8JA4

Structure of the alginate epimerase/lyase

PDB DOI: https://doi.org/10.2210/pdb8JA4/pdb

Classification: ISOMERASE
Organism(s): Azotobacter chroococcum NCIMB 8003
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-05-05 Released: 2024-05-08
Deposition Author(s): Fujiwara, T.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.04 Å
R-Value Free: 0.172
R-Value Work: 0.167
R-Value Observed: 0.167

wwPDB Validation 3D Report Full Report

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

Literature

Structural basis for the minimal bifunctional alginate epimerase AlgE3 from Azotobacter chroococcum.

Fujiwara, T., Mano, E., Nango, E.

(2024) FEBS Lett 598: 1422-1437

PubMed: 38649293 Search on PubMed
DOI: https://doi.org/10.1002/1873-3468.14886
Primary Citation of Related Structures:
8JA4, 8JA6, 8JAZ, 8XFQ, 8XFR

PubMed Abstract:
Among the epimerases specific to alginate, some of them in Azotobacter genera convert β-d-mannuronic acid to α-l-guluronic acid but also have lyase activity to degrade alginate. The remarkable characteristics of these epimerases make it a promising enzyme for tailoring alginates to meet specific demands. Here, we determined the structure of the bifunctional mannuronan C-5 epimerase AlgE3 from Azotobacter chroococcum (AcAlgE3) in complex with several mannuronic acid oligomers as well as in apo form, which allowed us to elucidate the binding manner of each mannuronic acid oligomer, and the structural plasticity, which is dependent on calcium ions. Moreover, a comprehensive analysis of the lyase activity profiles of AcAlgE3 combined with structural characteristics explained the preference for different chain length oligomers.

Organizational Affiliation

Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Japan.

Macromolecule Content

Total Structure Weight: 53.54 kDa
Atom Count: 3,840
Modelled Residue Count: 480
Deposited Residue Count: 493
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mannuronan 5-epimerase	A	493	Azotobacter chroococcum NCIMB 8003	Mutation(s): 0 Gene Names: algE7, Achr_39570 EC: 5.1.3.37
UniProt
Find proteins for A0A0C4WKK2 (Azotobacter chroococcum NCIMB 8003) Explore A0A0C4WKK2 Go to UniProtKB: A0A0C4WKK2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0C4WKK2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A]	K [auth A], L [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain K [auth A] Focus chain L [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A]	H [auth A], I [auth A], J [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]