HARP Hansen's Disease Antimicrobial Resistance Profiles

Ofloxacin Structural impacts of mutations in DNA gyrase (GYR) of Mycobacterium leprae

GYR: DNA gyrase (GYR) is an essential enzyme in mycobacteria that catalyses the ATP-dependent transient cleavage and negative supercoiling of closed circular DNA. The heterotetrameric protein (GyrA2GyrB2) has four chains (A, B, C and D), encoded by gyrA (ML0006) and gyrB (ML0005) in Mycobacterium leprae. Mutations in the GyrA subunit are associated with resistance to ofloxacin, a second-line bactericidal drug for leprosy. HARP contains only missense mutations, represented as amino acid substitutions at each residue position in every chain of the GYR structure. All 19 possible substitutions at each position are analysed with a range of computational tools. Submit a single mutation or a residue position below. You can also upload AB1 chromatogram files or FASTA sequences and view the BLASTX results.

Note: The GYR model of Mycobacterium leprae was built with PDB ID 5BS8 as the template. The intein region of chain A (residue positions 131–550) was removed during modelling, and residue numbering follows the template alignment.

Query Mutations:

Note: Query mutations and residue positions here. See the Help page for more information.

Single Mutation:

Note: Submit a single amino acid substitution identified by translating your sequencing reads.

Drug Target:
Chain:
Mutation:

For example, A91V. Select Help for more information.

Systematic Mutations:

Note: Submit a residue position from the modelled region. Select Help for more information.

Drug Target:
Chain:
Residue Position:

For example, 91. Select Help for more information.

Upload AB1 File:

Note: Upload AB1 files from Sanger or next-generation sequencing.

Upload AB1 File

Note: Once uploaded, the AB1 file is processed automatically. Select Processed AB1 File above to see the results.

Upload FASTA File:

Note: Upload a DNA FASTA sequence. It is translated and searched with BLASTX against the Lep-AMR reference amplicons for rpoB, folP1 and gyrA.

Upload FASTA File

...or paste a DNA sequence (FASTA or plain bases):

Note: Every amino acid difference between the translated query and the reference amplicon is reported as a HARP substitution (e.g. A91V). Press "Mutation Results" to list them and open any mutation on HARP.

3D Visualisation of the Ofloxacin-Binding Site in GYR and the Chemical Structure of Ofloxacin

Note: Hold the left mouse button and move over the viewers to see the structures in 3D. Scroll to zoom.

Interactive 3D Viewer: Interatomic interactions of ofloxacin with the surrounding residue environment in chain 'B' of wild-type GYR. Hydrogen bonds (blue), weak hydrogen bonds (light blue) and metal interactions (purple) are shown.

Ofloxacin in 3D

Structure: PubChem 3D conformer.

Note: Hold the left mouse button and move to see the structure of Ofloxacin in 3D. Scroll to zoom.

Predict the pharmacokinetic properties of Ofloxacin.
Protein Feature Viewer:
Note: The protein feature viewer shows sequence-based annotations of the drug target. Adjust the scale sliders at the top of the viewer to see the sequence. See the Help page for more information. Only GyrA (chain A) is loaded, for quick access to the quinolone resistance-determining region (QRDR) of the GYR Structure. As the intein region from residue numbers 131-550 has been removed in the model, the sequence numbers correspond with the structure from 16-130 and 550-921 (eg: residue position 131 in the model corresponds to sequence number 551 and so on).