Structural genomics analysis of uncharacterized protein families overrepresented in human gut bacteria identifies a novel glycoside hydrolase

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• 作者：Anna Sheydina (49) (50)
  Ruth Y Eberhardt (51) (52)
  Daniel J Rigden (53)
  Yuanyuan Chang (49) (50)
  Zhanwen Li (50)
  Christian C Zmasek (50)
  Herbert L Axelrod (49) (54)
  Adam Godzik (49) (50) (55)
  
  49. Joint Center for Structural Genomics ; 10550 North Torrey Pines Road ; BCC-206 ; La Jolla ; California ; 92037 ; USA
  50. Bioinformatics and Systems Biology Program ; Sanford-Burnham Medical Research Institute ; La Jolla ; CA ; 92037 ; USA
  51. Wellcome Trust Sanger Institute ; Wellcome Trust Genome Campus ; Hinxton ; Cambridgeshire ; CB10 1SA ; UK
  52. European Molecular Biology Laboratory ; European Bioinformatics Institute ; Wellcome Trust Genome Campus ; Hinxton ; Cambridgeshire ; CB10 1SD ; UK
  53. Institute of Integrative Biology ; University of Liverpool ; Crown Street ; Liverpool ; L69 7ZB ; UK
  54. Stanford Synchrotron Radiation Lightsource ; Menlo Park ; CA ; 94025 ; USA
  55. Center for Research in Biological Systems ; University of California ; 9500 Gilman Dr ; La Jolla ; CA ; 92093-0446 ; USA
  
• 关键词：Glycoside hydrolase ; Carbohydrate metabolism ; 3D structure ; Protein family ; Protein function prediction ; Domain of unknown function ; DUF
• 刊名：BMC Bioinformatics
• 出版年：2014
• 出版时间：December 2014
• 年：2014
• 卷：15
• 期：1
• 全文大小：3,619 KB
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• 刊物主题：Bioinformatics; Microarrays; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Combinatorial Libraries; Algorithms;
• 出版者：BioMed Central
• ISSN：1471-2105

文摘

Background Bacteroides spp. form a significant part of our gut microbiome and are well known for optimized metabolism of diverse polysaccharides. Initial analysis of the archetypal Bacteroides thetaiotaomicron genome identified 172 glycosyl hydrolases and a large number of uncharacterized proteins associated with polysaccharide metabolism. Results BT_1012 from Bacteroides thetaiotaomicron VPI-5482 is a protein of unknown function and a member of a large protein family consisting entirely of uncharacterized proteins. Initial sequence analysis predicted that this protein has two domains, one on the N- and one on the C-terminal. A PSI-BLAST search found over 150 full length and over 90 half size homologs consisting only of the N-terminal domain. The experimentally determined three-dimensional structure of the BT_1012 protein confirms its two-domain architecture and structural analysis of both domains suggests their specific functions. The N-terminal domain is a putative catalytic domain with significant similarity to known glycoside hydrolases, the C-terminal domain has a beta-sandwich fold typically found in C-terminal domains of other glycosyl hydrolases, however these domains are typically involved in substrate binding. We describe the structure of the BT_1012 protein and discuss its sequence-structure relationship and their possible functional implications. Conclusions Structural and sequence analyses of the BT_1012 protein identifies it as a glycosyl hydrolase, expanding an already impressive catalog of enzymes involved in polysaccharide metabolism in Bacteroides spp. Based on this we have renamed the Pfam families representing the two domains found in the BT_1012 protein, PF13204 and PF12904, as putative glycoside hydrolase and glycoside hydrolase-associated C-terminal domain respectively.