Protein profile

KP13_01731

Ubiquinone/menaquinone biosynthesis methyltransferase ubiE

Genome: KpKP13

Gene: ubiE AHE46966.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GLM9
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Amino acids 251
Annotations 8
Features 18
PDB binders 8
Druggability 0.988

Overview

Basic information about this protein and its source genome.

Accession
KP13_01731
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
ubiE AHE46966.1
Status
annotated
Amino acids
251
Structure source
AlphaFold + ColabFold
EC
2.1.1.163 2.1.1.201
GO
GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule. 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.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
56.0
Human E-value
9.14e-11
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
92.032
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
91.25

Selected Druggability evidence

AlphaFold / UniProt model

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 0.988
Structure A0A0H3GLM9
Pocket Pocket 1
P2Rank 0.976
Structure A0A0H3GLM9
Pocket Pocket 1
ColabFold model
FPocket 0.986 · Pocket 1
P2Rank 0.948 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 241 / 4744 genomes with a hit
Normalized 0.051

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 EC 6 GO

Enzyme Commission (EC)

2

Gene Ontology (GO)

6
  • GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule.
  • 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.

Sequence Features

Domain/signature hits from InterPro and related databases.

18 records
Show feature table
Start End DB Term Name
36 51 ProSitePatterns PS01183 ubiE/COQ5 methyltransferase family signature 1.
36 51 InterPro IPR023576 UbiE/COQ5 methyltransferase, conserved site
27 233 PANTHER PTHR43591 METHYLTRANSFERASE
25 250 NCBIfam TIGR01934 ubiquinone/menaquinone biosynthesis methyltransferase
25 250 InterPro IPR004033 UbiE/COQ5 methyltransferase
18 249 SUPERFAMILY SSF53335 S-adenosyl-L-methionine-dependent methyltransferases
18 249 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
31 251 FunFam G3DSA:3.40.50.150:FF:000014 Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE
16 250 Hamap MF_01813 Ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE [ubiE].
16 250 InterPro IPR004033 UbiE/COQ5 methyltransferase
20 250 ProSiteProfiles PS51608 UbiE family SAM-binding methyltransferase profile.
20 250 InterPro IPR004033 UbiE/COQ5 methyltransferase
31 251 Gene3D G3DSA:3.40.50.150 Vaccinia Virus protein VP39
31 251 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
15 250 Pfam PF01209 ubiE/COQ5 methyltransferase family
66 168 CDD cd02440 AdoMet_MTases
158 172 ProSitePatterns PS01184 ubiE/COQ5 methyltransferase family signature 2.
158 172 InterPro IPR023576 UbiE/COQ5 methyltransferase, conserved site

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

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Structural evidence

0 + 2

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

Entry Method Resolution Chain Coverage Links Status
AlphaFold AF_A0A0H3GLM9
AlphaFold — — full sequence — Viewing
ColabFold KP13_01731
ColabFold — — full sequence — Loaded
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 0.988
2 0.978

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 38.24 0.959
2 1.91 0.039

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.

58 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
ARS
4FSD
C0JV69 74.9 Da LogP -0.38 TPSA 0.0 ✓ Ro5 ✓ Clean [As]
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…
DTT
4RSR
C0JV69 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@@H]([C@H](CS)O)O)S
MLI
4PNE
Q9ALM7 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
PA0
4KW7
C0JV69 168.0 Da LogP 0.36 TPSA 17.1 ✓ Ro5 ✓ Clean c1ccc(cc1)[As]=O
PC
5WP4
Q9FR44 184.2 Da LogP -0.20 TPSA 66.8 ✓ Ro5 ✓ Clean C[N+](C)(C)CCOP(=O)(O)O
RXO
4RSR
C0JV69 215.0 Da LogP -0.44 TPSA 63.4 ✓ Ro5 ✓ Clean c1cc(c(cc1[AsH2])[N+](=O)[O-])O
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.