9GEF | pdb_00009gef

Experimental localization of metal-binding sites reveals the role of metal ions in the delafloxacin-stabilized Streptococcus pneumoniae topoisomerase IV DNA cleavage complex

PDB DOI: https://doi.org/10.2210/pdb9GEF/pdb
NAKB: 9GEF

Classification: DNA BINDING PROTEIN
Organism(s): Streptococcus pneumoniae, Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-08-08 Released: 2024-10-16
Deposition Author(s): Wang, B., Najmudin, S., Pan, X.-S., Mykhaylyk, V., Orr, C., Wagner, A., Govada, L., Chayen, N.E., Fisher, L.M., Sanderson, M.R.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.62 Å
R-Value Free:
0.208 (Depositor), 0.209 (DCC)
R-Value Work:
0.180 (Depositor), 0.189 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Experimental localization of metal-binding sites reveals the role of metal ions in type II DNA topoisomerases.

Wang, B., Najmudin, S., Pan, X.S., Mykhaylyk, V., Orr, C., Wagner, A., Govada, L., Chayen, N.E., Fisher, L.M., Sanderson, M.R.

(2024) Proc Natl Acad Sci U S A 121: e2413357121-e2413357121

PubMed: 39361644 Search on PubMed
DOI: https://doi.org/10.1073/pnas.2413357121
Primary Citation of Related Structures:
9GEF

PubMed Abstract:
Metal ions have important roles in supporting the catalytic activity of DNA-regulating enzymes such as topoisomerases (topos). Bacterial type II topos, gyrases and topo IV, are primary drug targets for fluoroquinolones, a class of clinically relevant antibacterials requiring metal ions for efficient drug binding. While the presence of metal ions in topos has been elucidated in biochemical studies, accurate location and assignment of metal ions in structural studies have historically posed significant challenges. Recent advances in X-ray crystallography address these limitations by extending the experimental capabilities into the long-wavelength range, exploiting the anomalous contrast from light elements of biological relevance. This breakthrough enables us to confirm experimentally the locations of Mg ²⁺ in the fluoroquinolone-stabilized Streptococcus pneumoniae topo IV complex. Moreover, we can unambiguously identify the presence of K ⁺ and Cl ^- ions in the complex with one pair of K ⁺ ions functioning as an additional intersubunit bridge. Overall, our data extend current knowledge on the functional and structural roles of metal ions in type II topos.

Organizational Affiliation

Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom.

Macromolecule Content

Total Structure Weight: 176.7 kDa
Atom Count: 12,454
Modeled Residue Count: 1,482
Deposited Residue Count: 1,482
Unique protein chains: 1
Unique nucleic acid chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA TOPOISOMERASE (ATP-HYDROLYZING),DNA TOPOISOMERASE 4	A, B	723	Streptococcus pneumoniae	Mutation(s): 0 Gene Names: AMCSP13_000989, PARC, SP_0855 EC: 5.6.2.2
UniProt
Find proteins for P72525 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore P72525 Go to UniProtKB: P72525
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P72525
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(TPGPTPGPGPAP*T)-3')	C [auth E]	7	Escherichia coli
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(PGPGPTPTPAPTPCPCPAPCP*A)-3')	D [auth F]	11	Escherichia coli
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(GPTPAPAPTPAP*C)-3')	E [auth G]	7	Escherichia coli
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (5'-D(PAPAPCPCPGPTPAPTPTPAP*C)-3')	F [auth H]	11	Escherichia coli
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TE9 Query on TE9 Download Ideal Coordinates CCD File SDF format, chain Y [auth F] SDF format, chain Z [auth H] MOL2 format, chain Y [auth F] MOL2 format, chain Z [auth H] mmCIF format, chain Y [auth F] mmCIF format, chain Z [auth H]	Y [auth F], Z [auth H]	delafloxacin C₁₈ H₁₂ Cl F₃ N₄ O₄ DYDCPNMLZGFQTM-UHFFFAOYSA-N		Interactions Focus chain Y [auth F] Focus chain Z [auth H] Interactions & Density Focus chain Y [auth F] Focus chain Z [auth H]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain G [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain G [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain G [auth A]	G [auth A], N [auth A], O [auth B], P [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain G [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain G [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain X [auth B] MOL2 format, chain X [auth B] mmCIF format, chain X [auth B]	X [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain X [auth B] Interactions & Density Focus chain X [auth B]
K Query on K Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain R [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain R [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain R [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B]	J [auth A] K [auth A] L [auth A] R [auth B] S [auth B] J [auth A], K [auth A], L [auth A], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain W [auth B] MOL2 format, chain M [auth A] MOL2 format, chain W [auth B] mmCIF format, chain M [auth A] mmCIF format, chain W [auth B]	M [auth A], W [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain M [auth A] Focus chain W [auth B] Interactions & Density Focus chain M [auth A] Focus chain W [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth H] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain Q [auth B] MOL2 format, chain AA [auth H] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain AA [auth H] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain Q [auth B]	AA [auth H], H [auth A], I [auth A], Q [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth H] Focus chain H [auth A] Focus chain I [auth A] Focus chain Q [auth B] Interactions & Density Focus chain AA [auth H] Focus chain H [auth A] Focus chain I [auth A] Focus chain Q [auth B]