FEATURED MACHINE 08 / 12

DNA gyrase

Controls DNA supercoiling and relieves twisting stress.

LIBRARY BASIS · BACTERIAL ACCOUNT

The question behind this machine

The library highlights a distinctive coordination problem: opening DNA to permit strand passage while preserving the ability to reseal it. This bacterial account separates gyrase’s supercoiling role from the related chromosome-unlinking role commonly associated with topoisomerase IV.^L1

A controlled change in DNA topology

Bacterial gyrase couples DNA binding and wrapping to strand passage through a transient gate. Structural work on a Thermus thermophilus gyrase construct supports a role for the ATPase region in organizing a DNA crossover. A deletion changed the observed supercoiling behaviour, showing that the arrangement of modules affects the topological outcome.^P1

Subunits and coordinated gates

The native enzyme is an assembly of GyrA and GyrB components. The experimental fusion used for structural analysis must not be confused with an assertion that bacterial gyrase is naturally one chain. Its useful operation requires DNA capture, catalytic events and conformational changes to remain coordinated.^P1

Interfaces that can be perturbed

A drug-bound Staphylococcus aureus gyrase–DNA structure shows how an inhibitor can occupy a specific protein–DNA interface. Such experiments test molecular recognition and reveal why a bound complex can behave differently from a productive one. They support specificity without measuring a probability of historical origin.^P2

Failure and the appropriate inference

Failure to complete a DNA-handling cycle can have different consequences from reduced ATPase activity or altered supercoiling. Gyrase and topoisomerase IV should not be treated as interchangeable in every organism. A cautious origin comparison examines related topoisomerases, usable intermediate functions and the coordinated gate mechanism.^P1

Connected to the rest of the cell

This machine depends on resources and supporting systems, and its work supplies other cellular processes.

FUNCTIONAL ORGANIZATION · AUTHOR’S FRAMEWORK

Hallmarks of design

DNA gyrase illustrates the following organizational features in the supplied papers. These descriptions identify biological functions; interpreting their origin as design is the author’s comparative argument.^{H1, H2}

H19Topological control

Strand passage changes DNA topology rather than simply binding DNA.

H21Energy currency

ATP-dependent transitions coordinate DNA handling.

H15Molecular machines

DNA gates must open, pass strands and reseal in a compatible sequence.

Origin hurdles and abductive assessment · Assessment method · All 40 hallmarks. Biological evidence: the mechanism, accession records and scientific references on this page.

Origins and explanatory assessment

INFERENCE TO THE BEST EXPLANATION · PROVISIONAL ASSESSMENT

From origin hurdles to a cautious inference

What needs explaining. Explain coordinated DNA cleavage, strand passage and resealing with useful topology control, considering other topoisomerase mechanisms and lineage history.

Positive observations. Strand passage changes DNA topology rather than simply binding DNA. ATP-dependent transitions coordinate DNA handling.

Compare the explanations. The design proposal appeals to coordinated functional organization, not complexity alone. A natural account can include chemical affinities, self-assembly, co-option, duplication, common ancestry and selection where heredity exists; it need not draw a complete modern system in one random trial. Present operation, historical emergence and first-cell origins are separate questions.

Abductive conclusion. The coordinated features give the author a positive reason to consider design within the wider cellular architecture. For this local system alone, they do not establish that design is uniquely the best historical explanation. The conservative inference is that the system contributes to a cumulative design case, with its weight conditional on the comparative evidence and on how much plausible natural pathways explain.

What could change the assessment. Functional intermediates, sequence-family relationships and experimentally connected steps would strengthen a natural account in proportion to what they explain. Loss of a claimed dependency or discovery of functional alternatives would weaken the corresponding design argument. Gaps in the record do not supply a numerical likelihood for either explanation.

Method, assumptions and revision criteria^{H1, H2}. Evaluate alongside the origin discussion and scientific sources on this page.

Represented in the 912-protein inventory

2 selected protein entries. These entries identify selected components represented in the working inventory; they do not establish the complete composition or copy numbers of an assembled machine.

Gene / locus	Protein entry	Source record
gyrBaq_1026	Type 2 topoisomerase subunit B (EC 5.6.2.2) (DNA gyrase subunit B)	O67137 ↗
gyrAaq_980	Type 2 topoisomerase subunit A (EC 5.6.2.2) (DNA gyrase subunit A)	O67108 ↗

Follow the evidence

Each source-record link opens its UniProt entry. Gene links open the corresponding entry in this atlas’s working inventory.

Related scientific references ↗

Sources for the developed article

Library essays and topic discussions

L1. Otangelo Grasso, Topoisomerase II enzymes, amazing evidence of design. Machine or family-level discussion.

Primary scientific evidence

P1. Papillon et al. (2013), Structural insight into negative DNA supercoiling by DNA gyrase, a bacterial type 2A DNA topoisomerase.
P2. Bax et al. (2010), Type IIA topoisomerase inhibition by a new class of antibacterial agents.

Numbered protein records establish the selected inventory entries; these experimental examples establish the mechanisms identified above. Results from another bacterial species are not automatically Aquifex-specific measurements. Explore the library-to-atlas source guide →