8B4H | pdb_00008b4h

IstA transposase cleaved donor complex

PDB DOI: https://doi.org/10.2210/pdb8B4H/pdb
EM Map EMD-15848: EMDB EMDataResource
NAKB: 8B4H

Classification: DNA BINDING PROTEIN
Organism(s): Geobacillus stearothermophilus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-09-20 Released: 2023-05-03
Deposition Author(s): Spinola-Amilibia, M., de la Gandara, A., Araujo-Bazan, L., Berger, J.M., Arias-Palomo, E.
Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.35 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

IS21 family transposase cleaved donor complex traps two right-handed superhelical crossings.

Spinola-Amilibia, M., Araujo-Bazan, L., de la Gandara, A., Berger, J.M., Arias-Palomo, E.

(2023) Nat Commun 14: 2335-2335

PubMed: 37087515 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-023-38071-x
Primary Citation Related Structures:
8B4H

PubMed Abstract:
Transposases are ubiquitous enzymes that catalyze DNA rearrangement events with broad impacts on gene expression, genome evolution, and the spread of drug-resistance in bacteria. Here, we use biochemical and structural approaches to define the molecular determinants by which IstA, a transposase present in the widespread IS21 family of mobile elements, catalyzes efficient DNA transposition. Solution studies show that IstA engages the transposon terminal sequences to form a high-molecular weight complex and promote DNA integration. A 3.4 Å resolution structure of the transposase bound to transposon ends corroborates our biochemical findings and reveals that IstA self-assembles into a highly intertwined tetramer that synapses two supercoiled terminal inverted repeats. The three-dimensional organization of the IstA•DNA cleaved donor complex reveals remarkable similarities with retroviral integrases and classic transposase systems, such as Tn7 and bacteriophage Mu, and provides insights into IS21 transposition.

Organizational Affiliation

Department of Structural & Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Madrid, 28040, Spain.

Macromolecule Content

Total Structure Weight: 261.63 kDa
Atom Count: 16,568
Modeled Residue Count: 1,664
Deposited Residue Count: 1,854
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative transposase for insertion sequence element IS5376	A, B, C, D	406	Geobacillus stearothermophilus	Mutation(s): 0
UniProt
Find proteins for Q45618 (Geobacillus stearothermophilus) Explore Q45618 Go to UniProtKB: Q45618
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q45618
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 2
DNA (57-MER) / right IS21 transposon end (insertion sequence IS5376)	E, G	60	Geobacillus stearothermophilus
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 3
DNA (55-MER) / right IS21 transposon end (insertion sequence IS5376)	F, H	55	Geobacillus stearothermophilus
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth A]	I [auth A], J [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.35 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.1
MODEL REFINEMENT	PHENIX	1.19

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-05-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Spanish Ministry of Science, Innovation, and Universities	Spain	PID2020-120275GB-I00
Spanish Ministry of Science, Innovation, and Universities	Spain	BFU2017-89143-P