Rv3577 Resolved · high
H37Rv Rv3577 · MTBC0 - ·
288 aa · 4019262–4020128 (+) ·
RefSeq NP_218094.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Binuclear metallo-beta-lactamase (MBL)-fold metallo-hydrolase of the UPF0173/UlaG family (InterPro IPR050114), substrate unassigned. RefSeq leaves it 'hypothetical protein'. The MBL HxHxDH motif (His74-His76-Asp78-His79) was confirmed as a genuine two-metal centre by co-folding the chain with two metal ions on AlphaFold Server (independent Zn and Fe jobs, top model iPTM 0.98): the ions bind a single bridged binuclear site 3.2-3.4 A apart, partitioned into a three-histidine metal (His74/His76/His137) and an aspartate-plus-two-histidine metal (Asp78/His79/His235), with identical geometry for Zn or Fe. HHpred top hits (>=99.8%) are UPF0173/UlaG metal-dependent hydrolases (UlaG 2wyl; COG2220). The fold-paralogue safeguard withholds the RNase Z (held by Rv2407) and glyoxalase II (Rv0634c/Rv2581c) labels: only the fold-level family is claimed. The six metal ligands are effectively invariant across ~250,724 genomes (most frequent non-synonymous ligand variant 0.0032%). A structural prediction, not a biochemical assay. |
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P96859
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | MBL fold metallo-hydrolase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Zn-dependent hydrolases of the beta-lactamase fold |
| Orthologous group | COG2220 |
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 | 0.551 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 3 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.57% of strains (821) · clonal |
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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 97.1 (very high). A confident model makes the fold comparison meaningful.
Best matches against the PDB, ranked by Foldseek homology probability. A high probability / TM-score suggests a shared fold; unless flagged sig (E < 0.01) these are fold hypotheses, not assignments.
| Target | Prob | TM | E-value | Description |
|---|---|---|---|---|
3bv6-assembly1_C |
1.00 | 0.61 | 9.6e-13 sig | 3bv6-assembly1_C Crystal structure of uncharacterized metallo protein from Vibrio cholerae with beta-lactamase like fold |
3x2y-assembly1_C |
1.00 | 0.71 | 2.9e-11 sig | 3x2y-assembly1_C Crystal structure of metallo-beta-lactamase H8A from Thermotoga maritima |
3x2z-assembly1_C |
1.00 | 0.72 | 6.7e-11 sig | 3x2z-assembly1_C Crystal structure of metallo-beta-lactamase in complex with nickel from Thermotoga maritima |
2wyl-assembly1_B |
1.00 | 0.64 | 3.5e-11 sig | 2wyl-assembly1_B Apo structure of a metallo-b-lactamase |
3x2x-assembly1_C |
1.00 | 0.70 | 5.6e-11 sig | 3x2x-assembly1_C Crystal structure of metallo-beta-lactamase H48A from Thermotoga maritima |
2wyl-assembly1_C |
1.00 | 0.61 | 1.3e-11 sig | 2wyl-assembly1_C Apo structure of a metallo-b-lactamase |
2wyl-assembly1_F |
1.00 | 0.63 | 2.3e-11 sig | 2wyl-assembly1_F Apo structure of a metallo-b-lactamase |
2wyl-assembly1_A |
1.00 | 0.63 | 2.7e-11 sig | 2wyl-assembly1_A Apo structure of a metallo-b-lactamase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: arsB2 (arsenic transport integral membrane protein ArsB), high confidence from genomic context alone (score 875 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3578 arsB2 |
arsenic transport integral membrane protein ArsB | 875 | 875 ctx | neighborhood:867 |
Rv3576 lppH |
lipoprotein LppH | 746 | 746 ctx | neighborhood:738 |
Rv3575c |
LacI family transcriptional regulator | 676 | 676 ctx | neighborhood:674 |
Rv1874 hyp |
hypothetical protein | 645 | 645 ctx | cooccurence:645 |
Rv0138 hyp |
hypothetical protein | 542 | 543 ctx | cooccurence:540 |
Rv2015c hyp |
hypothetical protein | 538 | 538 ctx | cooccurence:537 |
Rv2574 hyp |
hypothetical protein | 513 | 513 ctx | cooccurence:510 |
Rv0941c hyp |
hypothetical protein | 512 | 512 ctx | cooccurence:509 |
Rv1765c hyp |
hypothetical protein | 511 | 512 ctx | cooccurence:509 |
Rv3169 hyp |
hypothetical protein | 496 | 496 ctx | cooccurence:496 |
Rv1976c hyp |
hypothetical protein | 468 | 469 ctx | cooccurence:467 |
Rv1401 |
membrane protein | 457 | 457 ctx | cooccurence:454 |
Rv0272c hyp |
hypothetical protein | 440 | 440 ctx | cooccurence:436 |
Rv0293c hyp |
hypothetical protein | 425 | 425 ctx | cooccurence:418 |
Rv2721c hyp |
hypothetical protein | 412 | 412 ctx | cooccurence:409 |
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
- RefSeq: hypothetical protein; eggNOG COG2220 (Zn-dependent beta-lactamase-fold hydrolases)
- MBL motif HxHxDH (His74/His76/Asp78/His79); Foldseek 3bv6 / 2wyl (prob 1.00)
- AlphaFold Server metal co-folding (Zn + Fe): bridged binuclear site 3.2-3.4 A; ligands His74/His76/His137 + Asp78/His79/His235; iPTM 0.98
- HHpred >=99.8%: UPF0173/UlaG metal-dependent hydrolases (UlaG 2wyl, COG2220)
- Fold-paralogue safeguard: RNase Z (Rv2407) and glyoxalase II (Rv0634c/Rv2581c) labels withheld
- Six metal-ligand codons effectively invariant across ~250,724 genomes (most frequent NS 0.0032%)
- Curated against the companion dark-enzymes re-annotation (Guyeux 2026)
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_218094.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
COG2220 - Curated reference: UniProt P96859 (TrEMBL, unreviewed; Predicted)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Model confidence: ESMFold per-residue pLDDT (mean 97.1, very high)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
17 functional partner(s); context anchor
arsB2 - Primary literature: Guyeux C (2026). Structure-guided functional hypotheses for uncharacterised enzymes of Mycobacterium tuberculosis in preparation. doi:10.5281/zenodo.20571950
Ancestral MTBC0 protein sequence
>H37Rv|Rv3577| MPTARSDAPLSVTWMGVATLLVDDGSSALMTDGYFSRPGLARVAAGKVSPSAERVDGCLARANVSRLTAVIPVHTHIDHAMDSALVADRTGAQLVGGESAANVGRGYGLPEESLVVAVPGEPIQLGAFDVTLVESHHCPPDRFPGVISAPLTPPVKASAYRCGEAWSTLVHHRPSGRRLLIQDSAGFVSGALAGYRADAAYLSVGQLGLQPPSYLLEYWTETVRTVGVRRVILIHWDDFFRPLSKPLRALPYAADDLDLSIRILDELAAQDGVALQMPTVWRREDPWM