"Newton's cradle" proton relay with amide-imidic acid tautomerization in inverting cellulase visualized by neutron crystallography.
Identifieur interne : 000286 ( Main/Exploration ); précédent : 000285; suivant : 000287"Newton's cradle" proton relay with amide-imidic acid tautomerization in inverting cellulase visualized by neutron crystallography.
Auteurs : Akihiko Nakamura [Japon] ; Takuya Ishida [Japon] ; Katsuhiro Kusaka [Japon] ; Taro Yamada [Japon] ; Shinya Fushinobu [Japon] ; Ichiro Tanaka [Japon] ; Satoshi Kaneko [Japon] ; Kazunori Ohta [Japon] ; Hiroaki Tanaka [Japon] ; Koji Inaka [Japon] ; Yoshiki Higuchi [Japon] ; Nobuo Niimura [Japon] ; Masahiro Samejima [Japon] ; Kiyohiko Igarashi [Japon]Source :
- Science advances [ 2375-2548 ] ; 2015.
Abstract
Hydrolysis of carbohydrates is a major bioreaction in nature, catalyzed by glycoside hydrolases (GHs). We used neutron diffraction and high-resolution x-ray diffraction analyses to investigate the hydrogen bond network in inverting cellulase PcCel45A, which is an endoglucanase belonging to subfamily C of GH family 45, isolated from the basidiomycete Phanerochaete chrysosporium. Examination of the enzyme and enzyme-ligand structures indicates a key role of multiple tautomerizations of asparagine residues and peptide bonds, which are finally connected to the other catalytic residue via typical side-chain hydrogen bonds, in forming the "Newton's cradle"-like proton relay pathway of the catalytic cycle. Amide-imidic acid tautomerization of asparagine has not been taken into account in recent molecular dynamics simulations of not only cellulases but also general enzyme catalysis, and it may be necessary to reconsider our interpretation of many enzymatic reactions.
DOI: 10.1126/sciadv.1500263
PubMed: 26601228
PubMed Central: PMC4643802
Affiliations:
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<front><div type="abstract" xml:lang="en">Hydrolysis of carbohydrates is a major bioreaction in nature, catalyzed by glycoside hydrolases (GHs). We used neutron diffraction and high-resolution x-ray diffraction analyses to investigate the hydrogen bond network in inverting cellulase PcCel45A, which is an endoglucanase belonging to subfamily C of GH family 45, isolated from the basidiomycete Phanerochaete chrysosporium. Examination of the enzyme and enzyme-ligand structures indicates a key role of multiple tautomerizations of asparagine residues and peptide bonds, which are finally connected to the other catalytic residue via typical side-chain hydrogen bonds, in forming the "Newton's cradle"-like proton relay pathway of the catalytic cycle. Amide-imidic acid tautomerization of asparagine has not been taken into account in recent molecular dynamics simulations of not only cellulases but also general enzyme catalysis, and it may be necessary to reconsider our interpretation of many enzymatic reactions. </div>
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<Abstract><AbstractText>Hydrolysis of carbohydrates is a major bioreaction in nature, catalyzed by glycoside hydrolases (GHs). We used neutron diffraction and high-resolution x-ray diffraction analyses to investigate the hydrogen bond network in inverting cellulase PcCel45A, which is an endoglucanase belonging to subfamily C of GH family 45, isolated from the basidiomycete Phanerochaete chrysosporium. Examination of the enzyme and enzyme-ligand structures indicates a key role of multiple tautomerizations of asparagine residues and peptide bonds, which are finally connected to the other catalytic residue via typical side-chain hydrogen bonds, in forming the "Newton's cradle"-like proton relay pathway of the catalytic cycle. Amide-imidic acid tautomerization of asparagine has not been taken into account in recent molecular dynamics simulations of not only cellulases but also general enzyme catalysis, and it may be necessary to reconsider our interpretation of many enzymatic reactions. </AbstractText>
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</ArticleIdList>
<ReferenceList><Reference><Citation>Appl Environ Microbiol. 2008 Sep;74(18):5628-34</Citation>
<ArticleIdList><ArticleId IdType="pubmed">18676702</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):486-501</Citation>
<ArticleIdList><ArticleId IdType="pubmed">20383002</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Am Chem Soc. 2002 Aug 28;124(34):10015-24</Citation>
<ArticleIdList><ArticleId IdType="pubmed">12188666</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nature. 2015 Apr 23;520(7548):571-4</Citation>
<ArticleIdList><ArticleId IdType="pubmed">25624102</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Proc Natl Acad Sci U S A. 2007 Mar 6;104(10):4200-5</Citation>
<ArticleIdList><ArticleId IdType="pubmed">17360500</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Curr Opin Struct Biol. 1994 Dec;4(6):885-92</Citation>
<ArticleIdList><ArticleId IdType="pubmed">7712292</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Acta Crystallogr D Biol Crystallogr. 2010 Nov;66(Pt 11):1194-7</Citation>
<ArticleIdList><ArticleId IdType="pubmed">21041936</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nature. 2013 Feb 28;494(7438):443-8</Citation>
<ArticleIdList><ArticleId IdType="pubmed">23417064</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Biol Chem. 2009 Apr 24;284(17):11676-89</Citation>
<ArticleIdList><ArticleId IdType="pubmed">19181667</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Acta Crystallogr D Biol Crystallogr. 2009 Jun;65(Pt 6):567-73</Citation>
<ArticleIdList><ArticleId IdType="pubmed">19465771</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Synchrotron Radiat. 2013 Nov;20(Pt 6):859-63</Citation>
<ArticleIdList><ArticleId IdType="pubmed">24121328</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Biol Chem. 2009 Apr 10;284(15):10100-9</Citation>
<ArticleIdList><ArticleId IdType="pubmed">19193645</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):235-42</Citation>
<ArticleIdList><ArticleId IdType="pubmed">21460441</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Acta Crystallogr A. 2008 Jan;64(Pt 1):12-22</Citation>
<ArticleIdList><ArticleId IdType="pubmed">18156668</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Mol Biol. 2008 Jan 11;375(2):499-510</Citation>
<ArticleIdList><ArticleId IdType="pubmed">18035374</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nucleic Acids Res. 2014 Jan;42(Database issue):D490-5</Citation>
<ArticleIdList><ArticleId IdType="pubmed">24270786</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Methods Enzymol. 1997;276:307-26</Citation>
<ArticleIdList><ArticleId IdType="pubmed">27754618</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213-21</Citation>
<ArticleIdList><ArticleId IdType="pubmed">20124702</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Acta Crystallogr D Biol Crystallogr. 2010 Jun;66(Pt 6):698-708</Citation>
<ArticleIdList><ArticleId IdType="pubmed">20516622</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2184-95</Citation>
<ArticleIdList><ArticleId IdType="pubmed">15572771</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Am Chem Soc. 2002 Nov 13;124(45):13554-67</Citation>
<ArticleIdList><ArticleId IdType="pubmed">12418911</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Biochemistry. 1995 Dec 12;34(49):16210-20</Citation>
<ArticleIdList><ArticleId IdType="pubmed">8519779</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Acta Crystallogr D Biol Crystallogr. 2009 Oct;65(Pt 10):1074-80</Citation>
<ArticleIdList><ArticleId IdType="pubmed">19770504</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):125-32</Citation>
<ArticleIdList><ArticleId IdType="pubmed">20124692</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Synchrotron Radiat. 2013 Nov;20(Pt 6):994-8</Citation>
<ArticleIdList><ArticleId IdType="pubmed">24121355</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
</PubmedData>
</pubmed>
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