9HH4 | pdb_00009hh4

Crystal structure of the family S1_19 carrageenan sulfatase ZgCgsA from Zobellia galactanivorans in complex with hybrid b-k-neocarratetraose

PDB DOI: https://doi.org/10.2210/pdb9HH4/pdb

Classification: HYDROLASE
Organism(s): Zobellia galactanivorans
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-11-21 Released: 2025-06-04
Deposition Author(s): Chevenier, A., Czjzek, M., Michel, G., Ficko-Blean, E.
Funding Organization(s): Agence Nationale de la Recherche (ANR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free:
0.207 (Depositor), 0.206 (DCC)
R-Value Work:
0.167 (Depositor), 0.165 (DCC)
R-Value Observed:
0.169 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structure, function and catalytic mechanism of the carrageenan-sulfatases from the marine bacterium Zobellia galactanivorans Dsij T.

Chevenier, A., Fanuel, M., Sokolova, E., Mico Latorre, D., Jouanneau, D., Jeudy, A., Prechoux, A., Zuhlke, M.K., Bartel, J., Becher, D., Czjzek, M., Ropartz, D., Michel, G., Ficko-Blean, E.

(2025) Carbohydr Polym 358: 123487-123487

PubMed: 40383559 Search on PubMed
DOI: https://doi.org/10.1016/j.carbpol.2025.123487
Primary Citation of Related Structures:
9HH2, 9HH3, 9HH4

PubMed Abstract:
Carrageenans are highly diverse sulfated galactans found in red seaweeds. They play various physiological roles within macroalgae, but also serve as carbon sources for heterotrophic marine bacteria living at their surface. Carrageenan sulfatases catalyze the removal of sulfate esters from the glycans to expose the saccharide chain for further enzymatic processing. In the marine flavobacterium Zobellia galactanivorans, three carrageenan sulfatase genes are localized within a carrageenan utilization locus, belonging to three distinct SulfAtlas S1 (formylglycine-dependent sulfatases) subfamilies (S1_19, ZgCgsA; S1_7, ZgCgsB1; and S1_17, ZgCgsC). In this study we combined several techniques to characterize the detailed desulfurylation steps in the catabolic pathway of carrageenan in this model marine bacterium. High resolution UHPLC-MS/MS sequencing of the reaction species provides precise chemical localization of the enzymatic activities for the three carrageenan sulfatases on carrageenan polysaccharides and oligosaccharides. High resolution structures of the S1_19 endo-/exo-lytic carrageenan sulfatase (ZgCgsA) in complex with oligocarrageenan products show substrate plasticity which involve enzyme and glycan conformational rearrangements. A sulfo-enzyme covalent-intermediate sheds light on the catalytic mechanism and highlights the unique chemistry of formylglycine, an essential post-translationally modified catalytic residue in the active site of S1 family sulfatases.

Organizational Affiliation

Sorbonne Université, CNRS, Laboratoire de Biologie Intégrative des Modèles Marins, LBI2M, F-29680 Roscoff, France.

Macromolecule Content

Total Structure Weight: 224.46 kDa
Atom Count: 16,711
Modeled Residue Count: 1,861
Deposited Residue Count: 1,920
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sulfatase, family S1-19	A, B, C, D	480	Zobellia galactanivorans	Mutation(s): 0 Gene Names: zobellia_3145 EC: 3.1.6
UniProt
Find proteins for G0L000 (Zobellia galactanivorans (strain DSM 12802 / CCUG 47099 / CIP 106680 / NCIMB 13871 / Dsij)) Explore G0L000 Go to UniProtKB: G0L000
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G0L000
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
3,6-anhydro-alpha-D-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-D-galactopyranose-(1-3)-4-O-sulfo-beta-D-galactopyranose	E [auth I], F [auth J], G [auth K], H [auth L]	4		N/A	Interactions Focus chain E [auth I] Focus chain F [auth J] Focus chain G [auth K] Focus chain H [auth L] Interactions & Density Focus chain E [auth I] Focus chain F [auth J] Focus chain G [auth K] Focus chain H [auth L]
Glycosylation Resources
GlyTouCan: G69730VZ GlyCosmos: G69730VZ

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain YA [auth D] SDF format, chain ZA [auth D] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain YA [auth D] MOL2 format, chain ZA [auth D] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A] mmCIF format, chain YA [auth D] mmCIF format, chain ZA [auth D]	FA [auth B] GA [auth B] U [auth A] V [auth A] W [auth A] FA [auth B], GA [auth B], U [auth A], V [auth A], W [auth A], YA [auth D], ZA [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain FA [auth B] Focus chain GA [auth B] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain YA [auth D] Focus chain ZA [auth D] Interactions & Density Focus chain FA [auth B] Focus chain GA [auth B] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain YA [auth D] Focus chain ZA [auth D]
BR Query on BR Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain IA [auth C] SDF format, chain J [auth A] SDF format, chain JA [auth C] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain L [auth A] SDF format, chain RA [auth D] SDF format, chain SA [auth D] SDF format, chain TA [auth D] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain IA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain RA [auth D] MOL2 format, chain SA [auth D] MOL2 format, chain TA [auth D] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain IA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain RA [auth D] mmCIF format, chain SA [auth D] mmCIF format, chain TA [auth D] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	AA [auth B] IA [auth C] J [auth A] JA [auth C] K [auth A] AA [auth B], IA [auth C], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], RA [auth D], SA [auth D], TA [auth D], Y [auth B], Z [auth B]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain AA [auth B] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain TA [auth D] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain TA [auth D] Focus chain Y [auth B] Focus chain Z [auth B]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain HA [auth C] SDF format, chain I [auth A] SDF format, chain QA [auth D] SDF format, chain X [auth B] MOL2 format, chain HA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain QA [auth D] MOL2 format, chain X [auth B] mmCIF format, chain HA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain QA [auth D] mmCIF format, chain X [auth B]	HA [auth C], I [auth A], QA [auth D], X [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain HA [auth C] Focus chain I [auth A] Focus chain QA [auth D] Focus chain X [auth B] Interactions & Density Focus chain HA [auth C] Focus chain I [auth A] Focus chain QA [auth D] Focus chain X [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain LA [auth C] SDF format, chain M [auth A] SDF format, chain MA [auth C] SDF format, chain N [auth A] SDF format, chain NA [auth C] SDF format, chain O [auth A] SDF format, chain OA [auth C] SDF format, chain P [auth A] SDF format, chain PA [auth C] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain UA [auth D] SDF format, chain VA [auth D] SDF format, chain WA [auth D] SDF format, chain XA [auth D] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain LA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain UA [auth D] MOL2 format, chain VA [auth D] MOL2 format, chain WA [auth D] MOL2 format, chain XA [auth D] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain LA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain UA [auth D] mmCIF format, chain VA [auth D] mmCIF format, chain WA [auth D] mmCIF format, chain XA [auth D]	BA [auth B] CA [auth B] DA [auth B] EA [auth B] LA [auth C] BA [auth B], CA [auth B], DA [auth B], EA [auth B], LA [auth C], M [auth A], MA [auth C], N [auth A], NA [auth C], O [auth A], OA [auth C], P [auth A], PA [auth C], Q [auth A], R [auth A], S [auth A], T [auth A], UA [auth D], VA [auth D], WA [auth D], XA [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain WA [auth D] Focus chain XA [auth D] Interactions & Density Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain WA [auth D] Focus chain XA [auth D]