8U48
Crystal structure of Bacteroides thetaiotamicron BT1285 D161A-E163A inactive Endoglycosidase in complex with high-mannose N-glycan (Man9GlcNAc2) substrate
Summary for 8U48
| Entry DOI | 10.2210/pdb8u48/pdb |
| Descriptor | Endo-beta-N-acetylglucosaminidase, alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, PHOSPHATE ION, ... (4 entities in total) |
| Functional Keywords | inactive endoglycosidase, artificial lectin, high-mannose specific, bacteroides, gh18 family, carbohydrate |
| Biological source | Bacteroides thetaiotaomicron VPI-5482 |
| Total number of polymer chains | 2 |
| Total formula weight | 64854.31 |
| Authors | Sastre, D.E.,Sultana, N.,Navarro, M.V.A.S.,Sundberg, E.J. (deposition date: 2023-09-09, 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 Cited by 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: 38879612DOI: 10.1038/s41467-024-48802-3 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.9 Å) |
Structure validation
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