4ELY | pdb_00004ely

CCDBVFI:GYRA14EC

PDB DOI: https://doi.org/10.2210/pdb4ELY/pdb
Entry: 4ELY supersedes: 3KU8

Classification: TOXIN/ISOMERASE
Organism(s): Shigella flexneri, Aliivibrio fischeri
Expression System: Escherichia coli BL21(DE3), Escherichia coli
Mutation(s): No

Deposited: 2012-04-11 Released: 2012-05-30
Deposition Author(s): De Jonge, N., Simic, R., Buts, L., Haesaerts, S., Roelants, K., Garcia-Pino, A., Sterckx, Y., De Greve, H., Lah, J., Loris, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free:
0.217 (Depositor), 0.217 (DCC)
R-Value Work:
0.185 (Depositor), 0.181 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Alternative interactions define gyrase specificity in the CcdB family.

De Jonge, N., Simic, M., Buts, L., Haesaerts, S., Roelants, K., Garcia-Pino, A., Sterckx, Y., De Greve, H., Lah, J., Loris, R.

(2012) Mol Microbiol 84: 965-978

PubMed: 22582791 Search on PubMed
DOI: https://doi.org/10.1111/j.1365-2958.2012.08069.x
Primary Citation Related Structures:
4ELY, 4ELZ

PubMed Abstract:
Toxin-antitoxin (TA) modules are small operons associated with stress response of bacteria. F-plasmid CcdB(F) was the first TA toxin for which its target, gyrase, was identified. Plasmidic and chromosomal CcdBs belong to distinct families. Conserved residues crucial for gyrase poisoning activity of plasmidic CcdBs are not conserved among these families. Here we show that the chromosomal CcdB(Vfi) from Vibrio fischeri is an active gyrase poison that interacts with its target via an alternative energetic mechanism. Changes in the GyrA14-binding surface of the Vibrio and F-plasmid CcdB family members illustrate neutral drift where alternative interactions can be used to achieve the same functionality. Differences in affinity between V. fischeri and F-plasmid CcdB for gyrase and their corresponding CcdA antitoxin possibly reflect distinct roles for TA modules located on plasmids and chromosomes.

Organizational Affiliation

Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.

Macromolecule Content

Total Structure Weight: 59.06 kDa
Atom Count: 3,906
Modeled Residue Count: 466
Deposited Residue Count: 522
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA gyrase subunit A	A, B	156	Shigella flexneri	Mutation(s): 0 Gene Names: gyrA, GYRASE, S2444, SF2311 EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for P0AES5 (Shigella flexneri) Explore P0AES5 Go to UniProtKB: P0AES5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AES5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CcdB	C, D	105	Aliivibrio fischeri	Mutation(s): 0 Gene Names: ccdB
UniProt
Find proteins for Q84B82 (Aliivibrio fischeri) Explore Q84B82 Go to UniProtKB: Q84B82
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q84B82
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain G [auth D] SDF format, chain F [auth A] MOL2 format, chain G [auth D] MOL2 format, chain F [auth A] mmCIF format, chain G [auth D] mmCIF format, chain F [auth A]	F [auth A], G [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free: 0.217 (Depositor), 0.217 (DCC)
R-Value Work: 0.185 (Depositor), 0.181 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.073	α = 90
b = 90.833	β = 102.59
c = 58.13	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-05-30

Deposition Author(s):

This entry supersedes: 3KU8

Revision History (Full details and data files)

Version 1.0: 2012-05-30
Type: Initial release
Version 1.1: 2013-01-02
Changes: Database references
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description