Structural insights of RmXyn10A-A prebiotic-producing GH10 xylanase with a non-conserved aglycone binding region

Hydrolysis of arabinoxylan (AX) by glycoside hydrolase family 10 (GH10) xylanases produces xylo-and arabinoxylo-oligosaccharides ((A)XOS) which have shown prebiotic effects. The thermostable GH10 xylanase RmXyn10A has shown great potential to produce (A)XOS. In this study, the structure of RmXynlOA was investigated, the catalytic module by homology modelling and site-directed mutagenesis and the arrangement of its five domains by small-angle X-ray scattering (SAXS). Substrate specificity was explored in silico by manual docking and molecular dynamic simulations. It has been shown in the literature that the glycone subsites of GH10 xylanases are well conserved and our results suggest that RmXyn10A is no exception. The aglycone subsites are less investigated, and the modelled structure of RmXyn10A suggests that loop alpha(6)beta(6) in the aglycone part of the active site contains a non-conserved alpha-helix, which blocks the otherwise conserved space of subsite + 2. This structural feature has only been observed for one other GH10 xylanase. In RmXyn10A, docking revealed two alternative binding regions, one on either side of the alpha-helix. However, only one was able to accommodate arabinose-substitutions and the mutation study suggests that the same region is responsible for binding XOS. Several non-conserved structural features are most likely to be responsible for providing affinity for arabinose-substitutions in subsites +1 and + 2. The SAXS rigid model of the modular arrangement of RmXyn10A displays the catalytic module close to the cell-anchoring domain while the carbohydrate binding modules are further away, likely explaining the observed lack of contribution of the CBMs to activity.

Yazar Aronsson, Anna
Guler, Fatma
Petoukhov, Maxim V.
Crennell, Susan J.
Svergun, Dmitri I.
Linares-Pasten, Javier A.
Karlsson, Eva Nordberg
Yayın Türü Article
Tek Biçim Adres https://hdl.handle.net/20.500.12628/3376
Tek Biçim Adres 10.1016/j.bbapap.2017.11.006
Konu Başlıkları Homology modelling
Manual docking
Molecular dynamics
SAXS
Rhodothermus marinus
(A)XOS
Koleksiyonlar Araştırma Çıktıları | WoS | Scopus | TR-Dizin | PubMed | SOBİAD
PubMed İndeksli Yayınlar Koleksiyonu
WoS İndeksli Yayınlar Koleksiyonu
Dergi Adı BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
Dergi Cilt Bilgisi 1866
Dergi Sayısı 2
Sayfalar 292 - 306
Yayın Yılı 2018
Eser Adı
[dc.title]
Structural insights of RmXyn10A-A prebiotic-producing GH10 xylanase with a non-conserved aglycone binding region
Yazar
[dc.contributor.author]
Aronsson, Anna
Yazar
[dc.contributor.author]
Guler, Fatma
Yazar
[dc.contributor.author]
Petoukhov, Maxim V.
Yazar
[dc.contributor.author]
Crennell, Susan J.
Yazar
[dc.contributor.author]
Svergun, Dmitri I.
Yazar
[dc.contributor.author]
Linares-Pasten, Javier A.
Yazar
[dc.contributor.author]
Karlsson, Eva Nordberg
Yayın Yılı
[dc.date.issued]
2018
Yayıncı
[dc.publisher]
ELSEVIER SCIENCE BV
Yayın Türü
[dc.type]
article
Özet
[dc.description.abstract]
Hydrolysis of arabinoxylan (AX) by glycoside hydrolase family 10 (GH10) xylanases produces xylo-and arabinoxylo-oligosaccharides ((A)XOS) which have shown prebiotic effects. The thermostable GH10 xylanase RmXyn10A has shown great potential to produce (A)XOS. In this study, the structure of RmXynlOA was investigated, the catalytic module by homology modelling and site-directed mutagenesis and the arrangement of its five domains by small-angle X-ray scattering (SAXS). Substrate specificity was explored in silico by manual docking and molecular dynamic simulations. It has been shown in the literature that the glycone subsites of GH10 xylanases are well conserved and our results suggest that RmXyn10A is no exception. The aglycone subsites are less investigated, and the modelled structure of RmXyn10A suggests that loop alpha(6)beta(6) in the aglycone part of the active site contains a non-conserved alpha-helix, which blocks the otherwise conserved space of subsite + 2. This structural feature has only been observed for one other GH10 xylanase. In RmXyn10A, docking revealed two alternative binding regions, one on either side of the alpha-helix. However, only one was able to accommodate arabinose-substitutions and the mutation study suggests that the same region is responsible for binding XOS. Several non-conserved structural features are most likely to be responsible for providing affinity for arabinose-substitutions in subsites +1 and + 2. The SAXS rigid model of the modular arrangement of RmXyn10A displays the catalytic module close to the cell-anchoring domain while the carbohydrate binding modules are further away, likely explaining the observed lack of contribution of the CBMs to activity.
Açıklama
[dc.description]
WOS: 000423640800010
Açıklama
[dc.description]
PubMed: 29155107
Kayıt Giriş Tarihi
[dc.date.accessioned]
2019-12-23
Açık Erişim Tarihi
[dc.date.available]
2019-12-23
Yayın Dili
[dc.language.iso]
eng
Konu Başlıkları
[dc.subject]
Homology modelling
Konu Başlıkları
[dc.subject]
Manual docking
Konu Başlıkları
[dc.subject]
Molecular dynamics
Konu Başlıkları
[dc.subject]
SAXS
Konu Başlıkları
[dc.subject]
Rhodothermus marinus
Konu Başlıkları
[dc.subject]
(A)XOS
Haklar
[dc.rights]
info:eu-repo/semantics/openAccess
ISSN
[dc.identifier.issn]
1570-9639
ISSN
[dc.identifier.issn]
1878-1454
İlk Sayfa Sayısı
[dc.identifier.startpage]
292
Son Sayfa Sayısı
[dc.identifier.endpage]
306
Dergi Adı
[dc.relation.journal]
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
Dergi Sayısı
[dc.identifier.issue]
2
Dergi Cilt Bilgisi
[dc.identifier.volume]
1866
Tek Biçim Adres
[dc.identifier.uri]
https://dx.doi.org/10.1016/j.bbapap.2017.11.006
Tek Biçim Adres
[dc.identifier.uri]
https://hdl.handle.net/20.500.12628/3376
Görüntülenme Sayısı ( Şehir )
Görüntülenme Sayısı ( Ülke )
Görüntülenme Sayısı ( Zaman Dağılımı )
Görüntülenme
10
09.12.2022 tarihinden bu yana
İndirme
1
09.12.2022 tarihinden bu yana
Son Erişim Tarihi
08 Şubat 2024 03:51
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Tıklayınız
RmXyn10A binding subsites investigated structure catalytic module likely alpha-helix arrangement responsible arabinose-substitutions docking non-conserved aglycone suggests structural xylanases observed xylanase conserved blocks otherwise regions alternative subsite revealed feature either Hydrolysis modular activity contribution explaining further
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