8W04

Crystal structure of DUF1735-domain containing protein (GH18-like) from Bacteroides faecium at 2.9 A resolution (Space group P21)

Summary for 8W04

• Entry DOI: 10.2210/pdb8w04/pdb
• Descriptor: DUF1735 domain-containing protein (1 entity in total)
• Functional Keywords: duf1735-domain containing protein, gh18-like, inactive endoglycosidase, bacteroides faecium, gut microbiome, sugar binding protein
• Biological source: Bacteroides faecium
• Total number of polymer chains: 2
• Total formula weight: 114698.20

Authors

Sastre, D.E.,Navarro, M.V.A.S.,Sultana, N.,Sundberg, E.J. (deposition date: 2024-02-13, release date: 2024-05-29, Last modification date: 2024-06-26)

Primary citation

Sastre, D.E.,Sultana, N.,V A S Navarro, M.,Huliciak, M.,Du, J.,Cifuente, J.O.,Flowers, M.,Liu, X.,Lollar, P.,Trastoy, B.,Guerin, M.E.,Sundberg, E.J.
Human gut microbes express functionally distinct endoglycosidases to metabolize the same N-glycan substrate.
Nat Commun, 15:5123-5123, 2024

PubMed Abstract: Bacteroidales (syn. Bacteroidetes) are prominent members of the human gastrointestinal ecosystem mainly due to their efficient glycan-degrading machinery, organized into gene clusters known as polysaccharide utilization loci (PULs). A single PUL was reported for catabolism of high-mannose (HM) N-glycan glyco-polypeptides in the gut symbiont Bacteroides thetaiotaomicron, encoding a surface endo-β-N-acetylglucosaminidase (ENGase), BT3987. Here, we discover an ENGase from the GH18 family in B. thetaiotaomicron, BT1285, encoded in a distinct PUL with its own repertoire of proteins for catabolism of the same HM N-glycan substrate as that of BT3987. We employ X-ray crystallography, electron microscopy, mass spectrometry-based activity measurements, alanine scanning mutagenesis and a broad range of biophysical methods to comprehensively define the molecular mechanism by which BT1285 recognizes and hydrolyzes HM N-glycans, revealing that the stabilities and activities of BT1285 and BT3987 were optimal in markedly different conditions. BT1285 exhibits significantly higher affinity and faster hydrolysis of poorly accessible HM N-glycans than does BT3987. We also find that two HM-processing endoglycosidases from the human gut-resident Alistipes finegoldii display condition-specific functional properties. Altogether, our data suggest that human gut microbes employ evolutionary strategies to express distinct ENGases in order to optimally metabolize the same N-glycan substrate in the gastroinstestinal tract.

PubMed: 38879612
DOI: 10.1038/s41467-024-48802-3

Experimental method

X-RAY DIFFRACTION (2.91 Å)