7Y5Y

X-ray Structure of Stay-Green (SGR) from Anaerolineae bacterium.

PDB DOI: https://doi.org/10.2210/pdb7Y5Y/pdb

Classification: PLANT PROTEIN
Organism(s): Anaerolineae bacterium
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-06-18 Released: 2022-10-19
Deposition Author(s): Dey, D., Nishijima, M., Kurisu, G., Tanaka, H., Ito, H.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.239
R-Value Work: 0.218
R-Value Observed: 0.219

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure and reaction mechanism of a bacterial Mg-dechelatase homolog from the Chloroflexi Anaerolineae.

Dey, D., Nishijima, M., Tanaka, R., Kurisu, G., Tanaka, H., Ito, H.

(2022) Protein Sci 31: e4430-e4430

PubMed: 36173179 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/pro.4430
Primary Citation of Related Structures:
7Y5Y

PubMed Abstract:
Chlorophyll degradation plays a myriad of physiological roles in photosynthetic organisms, including acclimation to light environment and nutrient remobilization during senescence. Mg extraction from chlorophyll a is the first and committed step of the chlorophyll degradation pathway. This reaction is catalyzed by the Mg-dechelatase enzyme encoded by Stay-Green (SGR). The reaction mechanism of SGR protein remains elusive since metal ion extraction from organic molecules is not a common enzymatic reaction. Additionally, experimentally derived structural information about SGR or its homologs has not yet been reported. In this study, the crystal structure of the SGR homolog from Anaerolineae bacterium was determined using the molecular replacement method at 1.85 Å resolution. Our previous study showed that three residues-H32, D34, and D62 are essential for the catalytic activity of the enzyme. Biochemical analysis involving mutants of D34 residue further strengthened its importance in the functioning of the dechelatase. Docking simulation also revealed the interaction between the D34 side chain and central Mg ion of chlorophyll a. Structural analysis showed the arrangement of D34/H32/D62 in the form of a catalytic triad that is generally found in hydrolases. The probable reaction mechanism suggests that deprotonated D34 side chain coordinates and destabilizes Mg, resulting in Mg extraction. Besides, H32 possibly acts as a general base catalyst and D62 facilitates H32 to be a better proton acceptor. Taken together, the reaction mechanism of SGR partially mirrors the one observed in hydrolases.

Organizational Affiliation

Graduate School of Life Science, Hokkaido University, Sapporo, Japan.

Macromolecule Content

Total Structure Weight: 38.89 kDa
Atom Count: 2,756
Modelled Residue Count: 304
Deposited Residue Count: 322
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Staygreen domain-containing protein	A, B	161	Anaerolineae bacterium	Mutation(s): 0 Gene Names: G4O14_14785
UniProt
Find proteins for A0A7V2LBK3 (Anaerolineae bacterium) Explore A0A7V2LBK3 Go to UniProtKB: A0A7V2LBK3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7V2LBK3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B]	H [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B]	C [auth A], G [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B]	D [auth A], E [auth A], F [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B]