9GV9 | pdb_00009gv9

Structure of Heparinase I from Bacteroides eggerthii in complex with calcium cofactor and delta-UA(1-4)Glc 3, 6, N-Sulphated disaccharide

PDB DOI: https://doi.org/10.2210/pdb9GV9/pdb

Classification: LYASE
Organism(s): Bacteroides eggerthii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-09-23 Released: 2025-10-08
Deposition Author(s): Mycroft-West, C., Wu, L.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free:
0.241 (Depositor), 0.205 (DCC)
R-Value Work:
0.204 (Depositor), 0.205 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Functional characterization of a 3-O-sulfate tolerant heparin lyase from Bacteroides eggerthii.

Kandola, T.K., Mycroft-West, C.J., Lima, M.A., Turner, A., Gardini, C., Urso, E., Torode, T.A., Miller, G.J., Bisio, A., Yates, E.A., Guerrini, M., Skidmore, M.A., Wu, L.

(2026) Glycobiology

PubMed: 42867289 Search on PubMed
DOI: https://doi.org/10.1093/glycob/cwag097
Primary Citation Related Structures:
9GRW, 9GV9

PubMed Abstract:
Heparin is a sulfated glycosaminoglycan, and the most used pharmaceutical anticoagulant worldwide. Heparin is isolated primarily from porcine sources, and possesses a complex variable structure, wherein anticoagulant activity is principally derived from the pentasaccharide GlcNS6S-GlcA-GlcNS3S6S-IdoA2S-GlcNS6S (AGA*IA) motif, containing an infrequent 3-O-sulfated glucosamine that enhances antithrombin stabilization. Pedobacter heparinus heparin lyases are currently widely employed for characterization of heparin and its derivatives, but have limited activity near regions of 3-O-sulfation, hindering analyses of anticoagulation relevant sequences. Here, using a panel of biophysical and structural techniques, we show that Bacteroides eggerthii lyase I liberates ΔUA-GlcNS3S6S disaccharides from the defined pentasaccharide, fondaparinux. This activity provides improved access to 3-O-sulfated heparin standards, with potential to aid heparin quality control.

Organizational Affiliation

CEMACS, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia.

Macromolecule Content

Total Structure Weight: 90.18 kDa
Atom Count: 6,647
Modeled Residue Count: 734
Deposited Residue Count: 764
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heparin lyase I	A [auth B], B [auth A]	382	Bacteroides eggerthii	Mutation(s): 0 Gene Names: HMPREF1016_01920
UniProt
Find proteins for E5WZ15 (Bacteroides eggerthii 1_2_48FAA) Explore E5WZ15 Go to UniProtKB: E5WZ15
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E5WZ15
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-3,6-di-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose	C [auth E], D [auth G]	2		N/A	Interactions Focus chain C [auth E] Focus chain D [auth G] Interactions & Density Focus chain C [auth E] Focus chain D [auth G]

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A]	I [auth B] J [auth B] K [auth B] L [auth B] M [auth B] I [auth B], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain Q [auth A] SDF format, chain R [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A]	E [auth B] F [auth B] G [auth B] H [auth B] Q [auth A] E [auth B], F [auth B], G [auth B], H [auth B], Q [auth A], R [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain Q [auth A] Focus chain R [auth A] Interactions & Density Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain Q [auth A] Focus chain R [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain P [auth B] MOL2 format, chain AA [auth A] MOL2 format, chain P [auth B] mmCIF format, chain AA [auth A] mmCIF format, chain P [auth B]	AA [auth A], P [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain P [auth B] Interactions & Density Focus chain AA [auth A] Focus chain P [auth B]