- EMDB-14570: E.coli gyrase holocomplex with 217 bp DNA and albicidin -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: EMDB / ID: EMD-14570
Title
E.coli gyrase holocomplex with 217 bp DNA and albicidin
Map data
Gyrase-Mu217-albicidin
Sample
Complex: Escherichia coli gyrase holocomplex with 217 bp phage Mu SGS DNA and albicidin stabilised by ADPNP
Complex: Escherichia coli gyrase holocomplex
Protein or peptide: DNA gyrase subunit A
Protein or peptide: DNA gyrase subunit B
Complex: 217 bp phage Mu SGS DNA
DNA: DNA (5'-D(P*AP*AP*AP*TP*CP*TP*GP*TP*GP*CP*GP*GP*GP*T)-3')
DNA: DNA (5'-D(P*AP*GP*AP*AP*TP*CP*AP*GP*GP*CP*AP*TP*AP*A)-3')
DNA: DNA (5'-D(*AP*AP*TP*CP*AP*CP*CP*CP*GP*CP*AP*CP*AP*GP*AP*TP*TP*T)-3')
DNA: DNA (5'-D(*GP*AP*TP*TP*TP*TP*AP*TP*GP*CP*CP*TP*GP*AP*TP*TP*CP*T)-3')
Ligand: MAGNESIUM ION
Ligand: albicidin
Ligand: water
Keywords
type II topoisomerase / antibiotic / albicidin / DNA gyrase / ISOMERASE
Function / homology
Function and homology information
negative regulation of DNA-templated DNA replication / DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / ATP-dependent activity, acting on DNA / DNA-templated DNA replication / chromosome / response to xenobiotic stimulus ...negative regulation of DNA-templated DNA replication / DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / ATP-dependent activity, acting on DNA / DNA-templated DNA replication / chromosome / response to xenobiotic stimulus / response to antibiotic / DNA-templated transcription / DNA binding / ATP binding / membrane / identical protein binding / metal ion binding / cytoplasm / cytosol Similarity search - Function
: / GyrB, hook / DNA gyrase subunit B insert domain / DNA gyrase B subunit insert domain / DNA gyrase, subunit A / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase C-terminal domain, beta-propeller / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA gyrase subunit B, TOPRIM domain ...: / GyrB, hook / DNA gyrase subunit B insert domain / DNA gyrase B subunit insert domain / DNA gyrase, subunit A / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase C-terminal domain, beta-propeller / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site / DNA topoisomerase II signature. / TopoisomeraseII / DNA topoisomerase, type IIA, subunit B, C-terminal / Toprim domain / DNA topoisomerase, type IIA-like domain superfamily / Toprim domain profile. / TOPRIM domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold Similarity search - Domain/homology
Journal: Nat Catal / Year: 2023 Title: Molecular mechanism of topoisomerase poisoning by the peptide antibiotic albicidin. Authors: Elizabeth Michalczyk / Kay Hommernick / Iraj Behroz / Marcel Kulike / Zuzanna Pakosz-Stępień / Lukasz Mazurek / Maria Seidel / Maria Kunert / Karine Santos / Holger von Moeller / Bernhard ...Authors: Elizabeth Michalczyk / Kay Hommernick / Iraj Behroz / Marcel Kulike / Zuzanna Pakosz-Stępień / Lukasz Mazurek / Maria Seidel / Maria Kunert / Karine Santos / Holger von Moeller / Bernhard Loll / John B Weston / Andi Mainz / Jonathan G Heddle / Roderich D Süssmuth / Dmitry Ghilarov / Abstract: The peptide antibiotic albicidin is a DNA topoisomerase inhibitor with low-nanomolar bactericidal activity towards fluoroquinolone-resistant Gram-negative pathogens. However, its mode of action is ...The peptide antibiotic albicidin is a DNA topoisomerase inhibitor with low-nanomolar bactericidal activity towards fluoroquinolone-resistant Gram-negative pathogens. However, its mode of action is poorly understood. We determined a 2.6 Å resolution cryoelectron microscopy structure of a ternary complex between topoisomerase DNA gyrase, a 217 bp double-stranded DNA fragment and albicidin. Albicidin employs a dual binding mechanism where one end of the molecule obstructs the crucial gyrase dimer interface, while the other intercalates between the fragments of cleaved DNA substrate. Thus, albicidin efficiently locks DNA gyrase, preventing it from religating DNA and completing its catalytic cycle. Two additional structures of this trapped state were determined using synthetic albicidin analogues that demonstrate improved solubility, and activity against a range of gyrase variants and topoisomerase IV. The extraordinary promiscuity of the DNA-intercalating region of albicidins and their excellent performance against fluoroquinolone-resistant bacteria holds great promise for the development of last-resort antibiotics.
Entire : Escherichia coli gyrase holocomplex with 217 bp phage Mu SGS DNA ...
Entire
Name: Escherichia coli gyrase holocomplex with 217 bp phage Mu SGS DNA and albicidin stabilised by ADPNP
Components
Complex: Escherichia coli gyrase holocomplex with 217 bp phage Mu SGS DNA and albicidin stabilised by ADPNP
Complex: Escherichia coli gyrase holocomplex
Protein or peptide: DNA gyrase subunit A
Protein or peptide: DNA gyrase subunit B
Complex: 217 bp phage Mu SGS DNA
DNA: DNA (5'-D(P*AP*AP*AP*TP*CP*TP*GP*TP*GP*CP*GP*GP*GP*T)-3')
DNA: DNA (5'-D(P*AP*GP*AP*AP*TP*CP*AP*GP*GP*CP*AP*TP*AP*A)-3')
DNA: DNA (5'-D(*AP*AP*TP*CP*AP*CP*CP*CP*GP*CP*AP*CP*AP*GP*AP*TP*TP*T)-3')
DNA: DNA (5'-D(*GP*AP*TP*TP*TP*TP*AP*TP*GP*CP*CP*TP*GP*AP*TP*TP*CP*T)-3')
Ligand: MAGNESIUM ION
Ligand: albicidin
Ligand: water
+
Supramolecule #1: Escherichia coli gyrase holocomplex with 217 bp phage Mu SGS DNA ...
Supramolecule
Name: Escherichia coli gyrase holocomplex with 217 bp phage Mu SGS DNA and albicidin stabilised by ADPNP type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Organism: Escherichia coli str. K-12 substr. MG1655 (bacteria)
+
Supramolecule #3: 217 bp phage Mu SGS DNA
Supramolecule
Name: 217 bp phage Mu SGS DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#6
Source (natural)
Organism: Escherichia phage Mu (virus)
+
Macromolecule #1: DNA gyrase subunit A
Macromolecule
Name: DNA gyrase subunit A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA topoisomerase (ATP-hydrolysing)
Source (natural)
Organism: Escherichia coli str. K-12 substr. MG1655 (bacteria) Strain: K12
Name: DNA gyrase subunit B / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA topoisomerase (ATP-hydrolysing)
Source (natural)
Organism: Escherichia coli str. K-12 substr. MG1655 (bacteria) Strain: K12
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi