Protein profile

PA5063

ubiquinone/menaquinone biosynthesis methyltransferase

Genome: NC_002516.2

Gene: PA5063 ubiE Structure source: AlphaFold UniProt Q9HUC0
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Amino acids 256
Annotations 9
Features 18
PDB binders 5
Druggability 0.787

Overview

Basic information about this protein and its source genome.

Accession
PA5063
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA5063 ubiE
Status
annotated
Amino acids
256
Structure source
AlphaFold
EC
2.1.1.163 2.1.1.201
GO
GO:0008425 Catalysis of the reaction: a 2-methoxy-6-all-trans-polyprenyl-1,4-benzoquinol + S-adenosyl-L-methionine = a 6-methoxy-3-methyl-2-all-trans-polyprenyl-1,4-benzoquinol + S-adenosyl-L-homocysteine + H+. GO:0043770 Catalysis of the reaction: a 2-demethylmenaquinol + S-adenosyl-L-methionine = a menaquinol + H+ + S-adenosyl-L-homocysteine. Reaction substrates can have varying polyprenyl side chain length. GO:0009060 The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which requires oxygen as the terminal electron acceptor. GO:0009234 The chemical reactions and pathways resulting in the formation of any of the menaquinones. Structurally, menaquinones consist of a methylated naphthoquinone ring structure and side chains composed of a variable number of unsaturated isoprenoid residues. Menaquinones that have vitamin K activity and are known as vitamin K2. GO:0032259 The process in which a methyl group is covalently attached to a molecule. GO:0006744 The chemical reactions and pathways resulting in the formation of ubiquinone, a lipid-soluble electron-transporting coenzyme.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
56.667
Human E-value
3.23e-16
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 0.787
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 EC 7 GO

Enzyme Commission (EC)

2

Gene Ontology (GO)

7
  • GO:0008425 Catalysis of the reaction: a 2-methoxy-6-all-trans-polyprenyl-1,4-benzoquinol + S-adenosyl-L-methionine = a 6-methoxy-3-methyl-2-all-trans-polyprenyl-1,4-benzoquinol + S-adenosyl-L-homocysteine + H+.
  • GO:0043770 Catalysis of the reaction: a 2-demethylmenaquinol + S-adenosyl-L-methionine = a menaquinol + H+ + S-adenosyl-L-homocysteine. Reaction substrates can have varying polyprenyl side chain length.
  • GO:0009060 The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which requires oxygen as the terminal electron acceptor.
  • GO:0009234 The chemical reactions and pathways resulting in the formation of any of the menaquinones. Structurally, menaquinones consist of a methylated naphthoquinone ring structure and side chains composed of a variable number of unsaturated isoprenoid residues. Menaquinones that have vitamin K activity and are known as vitamin K2.
  • GO:0032259 The process in which a methyl group is covalently attached to a molecule.
  • GO:0006744 The chemical reactions and pathways resulting in the formation of ubiquinone, a lipid-soluble electron-transporting coenzyme.
  • GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule.

Sequence Features

Domain/signature hits from InterPro and related databases.

18 records
Show feature table
Start End DB Term Name
30 255 NCBIfam TIGR01934 ubiquinone/menaquinone biosynthesis methyltransferase
30 255 InterPro IPR004033 UbiE/COQ5 methyltransferase
36 256 FunFam G3DSA:3.40.50.150:FF:000014 Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE
36 256 Gene3D G3DSA:3.40.50.150 Vaccinia Virus protein VP39
36 256 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
71 173 CDD cd02440 AdoMet_MTases
25 255 Pfam PF01209 ubiE/COQ5 methyltransferase family
21 255 Hamap MF_01813 Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE [ubiE].
21 255 InterPro IPR004033 UbiE/COQ5 methyltransferase
25 238 PANTHER PTHR43591 METHYLTRANSFERASE
41 56 ProSitePatterns PS01183 ubiE/COQ5 methyltransferase family signature 1.
41 56 InterPro IPR023576 UbiE/COQ5 methyltransferase, conserved site
163 177 ProSitePatterns PS01184 ubiE/COQ5 methyltransferase family signature 2.
163 177 InterPro IPR023576 UbiE/COQ5 methyltransferase, conserved site
25 255 ProSiteProfiles PS51608 UbiE family SAM-binding methyltransferase profile.
25 255 InterPro IPR004033 UbiE/COQ5 methyltransferase
18 253 SUPERFAMILY SSF53335 S-adenosyl-L-methionine-dependent methyltransferases
18 253 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily

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 PA5063
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 0.787

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.

55 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
BY9
6UV6
Q0H2W9 487.5 Da LogP 1.29 TPSA 157.0 1 viol. ✓ Clean c1ccc2c(c1)c3c4c(c5c6ccccc6n(c5c3[nH]2)[C@H]7[C…
MLI
4PNE
Q9ALM7 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
PC
5WP4
Q9FR44 184.2 Da LogP -0.20 TPSA 66.8 ✓ Ro5 ✓ Clean C[N+](C)(C)CCOP(=O)(O)O
SAI
2AVN
Q9X1A9 431.3 Da LogP -1.63 TPSA 182.6 ✓ Ro5 ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
TEX
5GM2
A0A077K7L1 437.6 Da LogP 4.85 TPSA 68.4 ✓ Ro5 Alert CC(C)[C@H]1C(=O)N[C@@H](Cc2c[nH]c3c2c(ccc3[C@](…

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.