8RZI

ZgGH129 from Zobellia galactanivorans soaked with 1,2-diF-ADG (3,6-Anhydro-2-deoxy-2-fluoro-a-D-galactopyranosyl fluoride) resulting in a trapped glycosyl-enzyme intermediate.

PDB DOI: https://doi.org/10.2210/pdb8RZI/pdb

Classification: HYDROLASE
Organism(s): Zobellia galactanivorans
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-02-12 Released: 2024-07-31
Deposition Author(s): Roret, T., Czjzek, M., Ficko-Blean, E.
Funding Organization(s): Agence Nationale de la Recherche (ANR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free: 0.183
R-Value Work: 0.154
R-Value Observed: 0.156

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Constrained Catalytic Itinerary of a Retaining 3,6-Anhydro-D-Galactosidase, a Key Enzyme in Red Algal Cell Wall Degradation.

Wallace, M.D., Cuxart, I., Roret, T., Guee, L., Debowski, A.W., Czjzek, M., Rovira, C., Stubbs, K.A., Ficko-Blean, E.

(2024) Angew Chem Int Ed Engl 63: e202411171-e202411171

PubMed: 39022920 Search on PubMed
DOI: https://doi.org/10.1002/anie.202411171
Primary Citation of Related Structures:
8RZG, 8RZH, 8RZI, 8RZJ, 8RZK

PubMed Abstract:
The marine Bacteroidota Zobellia galactanivorans has a polysaccharide utilization locus dedicated to the catabolism of the red algal cell wall galactan carrageenan and its unique and industrially important α-3,6-anhydro-D-galactose (ADG) monosaccharide. Here we present the first analysis of the specific molecular interactions the exo-(α-1,3)-3,6-anhydro-D-galactosidase ZgGH129 uses to cope with the strict steric restrictions imposed by its bicyclic ADG substrate - which is ring flipped relative to D-galactose. Crystallographic snapshots of key catalytic states obtained with the natural substrate and novel chemical tools designed to mimic species along the reaction coordinate, together with quantum mechanics/molecular mechanics (QM/MM) metadynamics methods and kinetic studies, demonstrate a retaining mechanism where the second step is rate limiting. The conformational landscape of the constrained 3,6-anhydro-D-galactopyranose ring proceeds through enzyme glycosylation B1,4 → [E4]‡ → E4/1C4 and deglycosylation E4/1C4 → [E4]‡ → B1,4 itineraries limited to the Southern Hemisphere of the Cremer-Pople sphere. These results demonstrate the conformational changes throughout catalysis in a non-standard, sterically restrained, bicyclic monosaccharide and provide a molecular framework for mechanism-based inhibitor design for anhydro-type carbohydrate-processing enzymes and for future applications involving carrageenan degradation. In addition, it provides a rare example of distinct niche-based conformational itineraries within the same carbohydrate-active enzyme family.

Organizational Affiliation

University of Western Australia School of Molecular Sciences, School of Molecular Sciences, AUSTRALIA.

Macromolecule Content

Total Structure Weight: 308.12 kDa
Atom Count: 23,331
Modelled Residue Count: 2,636
Deposited Residue Count: 2,704
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Conserved hypothetical periplasmic protein	A, B, C, D	676	Zobellia galactanivorans	Mutation(s): 0 Gene Names: zobellia_3152
UniProt
Find proteins for G0L004 (Zobellia galactanivorans (strain DSM 12802 / CCUG 47099 / CIP 106680 / NCIMB 13871 / Dsij)) Explore G0L004 Go to UniProtKB: G0L004
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G0L004
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TLA Query on TLA Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain F [auth A] SDF format, chain LA [auth D] SDF format, chain Q [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain Q [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain Q [auth B]	AA [auth C], F [auth A], LA [auth D], Q [auth B]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain AA [auth C] Focus chain F [auth A] Focus chain LA [auth D] Focus chain Q [auth B] Interactions & Density Focus chain AA [auth C] Focus chain F [auth A] Focus chain LA [auth D] Focus chain Q [auth B]
A1H37 (Subject of Investigation/LOI) Query on A1H37 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain KA [auth D] SDF format, chain P [auth B] SDF format, chain Z [auth C] MOL2 format, chain E [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain P [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain E [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain P [auth B] mmCIF format, chain Z [auth C]	E [auth A], KA [auth D], P [auth B], Z [auth C]	(1~{R},4~{S},5~{S},8~{S})-4-fluoranyl-2,6-dioxabicyclo[3.2.1]octan-8-ol C₆ H₉ F O₃ BIAPWCHZUDCPBP-BGPJRJDNSA-N		Interactions Focus chain E [auth A] Focus chain KA [auth D] Focus chain P [auth B] Focus chain Z [auth C] Interactions & Density Focus chain E [auth A] Focus chain KA [auth D] Focus chain P [auth B] Focus chain Z [auth C]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain R [auth B] MOL2 format, chain G [auth A] MOL2 format, chain R [auth B] mmCIF format, chain G [auth A] mmCIF format, chain R [auth B]	G [auth A], R [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain R [auth B] Interactions & Density Focus chain G [auth A] Focus chain R [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain PA [auth D] SDF format, chain QA [auth D] SDF format, chain RA [auth D] SDF format, chain SA [auth D] SDF format, chain TA [auth D] SDF format, chain UA [auth D] SDF format, chain V [auth B] SDF format, chain VA [auth D] SDF format, chain W [auth B] SDF format, chain WA [auth D] SDF format, chain X [auth B] SDF format, chain Y [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain QA [auth D] MOL2 format, chain RA [auth D] MOL2 format, chain SA [auth D] MOL2 format, chain TA [auth D] MOL2 format, chain UA [auth D] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth D] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain QA [auth D] mmCIF format, chain RA [auth D] mmCIF format, chain SA [auth D] mmCIF format, chain TA [auth D] mmCIF format, chain UA [auth D] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth D] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B]	EA [auth C] FA [auth C] GA [auth C] HA [auth C] IA [auth C] EA [auth C], FA [auth C], GA [auth C], HA [auth C], IA [auth C], JA [auth C], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], PA [auth D], QA [auth D], RA [auth D], SA [auth D], TA [auth D], UA [auth D], V [auth B], VA [auth D], W [auth B], WA [auth D], X [auth B], Y [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain TA [auth D] Focus chain UA [auth D] Focus chain V [auth B] Focus chain VA [auth D] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain TA [auth D] Focus chain UA [auth D] Focus chain V [auth B] Focus chain VA [auth D] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain Y [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain NA [auth D] SDF format, chain OA [auth D] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain OA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain OA [auth D] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B]	CA [auth C] DA [auth C] I [auth A] J [auth A] NA [auth D] CA [auth C], DA [auth C], I [auth A], J [auth A], NA [auth D], OA [auth D], T [auth B], U [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain T [auth B] Focus chain U [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain H [auth A] SDF format, chain MA [auth D] SDF format, chain S [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain S [auth B] mmCIF format, chain BA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain S [auth B]	BA [auth C], H [auth A], MA [auth D], S [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain H [auth A] Focus chain MA [auth D] Focus chain S [auth B] Interactions & Density Focus chain BA [auth C] Focus chain H [auth A] Focus chain MA [auth D] Focus chain S [auth B]