8RZJ | pdb_00008rzj

ZgGH129 from Zobellia galactanivorans in complex with the inhibitor ADG-IF (3,6-anhydro-D-galacto-isofagomine).

PDB DOI: https://doi.org/10.2210/pdb8RZJ/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: 1.99 Å
R-Value Free:
0.185 (Depositor), 0.187 (DCC)
R-Value Work:
0.154 (Depositor)
R-Value Observed:
0.155 (Depositor)

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 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: 309.35 kDa
Atom Count: 23,417
Modeled Residue Count: 2,636
Deposited Residue Count: 2,704
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G0L004
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain ZA [auth D] SDF format, chain Z [auth B] SDF format, chain WA [auth D] SDF format, chain Q [auth A] SDF format, chain LA [auth C] SDF format, chain IA [auth C] SDF format, chain I [auth A] SDF format, chain AA [auth B] MOL2 format, chain ZA [auth D] MOL2 format, chain Z [auth B] MOL2 format, chain WA [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain AA [auth B] mmCIF format, chain ZA [auth D] mmCIF format, chain Z [auth B] mmCIF format, chain WA [auth D] mmCIF format, chain Q [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain AA [auth B]	AA [auth B] I [auth A] IA [auth C] LA [auth C] Q [auth A] AA [auth B], I [auth A], IA [auth C], LA [auth C], Q [auth A], WA [auth D], Z [auth B], ZA [auth D]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain I [auth A] Focus chain IA [auth C] Focus chain LA [auth C] Focus chain Q [auth A] Focus chain WA [auth D] Focus chain Z [auth B] Focus chain ZA [auth D] Interactions & Density Focus chain AA [auth B] Focus chain I [auth A] Focus chain IA [auth C] Focus chain LA [auth C] Focus chain Q [auth A] Focus chain WA [auth D] Focus chain Z [auth B] Focus chain ZA [auth D]
TLA Query on TLA Download:Ideal Coordinates CCD File SDF format, chain RA [auth C] SDF format, chain NA [auth C] SDF format, chain MA [auth C] SDF format, chain M [auth A] SDF format, chain J [auth A] SDF format, chain BA [auth B] SDF format, chain AB [auth D] MOL2 format, chain RA [auth C] MOL2 format, chain NA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain J [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain AB [auth D] mmCIF format, chain RA [auth C] mmCIF format, chain NA [auth C] mmCIF format, chain MA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain J [auth A] mmCIF format, chain BA [auth B] mmCIF format, chain AB [auth D]	AB [auth D] BA [auth B] J [auth A] M [auth A] MA [auth C] AB [auth D], BA [auth B], J [auth A], M [auth A], MA [auth C], NA [auth C], RA [auth C]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain AB [auth D] Focus chain BA [auth B] Focus chain J [auth A] Focus chain M [auth A] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain RA [auth C] Interactions & Density Focus chain AB [auth D] Focus chain BA [auth B] Focus chain J [auth A] Focus chain M [auth A] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain RA [auth C]
A1H36 (Subject of Investigation/LOI) Query on A1H36 Download:Ideal Coordinates CCD File SDF format, chain UA [auth D] SDF format, chain T [auth B] SDF format, chain GA [auth C] SDF format, chain E [auth A] MOL2 format, chain UA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain E [auth A] mmCIF format, chain UA [auth D] mmCIF format, chain T [auth B] mmCIF format, chain GA [auth C] mmCIF format, chain E [auth A]	E [auth A], GA [auth C], T [auth B], UA [auth D]	(1~{R},5~{R},8~{S})-6-oxa-3-azabicyclo[3.2.1]octan-8-ol C₆ H₁₁ N O₂ TWEISKJFQUHRBG-PBXRRBTRSA-N		Interactions Focus chain E [auth A] Focus chain GA [auth C] Focus chain T [auth B] Focus chain UA [auth D] Interactions & Density Focus chain E [auth A] Focus chain GA [auth C] Focus chain T [auth B] Focus chain UA [auth D]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain CA [auth B] MOL2 format, chain CA [auth B] mmCIF format, chain CA [auth B]	CA [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Interactions & Density Focus chain CA [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain R [auth A] SDF format, chain SA [auth C] SDF format, chain TA [auth C] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain XA [auth D] SDF format, chain Y [auth B] SDF format, chain YA [auth D] SDF format, chain V [auth B] SDF format, chain S [auth A] SDF format, chain QA [auth C] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain KA [auth C] SDF format, chain JA [auth C] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain FA [auth B] SDF format, chain DB [auth D] MOL2 format, chain P [auth A] MOL2 format, chain R [auth A] MOL2 format, chain SA [auth C] MOL2 format, chain TA [auth C] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth D] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth D] MOL2 format, chain V [auth B] MOL2 format, chain S [auth A] MOL2 format, chain QA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain DB [auth D] mmCIF format, chain P [auth A] mmCIF format, chain R [auth A] mmCIF format, chain SA [auth C] mmCIF format, chain TA [auth C] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain XA [auth D] mmCIF format, chain Y [auth B] mmCIF format, chain YA [auth D] mmCIF format, chain V [auth B] mmCIF format, chain S [auth A] mmCIF format, chain QA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain DB [auth D]	DB [auth D] FA [auth B] G [auth A] H [auth A] JA [auth C] DB [auth D], FA [auth B], G [auth A], H [auth A], JA [auth C], KA [auth C], N [auth A], O [auth A], P [auth A], QA [auth C], R [auth A], S [auth A], SA [auth C], TA [auth C], V [auth B], W [auth B], X [auth B], XA [auth D], Y [auth B], YA [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain DB [auth D] Focus chain FA [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain QA [auth C] Focus chain R [auth A] Focus chain S [auth A] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain XA [auth D] Focus chain Y [auth B] Focus chain YA [auth D] Interactions & Density Focus chain DB [auth D] Focus chain FA [auth B] Focus chain G [auth A] Focus chain H [auth A] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain QA [auth C] Focus chain R [auth A] Focus chain S [auth A] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain XA [auth D] Focus chain Y [auth B] Focus chain YA [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain VA [auth D] SDF format, chain U [auth B] SDF format, chain HA [auth C] SDF format, chain F [auth A] MOL2 format, chain VA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain HA [auth C] MOL2 format, chain F [auth A] mmCIF format, chain VA [auth D] mmCIF format, chain U [auth B] mmCIF format, chain HA [auth C] mmCIF format, chain F [auth A]	F [auth A], HA [auth C], U [auth B], VA [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain HA [auth C] Focus chain U [auth B] Focus chain VA [auth D] Interactions & Density Focus chain F [auth A] Focus chain HA [auth C] Focus chain U [auth B] Focus chain VA [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain PA [auth C] SDF format, chain OA [auth C] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain EA [auth B] SDF format, chain DA [auth B] SDF format, chain CB [auth D] SDF format, chain BB [auth D] MOL2 format, chain PA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain CB [auth D] MOL2 format, chain BB [auth D] mmCIF format, chain PA [auth C] mmCIF format, chain OA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain CB [auth D] mmCIF format, chain BB [auth D]	BB [auth D] CB [auth D] DA [auth B] EA [auth B] K [auth A] BB [auth D], CB [auth D], DA [auth B], EA [auth B], K [auth A], L [auth A], OA [auth C], PA [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain BB [auth D] Focus chain CB [auth D] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain OA [auth C] Focus chain PA [auth C] Interactions & Density Focus chain BB [auth D] Focus chain CB [auth D] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain OA [auth C] Focus chain PA [auth C]