9ryx: Difference between revisions

Latest revision as of 05:00, 27 May 2026

Aquifex aeolicus lumazine synthase I125A mutant 11-pentamer cage

Structural highlights

9ryx is a 55 chain structure with sequence from Aquifex aeolicus VF5. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 2.31Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RISB_AQUAE Catalyzes the formation of 6,7-dimethyl-8-ribityllumazine by condensation of 5-amino-6-(D-ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin.^[1] ^[2]

Publication Abstract from PubMed

Encapsulating metabolic enzymes within protein cages enhances catalytic efficiency through substrate channeling. The vitamin B2 biosynthesis system, in which a dodecahedral lumazine synthase (LS) cage encapsulates a homotrimeric riboflavin synthase (RS), exemplifies this strategy, yet the molecular basis for this stoichiometric enzyme encapsulation has remained elusive. Here, cryogenic electron microscopy structures reveal a hierarchical assembly mechanism that ensures the defined host-guest ratio. RS C-terminal cage-localization signal peptides anchor at LS pentamer-pentamer interfaces early during assembly, stabilizing open intermediates that, together with delayed later-stage cage closure, extend the loading window until guest incorporation is complete. RS spatial occupancy avoids overloading, while a molecular lock upon final closure prevents disassembly. The elucidated anchoring mechanism enabled structure-based phylogenetic analysis across diverse organisms, suggesting multiple independent evolutionary origins of this modular encapsulation strategy. This naturally occurring architecture provides design principles for engineering synthetic catalytic compartments with programmable stoichiometric control.

A molecular basis for stoichiometric enzyme encapsulation in the vitamin B2 biosynthesis compartment.,Koziej L, Pankowski J, Stefanska M, Jankowski D, Gawin A, Malolan VV, Huiskonen JT, Kosugi T, Azuma Y Nat Commun. 2026 May 16. doi: 10.1038/s41467-026-73260-4. PMID:42143052^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Haase I, Mortl S, Kohler P, Bacher A, Fischer M. Biosynthesis of riboflavin in archaea. 6,7-dimethyl-8-ribityllumazine synthase of Methanococcus jannaschii. Eur J Biochem. 2003 Mar;270(5):1025-32. PMID:12603336
↑ Zhang X, Meining W, Fischer M, Bacher A, Ladenstein R. X-ray structure analysis and crystallographic refinement of lumazine synthase from the hyperthermophile Aquifex aeolicus at 1.6 A resolution: determinants of thermostability revealed from structural comparisons. J Mol Biol. 2001 Mar 9;306(5):1099-114. PMID:11237620 doi:10.1006/jmbi.2000.4435
↑ Koziej L, Pankowski J, Stefanska M, Jankowski D, Gawin A, Malolan VV, Huiskonen JT, Kosugi T, Azuma Y. A molecular basis for stoichiometric enzyme encapsulation in the vitamin B2 biosynthesis compartment. Nat Commun. 2026 May 16. PMID:42143052 doi:10.1038/s41467-026-73260-4

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Haase I, Mortl S, Kohler P, Bacher A, Fischer M. Biosynthesis of riboflavin in archaea. 6,7-dimethyl-8-ribityllumazine synthase of Methanococcus jannaschii. Eur J Biochem. 2003 Mar;270(5):1025-32. PMID:12603336

[2] Zhang X, Meining W, Fischer M, Bacher A, Ladenstein R. X-ray structure analysis and crystallographic refinement of lumazine synthase from the hyperthermophile Aquifex aeolicus at 1.6 A resolution: determinants of thermostability revealed from structural comparisons. J Mol Biol. 2001 Mar 9;306(5):1099-114. PMID:11237620 doi:10.1006/jmbi.2000.4435

[3] Koziej L, Pankowski J, Stefanska M, Jankowski D, Gawin A, Malolan VV, Huiskonen JT, Kosugi T, Azuma Y. A molecular basis for stoichiometric enzyme encapsulation in the vitamin B2 biosynthesis compartment. Nat Commun. 2026 May 16. PMID:42143052 doi:10.1038/s41467-026-73260-4

[1]

[2]

[3]

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 9ryx is ON HOLD
+==Aquifex aeolicus lumazine synthase I125A mutant 11-pentamer cage==
+<StructureSection load='9ryx' size='340' side='right'caption='[[9ryx]], [[Resolution|resolution]] 2.31&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[9ryx]] is a 55 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus_VF5 Aquifex aeolicus VF5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9RYX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9RYX FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 2.31&#8491;</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=9ryx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9ryx OCA], [https://pdbe.org/9ryx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9ryx RCSB], [https://www.ebi.ac.uk/pdbsum/9ryx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9ryx ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RISB_AQUAE RISB_AQUAE] Catalyzes the formation of 6,7-dimethyl-8-ribityllumazine by condensation of 5-amino-6-(D-ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin.<ref>PMID:12603336</ref> <ref>PMID:11237620</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Encapsulating metabolic enzymes within protein cages enhances catalytic efficiency through substrate channeling. The vitamin B2 biosynthesis system, in which a dodecahedral lumazine synthase (LS) cage encapsulates a homotrimeric riboflavin synthase (RS), exemplifies this strategy, yet the molecular basis for this stoichiometric enzyme encapsulation has remained elusive. Here, cryogenic electron microscopy structures reveal a hierarchical assembly mechanism that ensures the defined host-guest ratio. RS C-terminal cage-localization signal peptides anchor at LS pentamer-pentamer interfaces early during assembly, stabilizing open intermediates that, together with delayed later-stage cage closure, extend the loading window until guest incorporation is complete. RS spatial occupancy avoids overloading, while a molecular lock upon final closure prevents disassembly. The elucidated anchoring mechanism enabled structure-based phylogenetic analysis across diverse organisms, suggesting multiple independent evolutionary origins of this modular encapsulation strategy. This naturally occurring architecture provides design principles for engineering synthetic catalytic compartments with programmable stoichiometric control.
-Authors: Koziej, L., Azuma, Y.
+A molecular basis for stoichiometric enzyme encapsulation in the vitamin B2 biosynthesis compartment.,Koziej L, Pankowski J, Stefanska M, Jankowski D, Gawin A, Malolan VV, Huiskonen JT, Kosugi T, Azuma Y Nat Commun. 2026 May 16. doi: 10.1038/s41467-026-73260-4. PMID:42143052<ref>PMID:42143052</ref>
-Description: Aquifex aeolicus lumazine synthase I125A mutant 11-pentamer cage
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Azuma, Y]]
+<div class="pdbe-citations 9ryx" style="background-color:#fffaf0;"></div>
-[[Category: Koziej, L]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Aquifex aeolicus VF5]]
+[[Category: Large Structures]]
+[[Category: Azuma Y]]
+[[Category: Koziej L]]

9ryx: Difference between revisions

Latest revision as of 05:00, 27 May 2026

Aquifex aeolicus lumazine synthase I125A mutant 11-pentamer cage

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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