8JC1

Crystal structure of Pectocin M1 from Pectobacterium carotovorum

PDB DOI: https://doi.org/10.2210/pdb8JC1/pdb

Classification: HYDROLASE
Organism(s): Pectobacterium carotovorum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-05-10 Released: 2024-09-04
Deposition Author(s): Jantarit, N., Kurisu, G., Tanaka, H.
Funding Organization(s): Japan Science and Technology

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.04 Å
R-Value Free: 0.238
R-Value Work: 0.195
R-Value Observed: 0.196

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

Crystal structure of pectocin M1 reveals diverse conformations and interactions during its initial step via the ferredoxin uptake system.

Jantarit, N., Tanaka, H., Lin, Y., Lee, Y.H., Kurisu, G.

(2024) FEBS Open Bio 14: 1731-1745

PubMed: 39123319 Search on PubMed
DOI: https://doi.org/10.1002/2211-5463.13874
Primary Citation of Related Structures:
8JC1

PubMed Abstract:
Pectocin M1 (PM1), the bacteriocin from phytopathogenic Pectobacterium carotovorum which causes soft rot disease, has a unique ferredoxin domain that allows it to use FusA of the plant ferredoxin uptake system. To probe the structure-based mechanism of PM1 uptake, we determined the X-ray structure of full-length PM1, containing an N-terminal ferredoxin and C-terminal catalytic domain connected by helical linker, at 2.04 Å resolution. Based on published FusA structure and NMR data for PM1 ferredoxin domain titrated with FusA, we modeled docking of the ferredoxin domain with FusA. Combining the docking models with the X-ray structures of PM1 and FusA enables us to propose the mechanism by which PM1 undergoes dynamic domain rearrangement to translocate across the target cell outer membrane.

Organizational Affiliation

Protein Crystallography Laboratory, Institute for Protein Research, Osaka University, Suita, Japan.

Macromolecule Content

Total Structure Weight: 119.1 kDa
Atom Count: 8,765
Modelled Residue Count: 1,068
Deposited Residue Count: 1,072
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
pectocin M1	A, B, C, D	268	Pectobacterium carotovorum	Mutation(s): 0 Gene Names: PC1_2303
UniProt
Find proteins for C6DJ69 (Pectobacterium carotovorum subsp. carotovorum (strain PC1)) Explore C6DJ69 Go to UniProtKB: C6DJ69
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C6DJ69
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FES (Subject of Investigation/LOI) Query on FES Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain R [auth C] SDF format, chain Z [auth D] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain R [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain R [auth C] mmCIF format, chain Z [auth D]	E [auth A], K [auth B], R [auth C], Z [auth D]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain R [auth C] Focus chain Z [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain R [auth C] Focus chain Z [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain U [auth C] MOL2 format, chain U [auth C] mmCIF format, chain U [auth C]	U [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain U [auth C] Interactions & Density Focus chain U [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain Q [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C]	M [auth B], Q [auth C], S [auth C], T [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Focus chain Q [auth C] Focus chain S [auth C] Focus chain T [auth C] Interactions & Density Focus chain M [auth B] Focus chain Q [auth C] Focus chain S [auth C] Focus chain T [auth C]
SO3 Query on SO3 Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain V [auth C] MOL2 format, chain L [auth B] MOL2 format, chain V [auth C] mmCIF format, chain L [auth B] mmCIF format, chain V [auth C]	L [auth B], V [auth C]	SULFITE ION O₃ S LSNNMFCWUKXFEE-UHFFFAOYSA-L		Interactions Focus chain L [auth B] Focus chain V [auth C] Interactions & Density Focus chain L [auth B] Focus chain V [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain X [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain X [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain X [auth C]	BA [auth D], X [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BA [auth D] Focus chain X [auth C] Interactions & Density Focus chain BA [auth D] Focus chain X [auth C]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain J [auth A] SDF format, chain P [auth B] SDF format, chain Y [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Y [auth C] mmCIF format, chain CA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Y [auth C]	CA [auth D], J [auth A], P [auth B], Y [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain J [auth A] Focus chain P [auth B] Focus chain Y [auth C] Interactions & Density Focus chain CA [auth D] Focus chain J [auth A] Focus chain P [auth B] Focus chain Y [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain W [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain W [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain W [auth C]	AA [auth D] F [auth A] G [auth A] H [auth A] I [auth A] AA [auth D], F [auth A], G [auth A], H [auth A], I [auth A], N [auth B], O [auth B], W [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain W [auth C] Interactions & Density Focus chain AA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain W [auth C]