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Contextual Overview of Simple Saccharides Amanda Ullmer Mahd Nishtar

Contextual Overview of Simple Saccharides Amanda Ullmer Mahd Nishtar. Presentation Overview. Last week: Improved queries to develop scenarios for various saccharide types. This week: Created appropriate amount of chemical classes to detect nearly all verified saccharides.

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Contextual Overview of Simple Saccharides Amanda Ullmer Mahd Nishtar

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  1. Contextual Overview of Simple Saccharides Amanda UllmerMahd Nishtar

  2. Presentation Overview Last week: • Improved queries to develop scenarios for various saccharide types. This week: • Created appropriate amount of chemical classes to detect nearly all verified saccharides. • Goal of Contextual Analysis: Identify PDB structures for simple ring and open-chain saccharides existing as free, linked, seqres ligands • Approach • Results • Examples with accompanying chimera images

  3. Approach 1. Created queries for simple ring and open-chain saccharides and generated ligand hits Results: • Rings: 20 ligands hits, 2358 structure hits • Open-Chains: 13 ligand hits, 46 structure hits

  4. Approach cont’d 2. Used Ligandsprogram to generate list of mmCIF link records for simple saccharides in order to distinguish between free and polymeric saccharides under “Free-Ligand” category. 3. Chose Reference Ligand: Mannose (MAN): • For mmCIF files with MAN as Partner 1/Partner 2:

  5. Mannose “As Free Ligands” “In Polymers” True Linked (Link record) True Free (No Link record) Linked, non-polymer Linked, polymer

  6. Instances of Free and Linked Saccharide Ligands Identifying instances of true free ligands of simple ring saccharides. Instructions for program: Finding Free Ligands.docx

  7. Mannose as Free Monosaccharide (True Free) MAN MAN 1I8L 1FZC

  8. Mannose in Chained Linkages (Linked, Polymer) • Complex N-Linked Glycan • Polymeric Structure • Covalent Linkage

  9. Mannose in Chained Linkages (Linked, Polymer) • N-Linked Glycan • Polymeric structure • Covalent Linkage

  10. Mannose in Chained Linkages (Linked, Polymer) NAG ASN NAG MAN 1BZB High Mannose N-linked Glycan

  11. Mannose as Terminal Ligand (Linked, non-polymer) MAN ASN 436. A MAN Terminal mannose covalently linked to an asparagine residue. 2HZH: Crystal structure of laccase from Corioluszonatus

  12. Mannose as Terminal Ligand (Linked, non-polymer) MAN TRP 550.A TRP 547.A TRP 11.A TRP 8.A Terminal mannoses covalently linked to tryptophan residues. 3T5O: Crystal Structure of human Complement Component C6

  13. Linked Polymer 1VBO Mannose tri-saccharide interacting with Artocarpin

  14. Unusual Linkage Types MAN Zn ASP 204.A HIS 471.A Mannose interacts with the metal zinc through a coordinate interaction. 3BUP: Golgi alpha-mannosidase II D341N acid-base catalyst mutant with bound mannose

  15. Unusual Linkage Types • Glycan chain includes Mannose at terminal and inner locations • In metal coordination with Calcium ion MAN 07B MAN AE9 CA 2XR6

  16. Mannose as Seqres (“In Polymers”) 1CAP covale1 covale ? A MAN 1 C1 ? ? ? 1_555 A BGC 2 O3 ? ? A MAN 1 A BGC 2 1_555 ? ? ? ? ? ? ? 1.416 ? covale4 covale ? A BDP 3 O4 ? ? ? 1_555 A MAN 5 C1 ? ? A BDP 3 A MAN 5 1_555 ? ? ? ? ? ? ? 1.428 ? covale5 covale ? A GAL 4 C1 ? ? ? 1_555 A MAN 7 O2 ? ? A GAL 4 A MAN 7 1_555 ? ? ? ? ? ? ? 1.414 ? covale6 covale ? A MAN 5 O2 ? ? ? 1_555 A CEG 6 C1 ? ? A MAN 5 A CEG 6 1_555 ? ? ? ? ? ? ? 1.388 ? covale7 covale ? A MAN 7 C1 ? ? ? 1_555 A BGC 8 O3 ? ? A MAN 7 A BGC 8 1_555 ? ? ? ? ? ? ? 1.416 ? covale10 covale ? A BDP 9 O4 ? ? ? 1_555 A MAN 11 C1 ? ? A BDP 9 A MAN 11 1_555 ? ? ? ? ? ? ? 1.428 ? covale11 covale ? A MAN 11 O2 ? ? ? 1_555 A CEG 12 C1 ? ? A MAN 11 A CEG 12 1_555 ? ? ? ? ? ? ? 1.388 ?

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