Protein profile

PA3622

RNA polymerase sigma factor RpoS

Genome: NC_002516.2

Gene: PA3622 rpoS Structure source: AlphaFold UniProt P45684
Amino acids 334
Annotations 16
Features 45
PDB binders 12
Druggability 0.64

Overview

Basic information about this protein and its source genome.

Accession
PA3622
Gene
PA3622 rpoS
Status
annotated
Amino acids
334
Structure source
AlphaFold
GO
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:1903865 A protein complex which is capable of sigma factor antagonist activity. GO:0003899 Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'. GO:0016987 Sigma factors act as the promoter specificity subunit of eubacterial and plant plastid multisubunit RNA polymerases, whose core subunit composition is often described as alpha(2)-beta-beta-prime. Although sigma does not bind DNA on its own, when combined with the core to form the holoenzyme, the sigma factor binds specifically to promoter elements. The sigma subunit is released once elongation begins. GO:0000976 Binding to a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon. GO:0006352 The initial step of transcription, consisting of the assembly of the RNA polymerase preinitiation complex (PIC) at a gene promoter, as well as the formation of the first few bonds of the RNA transcript. Transcription initiation includes abortive initiation events, which occur when the first few nucleotides are repeatedly synthesized and then released, and ends when promoter clearance takes place.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Gut microbiome off-target
hit
Essential (DEG)
Y
Localization
Cytoplasmic

Selected Druggability evidence

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.64
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

MALKKEGPEFDHDDEVLLLEPGIMLDESSADEQPSPRATPKATTSFSSKQHKHIDYTRALDATQLYLNEIGFSPLLTPEEEVHFARLAQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYLRAARELTHKLDHEPSPEEIANLLEKPVAEVKRMLGLNERVTSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLSESIDQWLTELTDKQREVVIRRFGLRGHESSTLEEVGQEIGLTRERVRQIQVEALKRLREILEKNGLSSDALFQ

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

16 GO

Gene Ontology (GO)

16
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:1903865 A protein complex which is capable of sigma factor antagonist activity.
  • GO:0003899 Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.
  • GO:0016987 Sigma factors act as the promoter specificity subunit of eubacterial and plant plastid multisubunit RNA polymerases, whose core subunit composition is often described as alpha(2)-beta-beta-prime. Although sigma does not bind DNA on its own, when combined with the core to form the holoenzyme, the sigma factor binds specifically to promoter elements. The sigma subunit is released once elongation begins.
  • GO:0000976 Binding to a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon.
  • GO:0006352 The initial step of transcription, consisting of the assembly of the RNA polymerase preinitiation complex (PIC) at a gene promoter, as well as the formation of the first few bonds of the RNA transcript. Transcription initiation includes abortive initiation events, which occur when the first few nucleotides are repeatedly synthesized and then released, and ends when promoter clearance takes place.
  • GO:1900377 Any process that stops, prevents or reduces the frequency, rate or extent of secondary metabolite biosynthetic process.
  • GO:0050921 Any process that activates or increases the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient.
  • GO:1900233 Any process that activates or increases the frequency, rate or extent of single-species biofilm formation on inanimate substrate.
  • GO:2000145 Any process that modulates the frequency, rate or extent of cell motility.
  • GO:1900034 Any process that modulates the frequency, rate or extent of cellular response to heat.
  • GO:1900407 Any process that modulates the frequency, rate or extent of cellular response to oxidative stress.
  • GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
  • GO:1901000 Any process that modulates the frequency, rate or extent of response to salt stress.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0003700 A transcription regulator activity that modulates transcription of gene sets via selective and non-covalent binding to a specific double-stranded genomic DNA sequence (sometimes referred to as a motif) within a cis-regulatory region. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons.

Sequence Features

Domain/signature hits from InterPro and related databases.

45 records
Show feature table
Start End DB Term Name
26 168 Gene3D G3DSA:1.10.601.10 RNA Polymerase Primary Sigma Factor
21 48 MobiDBLite mobidb-lite consensus disorder prediction
32 48 MobiDBLite mobidb-lite consensus disorder prediction
267 320 Pfam PF04545 Sigma-70, region 4
267 320 InterPro IPR007630 RNA polymerase sigma-70 region 4
172 248 FunFam G3DSA:1.10.10.10:FF:000046 RNA polymerase sigma factor RpoS
96 322 NCBIfam TIGR02937 sigma-70 family RNA polymerase sigma factor
96 322 InterPro IPR014284 RNA polymerase sigma-70 like domain
179 253 Pfam PF04539 Sigma-70 region 3
179 253 InterPro IPR007624 RNA polymerase sigma-70 region 3
99 168 Pfam PF04542 Sigma-70 region 2
99 168 InterPro IPR007627 RNA polymerase sigma-70 region 2
95 328 PANTHER PTHR30603 RNA POLYMERASE SIGMA FACTOR RPO
249 324 Gene3D G3DSA:1.10.10.10 -
249 324 InterPro IPR036388 Winged helix-like DNA-binding domain superfamily
91 171 FunFam G3DSA:1.10.601.10:FF:000001 RNA polymerase sigma factor SigA
292 318 ProSitePatterns PS00716 Sigma-70 factors family signature 2.
292 318 InterPro IPR000943 RNA polymerase sigma-70
172 247 Gene3D G3DSA:1.10.10.10 -
172 247 InterPro IPR036388 Winged helix-like DNA-binding domain superfamily
123 136 PRINTS PR00046 Major sigma-70 factor signature
123 136 InterPro IPR000943 RNA polymerase sigma-70
307 318 PRINTS PR00046 Major sigma-70 factor signature
307 318 InterPro IPR000943 RNA polymerase sigma-70
292 307 PRINTS PR00046 Major sigma-70 factor signature
292 307 InterPro IPR000943 RNA polymerase sigma-70
147 155 PRINTS PR00046 Major sigma-70 factor signature
147 155 InterPro IPR000943 RNA polymerase sigma-70
271 283 PRINTS PR00046 Major sigma-70 factor signature
271 283 InterPro IPR000943 RNA polymerase sigma-70
54 333 NCBIfam TIGR02394 RNA polymerase sigma factor RpoS
54 333 InterPro IPR012761 RNA polymerase sigma factor RpoS
172 246 SUPERFAMILY SSF88659 Sigma3 and sigma4 domains of RNA polymerase sigma factors
172 246 InterPro IPR013324 RNA polymerase sigma factor, region 3/4-like
123 136 ProSitePatterns PS00715 Sigma-70 factors family signature 1.
61 94 Pfam PF00140 Sigma-70 factor, region 1.2
61 94 InterPro IPR009042 RNA polymerase sigma-70 region 1.2
61 169 SUPERFAMILY SSF88946 Sigma2 domain of RNA polymerase sigma factors
61 169 InterPro IPR013325 RNA polymerase sigma factor, region 2
262 319 CDD cd06171 Sigma70_r4
4 333 Hamap MF_00959 RNA polymerase sigma factor RpoS [rpoS].
4 333 InterPro IPR012761 RNA polymerase sigma factor RpoS
230 327 SUPERFAMILY SSF88659 Sigma3 and sigma4 domains of RNA polymerase sigma factors
230 327 InterPro IPR013324 RNA polymerase sigma factor, region 3/4-like
250 323 FunFam G3DSA:1.10.10.10:FF:000044 RNA polymerase sigma factor RpoS

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

3D visualization script Full viewer

Loading 3D structure...

Legend High Medium Low

Structural evidence

0 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold PA3622
AlphaFold full sequence Viewing
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET Sticks Spheres Surfaces Druggability Labels Zoom Positions
1 0.64

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

62 records

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
118 P00579 430.2 Da LogP 3.06 TPSA 0.0 ✓ Ro5 ✓ Clean c1ccc(cc1)[Sb+](c2ccccc2)(c3ccccc3)c4ccccc4
1N7 P00579 631.9 Da LogP 2.20 TPSA 164.4 2 viol. ✓ Clean C[C@H](CCC(=O)NCCC[N+](C)(C)CC(CS(=O)(=O)O)O)[C…
1RL P00579 900.0 Da LogP 6.67 TPSA 216.4 3 viol. ✓ Clean CCN(CC)CCOc1cccc2c1N=C3c4c5c(c(c6c4C(=O)[C@](O6…
1RM P00579 1035.2 Da LogP 6.62 TPSA 237.5 3 viol. ✓ Clean Cc1c(c2c3c4c1O[C@@](C4=O)(O/C=C/[C@@H]([C@H]([C…
88G P9WGI1 358.4 Da LogP 3.97 TPSA 58.2 ✓ Ro5 ✓ Clean Cc1ccccc1NC(=O)[C@@H](Cc2ccccc2)NC(=O)c3ccccc3
BU3 A0A0H3CAV3 90.1 Da LogP -0.25 TPSA 40.5 ✓ Ro5 ✓ Clean C[C@H]([C@@H](C)O)O
FI8 P9WGI1 1058.1 Da LogP 6.23 TPSA 266.7 4 viol. ✓ Clean CCc1c(c(c(c(c1Cl)O)Cl)O)C(=O)O[C@@H]2[C@H](O[C@…
KNG A0QW02 986.1 Da LogP 5.64 TPSA 292.6 4 viol. Alert Cc1c(c2c3c(cc(c2O)NC(=O)/C(=C\CC[C@@H]([C@@H]([…
RBT Q5SKW1 847.0 Da LogP 4.62 TPSA 205.5 2 viol. Alert Cc1c(c2c3c4c1O[C@@](C4=O)(O\C=C\[C@@H]([C@H]([C…
RFP A0QW02 823.0 Da LogP 4.34 TPSA 220.1 3 viol. Alert Cc1c(c2c3c4c1O[C@@](C4=O)(O\C=C\[C@@H]([C@H]([C…
RFV Q5SKW1 699.8 Da LogP 4.60 TPSA 204.5 3 viol. ✓ Clean Cc1c(c2c3c(cc(c2O)NC(=O)C(=C/C=C/[C@@H]([C@@H](…
SRN A0QW02 807.0 Da LogP 6.80 TPSA 161.2 2 viol. ✓ Clean C[C@H]1[C@H]2C\C=C\[C@H]3[C@@H]([C@H]4C[C@@H](O…

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.