Target Pathogen

Overview

Basic information about this protein and its source genome.

Accession: PA5399
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA5399 dgcB
Status: annotated
Amino acids: 653
Structure source: AlphaFold

GO

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:0047865 Catalysis of the reaction: N,N-dimethylglycine + electron-transfer flavoprotein + H2O = sarcosine + formaldehyde + reduced electron-transfer flavoprotein. GO:0047866 Catalysis of the reaction: N,N-dimethylglycine + H2O + O2 = formaldehyde + H2O2 + sarcosine. GO:0046872 Binding to a metal ion. GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. GO:0042426 The chemical reactions and pathways resulting in the breakdown of choline (2-hydroxyethyltrimethylammonium), an amino alcohol that occurs widely in living organisms as a constituent of certain types of phospholipids and in the neurotransmitter acetylcholine.

Target profile

Computed evidence for target prioritization.

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

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 0.816

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

8 GO

Gene Ontology (GO)

8

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:0047865 Catalysis of the reaction: N,N-dimethylglycine + electron-transfer flavoprotein + H2O = sarcosine + formaldehyde + reduced electron-transfer flavoprotein.
GO:0047866 Catalysis of the reaction: N,N-dimethylglycine + H2O + O2 = formaldehyde + H2O2 + sarcosine.
GO:0046872 Binding to a metal ion.
GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
GO:0042426 The chemical reactions and pathways resulting in the breakdown of choline (2-hydroxyethyltrimethylammonium), an amino alcohol that occurs widely in living organisms as a constituent of certain types of phospholipids and in the neurotransmitter acetylcholine.
GO:0031457 The chemical reactions and pathways resulting in the breakdown of glycine betaine, N-trimethylglycine.
GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.

Sequence Features

Domain/signature hits from InterPro and related databases.

35 records

Show feature table

Start	End	DB	Term	Name
88	92	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
93	113	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
180	653	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
114	133	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
323	334	ProSitePatterns	PS00198	4Fe-4S ferredoxin-type iron-sulfur binding region signature.
323	334	InterPro	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site
311	342	ProSiteProfiles	PS51379	4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
311	342	InterPro	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain
218	357	FunFam	G3DSA:1.10.1060.10:FF:000014	DgcB, Dimethylglycine catabolism
134	153	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
68	87	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
4	26	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
525	611	Pfam	PF02754	Cysteine-rich domain
525	611	InterPro	IPR004017	Cysteine-rich domain
402	481	Pfam	PF02754	Cysteine-rich domain
402	481	InterPro	IPR004017	Cysteine-rich domain
154	158	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
6	26	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
93	113	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
236	266	ProSiteProfiles	PS51379	4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
236	266	InterPro	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain
67	89	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
157	179	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
19	632	PANTHER	PTHR43255	IRON-SULFUR-BINDING OXIDOREDUCTASE FADF-RELATED-RELATED
1	5	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
159	179	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
134	153	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
4	220	Pfam	PF11982	Domain of unknown function (DUF3483)
4	220	InterPro	IPR021872	Protein of unknown function DUF3483
222	352	SUPERFAMILY	SSF46548	alpha-helical ferredoxin
220	357	Gene3D	G3DSA:1.10.1060.10	-
220	357	InterPro	IPR009051	Alpha-helical ferredoxin
27	67	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
242	336	Pfam	PF13183	4Fe-4S dicluster domain
242	336	InterPro	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain

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 PA5399	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
2				0.816
13				0.325

PA5399