Protein profile

PA0916

ribosomal protein S12 methylthiotransferase RimO

Genome: NC_002516.2

Gene: rimO PA0916 Structure source: AlphaFold UniProt Q9I541
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Amino acids 440
Annotations 13
Features 40
PDB binders 2
Druggability 0.638

Overview

Basic information about this protein and its source genome.

Accession
PA0916
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
rimO PA0916
Status
annotated
Amino acids
440
Structure source
AlphaFold
EC
2.8.4.4
GO
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands. GO:0035599 Catalysis of the methylthiolation (-SCH3 addition) of the beta-carbon of peptidyl-aspartic acid to form peptidyl-L-beta-methylthioaspartic acid. GO:0046872 Binding to a metal ion. GO:0103039 Catalysis of the reaction: 2 S-adenosyl-L-methionine + a [ribosomal protein S12] L-aspartate89 + a sulfurated [sulfur carrier] + a reduced electron acceptor = S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 2 H+ + a [ribosomal protein S12] 3-methylthio-L-aspartate89 + an unsulfurated [sulfur carrier] + an oxidized electron acceptor. GO:0006400 The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
27.751
Human E-value
6.62e-09
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 0.638
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

MSTPTPKVGFVSLGCPKALVDSERILTQLRMEGYEVVPTYEDADVVVVNTCGFIDSAKAESLEVIGEAIAENGKVIVTGCMGVEEHAIRDVHPSVLAVTGPQQYEQVVTAVHEVVPPKTEHNPLVDLVPPQGVKLTPRHYAYLKISEGCNHSCSFCIIPSMRGKLVSRPVGDVLSEAERLVKAGVKELLVISQDTSAYGVDLKYKTDFWNGQPVKTRMKELCEALSSMGVWVRLHYVYPYPNVDDVIPLMAAGKLLPYLDIPFQHASPKVLKAMKRPAFEDKTLARIKQWREICPELTIRSTFIVGFPGETEEDFQYLLDWLTEAQLDRVGCFQYSPVEGAPANELGLEPVPDEVKQDRWERFMAHQQAISAARLQLKVGKEIEVLIDEVDEQGAVGRSWADAPEIDGNVFVDSDELKPGDKVRVRITDADEYDLWAELV

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 12 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

12
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
  • GO:0035599 Catalysis of the methylthiolation (-SCH3 addition) of the beta-carbon of peptidyl-aspartic acid to form peptidyl-L-beta-methylthioaspartic acid.
  • GO:0046872 Binding to a metal ion.
  • GO:0103039 Catalysis of the reaction: 2 S-adenosyl-L-methionine + a [ribosomal protein S12] L-aspartate89 + a sulfurated [sulfur carrier] + a reduced electron acceptor = S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 2 H+ + a [ribosomal protein S12] 3-methylthio-L-aspartate89 + an unsulfurated [sulfur carrier] + an oxidized electron acceptor.
  • GO:0006400 The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.
  • GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0016740 Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
  • GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.
  • GO:0035596 Catalysis of the addition of a methylthioether group (-SCH3) to a nucleic acid or protein acceptor.
  • GO:0018339 The modification of peptidyl-aspartic acid to form peptidyl-L-beta-methylthioaspartic acid, typical of bacterial ribosomal protein S12.

Sequence Features

Domain/signature hits from InterPro and related databases.

40 records
Show feature table
Start End DB Term Name
135 373 ProSiteProfiles PS51918 Radical SAM core domain profile.
135 373 InterPro IPR007197 Radical SAM
7 437 NCBIfam TIGR00089 MiaB/RimO family radical SAM methylthiotransferase
7 437 InterPro IPR005839 Methylthiotransferase
143 345 CDD cd01335 Radical_SAM
379 440 Pfam PF18693 TRAM domain
379 440 InterPro IPR041582 RimO, TRAM domain
137 379 FunFam G3DSA:3.80.30.20:FF:000001 tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase 2
143 163 ProSitePatterns PS01278 Methylthiotransferase radical SAM domain signature.
143 163 InterPro IPR020612 Methylthiotransferase, conserved site
137 379 Gene3D G3DSA:3.80.30.20 tm_1862 like domain
137 379 InterPro IPR023404 Radical SAM, alpha/beta horseshoe
376 440 ProSiteProfiles PS50926 TRAM domain profile.
376 440 InterPro IPR002792 TRAM domain
145 322 Pfam PF04055 Radical SAM superfamily
145 322 InterPro IPR007197 Radical SAM
6 439 Hamap MF_01865 Ribosomal protein S12 methylthiotransferase RimO [rimO].
6 439 InterPro IPR005840 Ribosomal protein S12 methylthiotransferase RimO
4 439 SFLD SFLDF00274 ribosomal protein S12 methylthiotransferase (RimO-like)
4 439 InterPro IPR005840 Ribosomal protein S12 methylthiotransferase RimO
7 125 Gene3D G3DSA:3.40.50.12160 -
7 125 InterPro IPR038135 Methylthiotransferase, N-terminal domain superfamily
139 365 SMART SM00729 MiaB
139 365 InterPro IPR006638 Elp3/MiaA/NifB-like, radical SAM core domain
4 439 SFLD SFLDG01061 methylthiotransferase
4 439 InterPro IPR005839 Methylthiotransferase
1 440 PANTHER PTHR43837 RIBOSOMAL PROTEIN S12 METHYLTHIOTRANSFERASE RIMO
1 440 InterPro IPR005840 Ribosomal protein S12 methylthiotransferase RimO
380 440 FunFam G3DSA:2.40.50.140:FF:000060 Ribosomal protein S12 methylthiotransferase RimO
7 124 FunFam G3DSA:3.40.50.12160:FF:000002 Ribosomal protein S12 methylthiotransferase RimO
7 436 NCBIfam TIGR01125 30S ribosomal protein S12 methylthiotransferase RimO
7 436 InterPro IPR005840 Ribosomal protein S12 methylthiotransferase RimO
123 364 SFLD SFLDG01082 B12-binding domain containing
380 440 Gene3D G3DSA:2.40.50.140 -
380 440 InterPro IPR012340 Nucleic acid-binding, OB-fold
6 116 ProSiteProfiles PS51449 Methylthiotransferase N-terminal domain profile.
6 116 InterPro IPR013848 Methylthiotransferase, N-terminal
7 96 Pfam PF00919 Uncharacterized protein family UPF0004
7 96 InterPro IPR013848 Methylthiotransferase, N-terminal
109 370 SUPERFAMILY SSF102114 Radical SAM enzymes

3D Structure

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

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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 PA0916
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 0.638

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.

15 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
CXS
2QGQ
Q9X2H6 221.3 Da LogP 1.19 TPSA 66.4 ✓ Ro5 ✓ Clean C1CCC(CC1)NCCCS(=O)(=O)O
FS5
4JC0
Q9X2H6 863.6 Da LogP 8.41 TPSA 0.0 2 viol. ✓ Clean S(SS[Fe]12[S]3[Fe]4[S]1[Fe]5[S]4[Fe]3[S]25)SS[F…

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.