9S1P | pdb_00009s1p

Crystal structure of the DABA transaminase EctB from the halophilic and cold-adapted Marinobacter sp. CK1 -Mutant K264A

PDB DOI: https://doi.org/10.2210/pdb9S1P/pdb

Classification: TRANSFERASE
Organism(s): Marinobacter sp. CK-1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-07-18 Released: 2026-02-18
Deposition Author(s): Erlandsen, H., Leiros, I., Skogvold, A.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.163 (Depositor), 0.174 (DCC)
R-Value Work:
0.138 (Depositor), 0.152 (DCC)
R-Value Observed:
0.139 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Biochemical characterization and mutational analysis of the tetrameric DABA transaminase EctB from the Arctic bacterium Marinobacter sp. CK1.

Skogvold, A.C.A., Leiros, I., Engh, R.A., Erlandsen, H.

(2026) FEBS J

PubMed: 41652856 Search on PubMed
DOI: https://doi.org/10.1111/febs.70441
Primary Citation of Related Structures:
9S1P, 9S1Q

PubMed Abstract:
Ectoine is a chemical chaperone and osmoprotectant discovered in halophilic bacteria where it is used to protect from osmotic stress in high-salt environments. Ectoine has become a valuable product in pharmaceutical, biotechnological, cosmetical, and other applications due to its protective and stabilizing properties. The rate-limiting step of ectoine biosynthesis is catalyzed by the l-2,4-diaminobutyric acid (DABA) transaminase enzyme EctB, which converts aspartate-β-semialdehyde (ASA) to DABA. We studied the structural and functional properties of EctB from a novel halophilic bacterium Marinobacter sp. CK1. Crystal structures of complexes with mEctB/pyridoxamine-5'-phosphate and an inactive mutant K264A/pyridoxal 5'-phosphate reveal that the enzyme forms tetramers. We also investigated the stability/activity relationship and validated residues important for activity and flexibility by characterizing mEctB and a series of 17 mutants for oligomerization, thermal stability, and catalytic activity. The wild-type enzyme retained > 50% activity over a pH range of 2.5 units, with an optimum at pH 8, all NaCl concentrations (0-1 m), and temperatures between 30 °C and 45 °C. Enzyme activity was highest using DABA and GABA as substrates. Mutations at the dimer-dimer interface (K150A, E194A, E194Q, and N134A) overall lowered the enzyme's thermal stability while two (E194Q and N134A) completely abolished activity. Mutation of Arg96 at the surface significantly lowered activity and melting temperature, but with little effect on oligomerization. The active site mutants K264, Y14 and R295 were shown to be vital for activity. Overall, this study provides new information regarding the structure, stability and function of EctB.

Organizational Affiliation

Department of Chemistry, Faculty of Science and Technology, The Norwegian Structural Biology Center, UiT the Arctic University of Norway, Tromsø, Norway.

Macromolecule Content

Total Structure Weight: 47.08 kDa
Atom Count: 3,769
Modeled Residue Count: 419
Deposited Residue Count: 428
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diaminobutyrate-2-oxoglutarate transaminase	A [auth H]	428	Marinobacter sp. CK-1	Mutation(s): 0 Gene Names: ectb EC: 2.6.1.76
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP (Subject of Investigation/LOI) Query on PLP Download Ideal Coordinates CCD File SDF format, chain B [auth H] MOL2 format, chain B [auth H] mmCIF format, chain B [auth H]	B [auth H]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain B [auth H] Interactions & Density Focus chain B [auth H]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth H] MOL2 format, chain D [auth H] mmCIF format, chain D [auth H]	D [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth H] Interactions & Density Focus chain D [auth H]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth H] MOL2 format, chain C [auth H] mmCIF format, chain C [auth H]	C [auth H]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth H] Interactions & Density Focus chain C [auth H]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain E [auth H] MOL2 format, chain E [auth H] mmCIF format, chain E [auth H]	E [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth H] Interactions & Density Focus chain E [auth H]