8R56
Crystal structure of GH31 family Sulfoquinovosidase BmSQase in covalent complex with SQ-aziridine (SQZ)
Summary for 8R56
| Entry DOI | 10.2210/pdb8r56/pdb |
| Descriptor | Glycosyl hydrolase, family 31, [(1~{S},2~{R},3~{R},4~{S},6~{R})-6-azanyl-2,3,4-tris(oxidanyl)cyclohexyl]methanesulfonic acid, POTASSIUM ION, ... (4 entities in total) |
| Functional Keywords | glycoside hydrolase, cazy family 31, sulfoquinovose, activity-based probe, hydrolase |
| Biological source | Priestia megaterium DSM 319 |
| Total number of polymer chains | 4 |
| Total formula weight | 323087.53 |
| Authors | Sharma, M.,Davies, G.J. (deposition date: 2023-11-16, release date: 2024-05-08, Last modification date: 2024-11-06) |
| Primary citation | Li, Z.,Pickles, I.B.,Sharma, M.,Melling, B.,Pallasdies, L.,Codee, J.D.C.,Williams, S.J.,Overkleeft, H.S.,Davies, G.J. Detection of Sulfoquinovosidase Activity in Cell Lysates Using Activity-Based Probes. Angew.Chem.Int.Ed.Engl., 63:e202401358-e202401358, 2024 Cited by PubMed Abstract: The sulfolipid sulfoquinovosyl diacylglycerol (SQDG), produced by plants, algae, and cyanobacteria, constitutes a major sulfur reserve in the biosphere. Microbial breakdown of SQDG is critical for the biological utilization of its sulfur. This commences through release of the parent sugar, sulfoquinovose (SQ), catalyzed by sulfoquinovosidases (SQases). These vanguard enzymes are encoded in gene clusters that code for diverse SQ catabolic pathways. To identify, visualize and isolate glycoside hydrolase CAZY-family 31 (GH31) SQases in complex biological environments, we introduce SQ cyclophellitol-aziridine activity-based probes (ABPs). These ABPs label the active site nucleophile of this enzyme family, consistent with specific recognition of the SQ cyclophellitol-aziridine in the active site, as evidenced in the 3D structure of Bacillus megaterium SQase. A fluorescent Cy5-probe enables visualization of SQases in crude cell lysates from bacteria harbouring different SQ breakdown pathways, whilst a biotin-probe enables SQase capture and identification by proteomics. The Cy5-probe facilitates monitoring of active SQase levels during different stages of bacterial growth which show great contrast to more traditional mRNA analysis obtained by RT-qPCR. Given the importance of SQases in global sulfur cycling and in human microbiota, these SQase ABPs provide a new tool with which to study SQase occurrence, activity and stability. PubMed: 38647177DOI: 10.1002/anie.202401358 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.45 Å) |
Structure validation
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