccharides and the degradation pattern of the catalytic domains may help to efficiently decompose the cell wall chitin through the contact surface. Furthermore, we clarify that other Gram-positive bacteria possess similar cell-surface-expressed multi-modular enzymes for cell wall polysaccharide degradation. Crystal Structure of Chitinase ChiW from Paenibacillus sp. str. FPU-7 Reveals a Novel Type of Bacterial Cell-Surface-Expressed Multi-Modular Enzyme Machinery.,Itoh T, Hibi T, Suzuki F, Sugimoto I, Fujiwara A, Inaka K, Tanaka H, Ohta K, Fujii Y, Taketo A, Kimoto H PLoS One. 2016 Dec 1;11(12):e0167310. doi: 10.1371/journal.pone.0167310., eCollection 2016. PMID:27907169[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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