9GCB image
Deposition Date 2024-08-01
Release Date 2025-09-10
Last Version Date 2025-10-29
Entry Detail
PDB ID:
9GCB
Title:
DUF4198 protein from Ideonella sakaiensis with Ni bound
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.44 Å
R-Value Free:
0.18
R-Value Work:
0.12
Space Group:
P 1
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nickel ECF transporter, additional periplasmic component NikK
Gene (Uniprot):ISF6_5495
Chain IDs:A, B (auth: C)
Chain Length:213
Number of Molecules:2
Biological Source:Piscinibacter sakaiensis
Primary Citation
Signal-strapping as a protein-sequence search method for the discovery of metalloproteins.
Nat Commun 16 9244 9244 (2025)
PMID: 41115942 DOI: 10.1038/s41467-025-64309-x

Abstact

Metalloprotein discovery is often made post hoc, in which activity studies following protein isolation reveal a metal-ion dependence. Herein we take a different approach to finding metalloproteins, by building on the discovery of copper-containing lytic polysaccharide monooxygenases (LPMOs), which include an N-terminal histidine as part of their sequence. This residue acts as a natural chelator for transition metal ions, irrespective of the structure of the protein. We report the method of signal strapping, where sequences of N-terminal signal peptides artificially appended with a histidine residue at their C-terminus are used to bootstrap a proteomic search. These searches return sequences of proteins with an N-terminal histidine capable of coordinating a metal ion. We exemplify the approach by the discovery and characterisation of four classes of bacterial metalloproteins, including two that we denote as anglerases reflecting their potential to capture transition metal ions from the bacterial environment.

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Primary Citation of related structures
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