9GOF | pdb_00009gof

MncA bound to nickel

PDB DOI: https://doi.org/10.2210/pdb9GOF/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Synechocystis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-09-05 Released: 2024-12-25
Deposition Author(s): Glasfeld, A., Robinson, N.J.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.177 (Depositor), 0.174 (DCC)
R-Value Work:
0.164 (Depositor), 0.167 (DCC)
R-Value Observed:
0.164 (Depositor)

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

A metal-trap tests and refines blueprints to engineer cellular protein metalation with different elements.

Clough, S.E., Young, T.R., Tarrant, E., Scott, A.J.P., Chivers, P.T., Glasfeld, A., Robinson, N.J.

(2025) Nat Commun 16: 810-810

PubMed: 39827241 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41467-025-56199-w
Primary Citation of Related Structures:
9GOF

PubMed Abstract:
It has been challenging to test how proteins acquire specific metals in cells. The speciation of metalation is thought to depend on the preferences of proteins for different metals competing at intracellular metal-availabilities. This implies mis-metalation may occur if proteins become mis-matched to metal-availabilities in heterologous cells. Here we use a cyanobacterial Mn ^II-cupin (MncA) as a metal trap, to test predictions of metalation. By re-folding MncA in buffered competing metals, metal-preferences are determined. Relating metal-preferences to metal-availabilities estimated using cellular metal sensors, predicts mis-metalation of MncA with Fe ^II in E. coli. After expression in E. coli, predominantly Fe ^II-bound MncA is isolated experimentally. It is predicted that in metal-supplemented viable cells metal-MncA speciation should switch. Mn ^II-, Co ^II-, or Ni ^II-MncA are recovered from the respective metal-supplemented cells. Differences between observed and predicted metal-MncA speciation are used to refine estimated metal availabilities. Values are provided as blueprints to guide engineering biological protein metalation.

Organizational Affiliation

Department of Biosciences, University of Durham, Durham, UK.

Macromolecule Content

Total Structure Weight: 119.49 kDa
Atom Count: 9,298
Modeled Residue Count: 1,066
Deposited Residue Count: 1,083
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sll1358 protein	A, B, C	361	Synechocystis	Mutation(s): 0 Gene Names: sll1358
UniProt
Find proteins for P73510 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore P73510 Go to UniProtKB: P73510
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P73510
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
GLY Query on GLY Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain O [auth C] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain O [auth C] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain O [auth C]	F [auth A], J [auth B], O [auth C]	GLYCINE C₂ H₅ N O₂ DHMQDGOQFOQNFH-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain O [auth C] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain O [auth C]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	K [auth B], L [auth B]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain K [auth B] Focus chain L [auth B]
NI (Subject of Investigation/LOI) Query on NI Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C]	D [auth A] E [auth A] H [auth B] I [auth B] M [auth C] D [auth A], E [auth A], H [auth B], I [auth B], M [auth C], N [auth C]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain M [auth C] Focus chain N [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain M [auth C] Focus chain N [auth C]