Entry: Q59533 Genes: gyrB ML0005 Length: 678 aa

DNA gyrase subunit B

GYRB_MYCLE • Mycobacterium leprae (strain TN)
Navigate Overview Model Scores RCSB 1D Mol* Pockets B-Cell Epitopes Function and interactions Ontology and localisation Sequence features and PTMs Evidence and cross-references

Summary

Download FASTA UniProt: Q59533 ML Locus: ML0005
Entry Q59533
Reviewed reviewed
Entry Name GYRB_MYCLE
Gene Names gyrB ML0005
ML locus tag ML0005
Organism Mycobacterium leprae (strain TN)
Length 678 aa
Mass 74674 Da
Annotation 5.0
Annotation Summary

Evidence and cross-references

PubMed ID 8969512; 11234002; 17325221
DOI ID 10.1099/13500872-142-11-3147; 10.1038/35059006; 10.1128/aac.01282-06
STRING 272631.gene:17573814;
KEGG mle:ML0005;
eggNOG COG0187;
OrthoDB 9802808at2;
InterPro IPR002288;IPR011557;IPR036890;IPR003594;IPR020568;IPR014721;IPR001241;IPR013760;IPR000565;IPR013759;IPR013506;IPR018522;IPR006171;

Oligomer Models

Best Boltz2 oligomer and local AlphaFold‑3 homooligomer structure models matched to ML0005, with the same model switching, Mol*, Nightingale, pLDDT, PAE, and download functionality as monomers.
Count: 1
Assembly Method Template / Source Overall Rank Download
hetero_4mer Boltz2 — — Download Model

Ligands

Curated ligands imported from the selected oligomer template/YAML rows. The displayed ligand code is the original template CCD code; predicted-model placeholders such as LIG1/LIG2 are not shown. Click a ligand code to focus the ligand in Mol*.
Ligands: 0
Ligand Code Ligand Name PubChem ID
No curated ligand rows were found for this oligomer in the database.

Monomer Models

Monomer structure models for ML0005, retaining all existing model selection, Mol*, Nightingale, pLDDT, PAE, and download functionality.
Count: 4
Assembly Method Model Overall Rank Download
Monomer Boltz2 0 0.776911 Download Model
Monomer AlphaFold‑3 4 0.832956 Download Model
Monomer Boltz 0 0.777813 Download Model
Monomer CHAI 3 0.153458 Download Model

Sequence & Feature Viewer

Residue-level feature tracks for the loaded model — pLDDT confidence colouring, mapped annotations, and interactive PAE selection ranges. Drag a region on the heatmap to highlight it here and in Mol*.
RCSB 1D
Sequence viewer will initialise once a structure model is loaded.
Mol* — ML0005

Mol* Structure Viewer

Local mmCIF model display for ML0005 with Mol* controls hidden.
Default: hetero_4mer • Boltz2
Preparing hetero_4mer • Boltz2 model 0 for ML0005…
Residue focus: none
Heterooligomer ML IDs / chain selection

PAE Map Panel

Predicted aligned error heatmap for the currently loaded model, when pairwise confidence data are available in the local mmCIF.
PAE • Waiting for Model
PAE Heatmap
Loading pairwise confidence data for the selected model…
Scored residue
Aligned residue
Hover over the heatmap to inspect residue-pair PAE values.
Click a cell or drag across the heatmap to select residue blocks and mirror them in the sequence viewer.

B-cell Epitope Propensity

Per-residue conformational B-cell epitope predictions from DiscoTope-3.0.
Epitope · Loading
Low
Epitope
Residue number Residue type DiscoTope-3.0 score Focus
Loading epitope predictions…
Click a residue to focus it in Mol*.
Annotation Summary

Function and interactions

EC number 5.6.2.2
Catalytic activity CATALYTIC ACTIVITY: Reaction=ATP-dependent breakage, passage and rejoining of double-stranded DNA.; EC=5.6.2.2; Evidence={ECO:0000255|HAMAP-Rule:MF_01898, ECO:0000305|PubMed:17325221};
Binding site BINDING 462; /ligand="Mg(2+)"; /ligand_id="ChEBI:CHEBI:18420"; /ligand_label="1"; /ligand_note="catalytic"; /evidence="ECO:0000255|HAMAP-Rule:MF_01898"; BINDING 535; /ligand="Mg(2+)"; /ligand_id="ChEBI:CHEBI:18420"; /ligand_label="1"; /ligand_note="catalytic"; /evidence="ECO:0000255|HAMAP-Rule:MF_01898"; BINDING 535; /ligand="Mg(2+)"; /ligand_id="ChEBI:CHEBI:18420"; /ligand_label="2"; /evidence="ECO:0000255|HAMAP-Rule:MF_01898"; BINDING 537; /ligand="Mg(2+)"; /ligand_id="ChEBI:CHEBI:18420"; /ligand_label="2"; /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
Cofactor COFACTOR: Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000255|HAMAP-Rule:MF_01898}; Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000255|HAMAP-Rule:MF_01898}; Name=Ca(2+); Xref=ChEBI:CHEBI:29108; Evidence={ECO:0000255|HAMAP-Rule:MF_01898}; Note=Binds two Mg(2+) per subunit. The magnesium ions form salt bridges with both the protein and the DNA. Can also accept other divalent metal cations, such as Mn(2+) or Ca(2+). {ECO:0000255|HAMAP-Rule:MF_01898};
Site SITE 487; /note="Interaction with DNA"; /evidence="ECO:0000255|HAMAP-Rule:MF_01898"; SITE 490; /note="Interaction with DNA"; /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
Subunit structure SUBUNIT: Heterotetramer, composed of two GyrA and two GyrB chains (PubMed:17325221). In the heterotetramer, GyrA contains the active site tyrosine that forms a transient covalent intermediate with the DNA, while GyrB binds cofactors catalyzes ATP hydrolysis. {ECO:0000255|HAMAP-Rule:MF_01898, ECO:0000269|PubMed:17325221}.
Annotation Summary

Ontology and localisation

Gene Ontology (biological process) DNA topological change [GO:0006265]; DNA-templated DNA replication [GO:0006261]
Gene Ontology (cellular component) chromosome [GO:0005694]; cytoplasm [GO:0005737]
Gene Ontology (GO) chromosome [GO:0005694]; cytoplasm [GO:0005737]; ATP binding [GO:0005524]; DNA binding [GO:0003677]; DNA negative supercoiling activity [GO:0034335]; metal ion binding [GO:0046872]; DNA topological change [GO:0006265]; DNA-templated DNA replication [GO:0006261]
Gene Ontology (molecular function) ATP binding [GO:0005524]; DNA binding [GO:0003677]; DNA negative supercoiling activity [GO:0034335]; metal ion binding [GO:0046872]
Gene Ontology IDs GO:0003677; GO:0005524; GO:0005694; GO:0005737; GO:0006261; GO:0006265; GO:0034335; GO:0046872
Subcellular location [CC] SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01898}.
Protein families Type II topoisomerase GyrB family
Sequence similarities SIMILARITY: Belongs to the type II topoisomerase GyrB family. {ECO:0000255|HAMAP-Rule:MF_01898}.
Annotation Summary

Sequence features and PTMs

Chain CHAIN 1..678; /note="DNA gyrase subunit B"; /id="PRO_0000145321"
Domain [FT] DOMAIN 456..570; /note="Toprim"; /evidence="ECO:0000255|HAMAP-Rule:MF_01898"