gyrB Family assigned · medium auto-curated
H37Rv Rv0005 · MTBC0 mtbc0_000005 ·
675 aa · 5240–7267 (+) ·
RefSeq NP_214519.2
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | DNA gyrase subunit B |
|---|---|
| MTBC0 PGAP re-annotation | DNA topoisomerase (ATP-hydrolyzing) subunit B |
| Revised (this work) | DNA topoisomerase (ATP-hydrolyzing) subunit B. Pfam: HATPase_c (PF02518.32), DNA_gyraseB (PF00204.32), Toprim (PF01751.29), DNA_gyraseB_C (PF00986.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WG45
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | DNA gyrase subunit B |
| EC (curated) |
EC 5.6.2.2
|
| Curated function | A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner to maintain chromosomes in an underwound state, while in the absence of ATP it relaxes supercoiled dsDNA. Also catalyzes the interconversion of other topological isomers of dsDNA rings, including catenanes. Gyrase from M.tuberculosis has higher decatenation than supercoiling activity compared to E.coli; as M.tuberculosis only has 1 type II topoisomerase, gyrase has to fulfill the decatenation function of topoisomerase IV as well. At comparable concentrations M.tuberculosis gyr. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | gyrB |
| eggNOG description | A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner to modulate DNA topology and maintain chromosomes in an underwound state. Negative supercoiling favors strand separation, and DNA replication, transcription, recombination and repair, all of which involve strand separation. Also able to catalyze the interconversion of other topological isomers of dsDNA rings, including catenanes and knotted rings. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP-dependent manner |
| Orthologous group | COG0187 |
| EC number |
EC 5.99.1.3
|
| KEGG orthology |
K02470
|
| Gene Ontology (69) |
GO:0000166, GO:0000287, GO:0003674, GO:0003824, GO:0003916, GO:0003918, GO:0005488, GO:0005524, GO:0005575, GO:0005618, GO:0005623, GO:0005886 +57 more
|
Orthology-based transfer (eggNOG 5.0.2, diamond). EC/KO/GO/CAZy are computed annotations, not manual curation; cross-check against the primary literature before treating a specific reaction as established.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | 0.401 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 11 synonymous, 14 missense, 0 nonsense, 0 frameshift |
pN/pS from segregating SNPs (singletons removed) normalised by possible sites. Low pN/pS = purifying selection (a strong signal that a "hypothetical" is a real, constrained gene). A high pN/pS is ambiguous: relaxed constraint or positive selection (drug resistance, antigenic variation) inflate it; e.g. rpoB/katG/pncA score high here for resistance, not loss of function. A clonal disruption (one allele over a clade) suggests lineage pseudogenisation; a convergent one (many independent alleles) is typical of resistance loss-of-function.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
HATPase_c | PF02518.32 | 3.2e-15 | 39–176 | Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase |
DNA_gyraseB | PF00204.32 | 1.7e-63 | 256–425 | DNA gyrase B |
Toprim | PF01751.29 | 5.3e-17 | 454–565 | Toprim domain |
DNA_gyraseB_C | PF00986.27 | 3.1e-26 | 606–663 | DNA gyrase B subunit, carboxyl terminus |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: gyrA (DNA gyrase subunit A), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0006 gyrA |
DNA gyrase subunit A | 999 | 1000 ctx | neighborhood:830 cooccurence:773 coexpression:942 experimental:981 textmining:989 |
Rv3361c mfpA hyp |
hypothetical protein | 997 | 997 | experimental:997 |
Rv0730 |
GCN5-like N-acetyltransferase | 956 | 951 | coexpression:726 experimental:818 |
Rv0003 recF |
DNA replication/repair protein RecF | 975 | 900 ctx | neighborhood:727 coexpression:650 textmining:769 |
Rv0002 dnaN |
DNA polymerase III subunit beta | 952 | 854 ctx | neighborhood:714 coexpression:446 textmining:685 |
Rv0004 hyp |
hypothetical protein | 797 | 785 ctx | neighborhood:727 |
Rv0007 |
membrane protein | 772 | 759 ctx | neighborhood:743 |
Rv2373c dnaJ2 |
chaperone protein DnaJ | 836 | 686 ctx | cooccurence:596 textmining:500 |
Rv2793c truB |
tRNA pseudouridine synthase B | 689 | 675 | experimental:412 |
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 820 | 658 ctx | neighborhood:473 textmining:496 |
Rv3769 hyp |
hypothetical protein | 652 | 615 | |
Rv2731 hyp |
hypothetical protein | 652 | 615 | |
Rv2922c smc |
chromosome partition protein Smc | 652 | 615 | |
Rv2614c thrS |
threonine--tRNA ligase | 655 | 596 ctx | cooccurence:567 |
Rv0352 dnaJ1 |
chaperone protein DnaJ | 793 | 589 ctx | cooccurence:472 textmining:519 |
STRING combines evidence channels (neighborhood, fusion, cooccurrence, coexpression, experimental, database, text-mining) into a 0–1000 score. The ctx badge marks edges carried by the genomic-context channels (conserved neighborhood, fusion, phylogenetic co-occurrence), which are independent of orthology and structure and the strongest signal for an unknown gene. The no text-mining column recomputes the score from data alone, so a link that does not depend on the literature is visible. Association is a function hypothesis, not proof: corroborate with the operon context and the primary literature before assigning a function.
Evidence
- Legacy H37Rv annotation: DNA gyrase subunit B
- MTBC0 PGAP product: DNA topoisomerase (ATP-hydrolyzing) subunit B
- Pfam (hmmscan --cut_ga): HATPase_c PF02518.32 (E=3e-15), DNA_gyraseB PF00204.32 (E=2e-63), Toprim PF01751.29 (E=5e-17), DNA_gyraseB_C PF00986.27 (E=3e-26)
- (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)
Sources
- Ancestral sequence & coordinates: Harrison LB et al. (2024), An imputed ancestral reference genome for the MTBC, doi:10.1101/2023.09.07.556366
- Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq NP_214519.2)
- Domains: Pfam-A via hmmscan --cut_ga — HATPase_c (PF02518.32), DNA_gyraseB (PF00204.32), Toprim (PF01751.29), DNA_gyraseB_C (PF00986.27)
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021,
doi:10.1093/molbev/msab293), eggNOG 5.0 DB
(Huerta-Cepas et al. 2019) — OG
COG0187 - Curated reference: UniProt P9WG45 (SwissProt, reviewed; Evidence at protein level)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
174 functional partner(s); context anchor
gyrA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000005|Rv0005|gyrB MAAQKKKAQDEYGAASITILEGLEAVRKRPGMYIGSTGERGLHHLIWEVVDNAVDEAMAGYATTVNVVLLEDGGVEVADDGRGIPVATHASGIPTVDVVMTQLHAGGKFDSDAYAISGGLHGVGVSVVNALSTRLEVEIKRDGYEWSQVYEKSEPLGLKQGAPTKKTGSTVRFWADPAVFETTEYDFETVARRLQEMAFLNKGLTINLTDERVTQDEVVDEVVSDVAEAPKSASERAAESTAPHKVKSRTFHYPGGLVDFVKHINRTKNAIHSSIVDFSGKGTGHEVEIAMQWNAGYSESVHTFANTINTHEGGTHEEGFRSALTSVVNKYAKDRKLLKDKDPNLTGDDIREGLAAVISVKVSEPQFEGQTKTKLGNTEVKSFVQKVCNEQLTHWFEANPTDAKVVVNKAVSSAQARIAARKARELVRRKSATDIGGLPGKLADCRSTDPRKSELYVVEGDSAGGSAKSGRDSMFQAILPLRGKIINVEKARIDRVLKNTEVQAIITALGTGIHDEFDIGKLRYHKIVLMADADVDGQHISTLLLTLLFRFMRPLIENGHVFLAQPPLYKLKWQRSDPEFAYSDRERDGLLEAGLKAGKKINKEDGIQRYKGLGEMDAKELWETTMDPSVRVLRQVTLDDAAAADELFSILMGEDVDARRSFITRNAKDVRFLDV