Protein profile

VK055_3252

1,4-dihydroxy-2-naphthoate octaprenyltransferase

Genome: KpATCC43816

Gene: AIK81813.1 menA Structure source: AlphaFold + ColabFold UniProt A0A0H3GGB8
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Amino acids 306
Annotations 8
Features 43
PDB binders 0
Druggability 0.995

Overview

Basic information about this protein and its source genome.

Accession
VK055_3252
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK81813.1 menA
Status
annotated
Amino acids
306
Structure source
AlphaFold + ColabFold
EC
2.5.1.74
GO
GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GO:0004659 Catalysis of the transfer of a prenyl group from one compound (donor) to another (acceptor). GO:0046428 Catalysis of the reaction: 1,4-dihydroxy-2-naphthoate + an all-trans-polyprenyl diphosphate + H+ = a 2-demethylmenaquinol + CO2 + diphosphate. 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:0016765 Catalysis of the transfer of an alkyl or aryl (but not methyl) group from one compound (donor) to another (acceptor). GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
28.618
Human E-value
1.07e-19
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
37.276
Localization
CytoplasmicMembrane
ColabFold pLDDT
93.01

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 0.995
Structure A0A0H3GGB8
Pocket Pocket 1
P2Rank 0.992
Structure A0A0H3GGB8
Pocket Pocket 1
ColabFold model
FPocket 0.972 · Pocket 1
P2Rank 0.993 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 128 / 4744 genomes with a hit
Normalized 0.027

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0004659 Catalysis of the transfer of a prenyl group from one compound (donor) to another (acceptor).
  • GO:0046428 Catalysis of the reaction: 1,4-dihydroxy-2-naphthoate + an all-trans-polyprenyl diphosphate + H+ = a 2-demethylmenaquinol + CO2 + diphosphate.
  • 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:0016765 Catalysis of the transfer of an alkyl or aryl (but not methyl) group from one compound (donor) to another (acceptor).
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0042371 The chemical reactions and pathways resulting in the formation of any of the forms of vitamin K, quinone-derived vitamins which are involved in the synthesis of blood-clotting factors in mammals.

Sequence Features

Domain/signature hits from InterPro and related databases.

43 records
Show feature table
Start End DB Term Name
96 118 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
123 142 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
18 28 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
24 270 Pfam PF01040 UbiA prenyltransferase family
24 270 InterPro IPR000537 UbiA prenyltransferase family
34 42 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
287 304 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
289 305 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
146 168 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
11 298 CDD cd13962 PT_UbiA_UBIAD1
11 298 InterPro IPR026046 UbiA prenyltransferase domain containing protein 1
178 200 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
250 269 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
231 253 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
245 249 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
178 197 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
173 177 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
62 95 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
270 288 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
306 306 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
184 305 Gene3D G3DSA:1.20.120.1780 UbiA prenyltransferase
1 17 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
5 299 Hamap MF_01937 1,4-dihydroxy-2-naphthoate octaprenyltransferase [menA].
5 299 InterPro IPR004657 1,4-dihydroxy-2-naphthoate octaprenyltransferase
198 225 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
154 172 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
43 61 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
226 244 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
96 117 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
13 32 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
143 153 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
118 122 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
15 298 NCBIfam TIGR00751 1,4-dihydroxy-2-naphthoate octaprenyltransferase
42 61 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 33 Phobius SIGNAL_PEPTIDE Signal peptide region
3 303 PANTHER PTHR13929 1,4-DIHYDROXY-2-NAPHTHOATE OCTAPRENYLTRANSFERASE
3 303 InterPro IPR026046 UbiA prenyltransferase domain containing protein 1
29 33 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
2 304 PIRSF PIRSF005355 UBIAD1
2 304 InterPro IPR026046 UbiA prenyltransferase domain containing protein 1
15 176 Gene3D G3DSA:1.10.357.140 UbiA prenyltransferase
15 176 InterPro IPR044878 UbiA prenyltransferase superfamily
122 141 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.

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_A0A0H3GGB8
AlphaFold — — full sequence — Viewing
ColabFold VK055_3252
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 0.995

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 57.14 0.985
2 1.83 0.035
3 1.6 0.025
4 1.58 0.025
5 1.36 0.016