8RO4 | pdb_00008ro4

The crystal structure of 2-hydroxy-3-keto-glucal hydratase AtHYD from A. tumefaciens

PDB DOI: https://doi.org/10.2210/pdb8RO4/pdb

Classification: LYASE
Organism(s): Agrobacterium tumefaciens
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2024-01-11 Released: 2024-08-07
Deposition Author(s): Grininger, C., Bitter, J., Pfeiffer, M., Nidetzky, B., Pavkov-Keller, T.
Funding Organization(s): Austrian Science Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.51 Å
R-Value Free:
0.217 (Depositor), 0.218 (DCC)
R-Value Work:
0.181 (Depositor), 0.181 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Enzyme Machinery for Bacterial Glucoside Metabolism through a Conserved Non-hydrolytic Pathway.

Kastner, K., Bitter, J., Pfeiffer, M., Grininger, C., Oberdorfer, G., Pavkov-Keller, T., Weber, H., Nidetzky, B.

(2024) Angew Chem Int Ed Engl 63: e202410681-e202410681

PubMed: 39041709 Search on PubMed
DOI: https://doi.org/10.1002/anie.202410681
Primary Citation Related Structures:
8RO4, 8RR2

PubMed Abstract:
The flexible acquisition of substrates from nutrient pools is critical for microbes to prevail in competitive environments. To acquire glucose from diverse glycoside and disaccharide substrates, many free-living and symbiotic bacteria have developed, alongside hydrolysis, a non-hydrolytic pathway comprised of four biochemical steps and conferred from a single glycoside utilization gene locus (GUL). Mechanistically, this pathway integrates within the framework of oxidation and reduction at the glucosyl/glucose C3, the eliminative cleavage of the glycosidic bond and the addition of water in two consecutive lyase-catalyzed reactions. Here, based on study of enzymes from the phytopathogen Agrobacterium tumefaciens, we reveal a conserved Mn ²⁺ metallocenter active site in both lyases and identify the structural requirements for specific catalysis to elimination of 3-keto-glucosides and water addition to the resulting 2-hydroxy-3-keto-glycal product, yielding 3-keto-glucose. Extending our search of GUL-encoded putative lyases to the human gut commensal Bacteroides thetaiotaomicron, we discover a Ca ²⁺ metallocenter active site in a putative glycoside hydrolase-like protein and demonstrate its catalytic function in the eliminative cleavage of 3-keto-glucosides of opposite (α) anomeric configuration as preferred by the A. tumefaciens enzyme (β). Structural and biochemical comparisons reveal the molecular-mechanistic origin of 3-keto-glucoside lyase stereo-complementarity. Our findings identify a basic set of GUL-encoded lyases for glucoside metabolism and assign physiological significance to GUL genetic diversity in the bacterial domain of life.

Organizational Affiliation

Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, A-8010, Graz, Austria.

Macromolecule Content

Total Structure Weight: 234.61 kDa
Atom Count: 16,102
Modeled Residue Count: 2,033
Deposited Residue Count: 2,094
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-hydroxy-3-keto-glucal hydratase	A B [auth C] C [auth D] D [auth B] E A, B [auth C], C [auth D], D [auth B], E, F	349	Agrobacterium tumefaciens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MN (Subject of Investigation/LOI) Query on MN Download:Ideal Coordinates CCD File SDF format, chain L [auth F] SDF format, chain K [auth E] SDF format, chain J [auth B] SDF format, chain I [auth D] SDF format, chain H [auth C] SDF format, chain G [auth A] MOL2 format, chain L [auth F] MOL2 format, chain K [auth E] MOL2 format, chain J [auth B] MOL2 format, chain I [auth D] MOL2 format, chain H [auth C] MOL2 format, chain G [auth A] mmCIF format, chain L [auth F] mmCIF format, chain K [auth E] mmCIF format, chain J [auth B] mmCIF format, chain I [auth D] mmCIF format, chain H [auth C] mmCIF format, chain G [auth A]	G [auth A] H [auth C] I [auth D] J [auth B] K [auth E] G [auth A], H [auth C], I [auth D], J [auth B], K [auth E], L [auth F]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth C] Focus chain I [auth D] Focus chain J [auth B] Focus chain K [auth E] Focus chain L [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth C] Focus chain I [auth D] Focus chain J [auth B] Focus chain K [auth E] Focus chain L [auth F]