dnaN Family assigned · medium auto-curated
H37Rv Rv0002 · MTBC0 mtbc0_000002 ·
402 aa · 2052–3260 (+) ·
RefSeq NP_214516.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | DNA polymerase III subunit beta |
|---|---|
| MTBC0 PGAP re-annotation | DNA polymerase III subunit beta |
| Revised (this work) | DNA polymerase III subunit beta. Pfam: DNA_pol3_beta (PF00712.25), DNA_pol3_beta_2 (PF02767.22), DNA_pol3_beta_3 (PF02768.21). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WNU1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Beta sliding clamp |
| Curated function | Confers DNA tethering and processivity to DNA polymerases and other proteins. Acts as a clamp, forming a ring around DNA (a reaction catalyzed by the clamp-loading complex) which diffuses in an ATP-independent manner freely and bidirectionally along dsDNA. Initially characterized for its ability to contact the catalytic subunit of DNA polymerase III (Pol III), a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria; Pol III exhibits 3'-5' exonuclease proofreading activity. The beta chain is required for initiation of replication as well as for processivity of. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | dnaN |
| eggNOG description | Confers DNA tethering and processivity to DNA polymerases and other proteins. Acts as a clamp, forming a ring around DNA (a reaction catalyzed by the clamp-loading complex) which diffuses in an ATP-independent manner freely and bidirectionally along dsDNA. Initially characterized for its ability to contact the catalytic subunit of DNA polymerase III (Pol III), a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria |
| Orthologous group | COG0592 |
| EC number |
EC 2.7.7.7
|
| KEGG orthology |
K02338
|
| KEGG pathways |
map00230, map00240, map01100, map03030, map03430, map03440
|
| KEGG modules |
M00260
|
| Gene Ontology (7) |
GO:0005575, GO:0005576, GO:0005618, GO:0005623, GO:0030312, GO:0044464, GO:0071944
|
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 | 0.365 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 synonymous, 7 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 |
|---|---|---|---|---|
DNA_pol3_beta | PF00712.25 | 3.4e-39 | 14–130 | DNA polymerase III beta subunit, N-terminal domain |
DNA_pol3_beta_2 | PF02767.22 | 3.6e-32 | 139–260 | DNA polymerase III beta subunit, central domain |
DNA_pol3_beta_3 | PF02768.21 | 1.4e-34 | 262–371 | DNA polymerase III beta subunit, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3644c (DNA polymerase), high confidence from genomic context alone (score 987 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1629 polA |
DNA polymerase I | 997 | 995 | coexpression:414 experimental:970 database:630 textmining:508 |
Rv1547 dnaE1 |
DNA polymerase III subunit alpha | 993 | 988 | experimental:858 database:900 textmining:490 |
Rv2413c hyp |
hypothetical protein | 989 | 988 | experimental:829 database:900 |
Rv3644c |
DNA polymerase | 988 | 987 ctx | cooccurence:454 experimental:773 database:900 |
Rv3721c dnaZX |
DNA polymerase III subunit gamma/tau | 997 | 980 | experimental:773 database:900 textmining:881 |
Rv0001 dnaA |
chromosomal replication initiator protein DnaA | 998 | 966 ctx | cooccurence:520 coexpression:711 experimental:737 textmining:965 |
Rv2191 hyp |
hypothetical protein | 967 | 954 | experimental:481 database:900 |
Rv3711c dnaQ |
DNA polymerase III subunit epsilon | 979 | 950 | experimental:481 database:900 textmining:600 |
Rv0003 recF |
DNA replication/repair protein RecF | 992 | 945 ctx | neighborhood:855 coexpression:481 textmining:863 |
Rv2090 |
5'-3' exonuclease | 948 | 944 | experimental:772 database:630 |
Rv2101 helZ |
helicase HelZ | 920 | 912 | experimental:769 database:614 |
Rv1537 dinX |
DNA polymerase IV | 941 | 907 | experimental:766 database:612 |
Rv3056 dinP |
DNA polymerase IV 2 | 919 | 907 | experimental:766 database:612 |
Rv3731 ligC |
DNA ligase C | 892 | 886 | experimental:629 database:609 |
Rv0938 ligD |
multifunctional non-homologous end joining DNA repair protein/ATP dependent DNA ligase LigD | 895 | 885 | experimental:629 database:609 |
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 polymerase III subunit beta
- MTBC0 PGAP product: DNA polymerase III subunit beta
- Pfam (hmmscan --cut_ga): DNA_pol3_beta PF00712.25 (E=3e-39), DNA_pol3_beta_2 PF02767.22 (E=4e-32), DNA_pol3_beta_3 PF02768.21 (E=1e-34)
- (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_214516.1)
- Domains: Pfam-A via hmmscan --cut_ga — DNA_pol3_beta (PF00712.25), DNA_pol3_beta_2 (PF02767.22), DNA_pol3_beta_3 (PF02768.21)
- 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
COG0592 - Curated reference: UniProt P9WNU1 (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
Rv3644c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000002|Rv0002|dnaN MDAATTRVGLTDLTFRLLRESFADAVSWVAKNLPARPAVPVLSGVLLTGSDNGLTISGFDYEVSAEAQVGAEIVSPGSVLVSGRLLSDITRALPNKPVDVHVEGNRVALTCGNARFSLPTMPVEDYPTLPTLPEETGLLPAELFAEAISQVAIAAGRDDTLPMLTGIRVEILGETVVLAATDRFRLAVRELKWSASSPDIEAAVLVPAKTLAEAAKAGIGGSDVRLSLGTGPGVGKDGLLGISGNGKRSTTRLLDAEFPKFRQLLPTEHTAVATMDVAELIEAIKLVALVADRGAQVRMEFADGSVRLSAGADDVGRAEEDLVVDYAGEPLTIAFNPTYLTDGLSSLRSERVSFGFTTAGKPALLRPVSGDDRPVAGLNGNGPFPAVSTDYVYLLMPVRLPG