Protein profile

PA5332

catabolite repression control protein

Genome: NC_002516.2

Gene: CAZ10_32350 DT376_09125 IPC1295_10410 exoA PAERUG_P19_London_7_VIM_2_05_10_01808 L4V69_36320 ALP65_01013 crc GUL26_21635 GNQ48_25180 PA5332 Structure source: Experimental + AlphaFold UniProt G3XDB0 UniProt Q51380
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Amino acids 259
Annotations 11
Features 14
PDB binders 1
Druggability 0.959

Overview

Basic information about this protein and its source genome.

Accession
PA5332
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
CAZ10_32350 DT376_09125 IPC1295_10410 exoA PAERUG_P19_London_7_VIM_2_05_10_01808 L4V69_36320 ALP65_01013 crc GUL26_21635 GNQ48_25180 PA5332
Status
annotated
Amino acids
259
Structure source
Experimental + AlphaFold
GO
GO:0003906 Catalysis of the cleavage of the C-O-P bond in the AP site created when DNA glycosylase removes a damaged base, involved in the DNA base excision repair pathway (BER). GO:0008311 Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of a double-stranded DNA molecule. GO:0046872 Binding to a metal ion. GO:0008081 Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group. GO:0006284 In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. GO:0009372 The cell-cell signaling process in which single-celled organisms carry out coordinated responses by monitoring their own population density, and often also that of other microbes, by producing small, diffusible, signal molecules, detecting the concentration of these molecules, and triggering a signal transduction pathway when a certain threshold is reached. Quorum sensing can occur amongst microbial communities in the environment or within host organisms.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
32.743
Human E-value
8.15e-11
Gut microbiome off-target
hit
Essential (DEG)
N
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 0.959
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

11 GO

Gene Ontology (GO)

11
  • GO:0003906 Catalysis of the cleavage of the C-O-P bond in the AP site created when DNA glycosylase removes a damaged base, involved in the DNA base excision repair pathway (BER).
  • GO:0008311 Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of a double-stranded DNA molecule.
  • GO:0046872 Binding to a metal ion.
  • GO:0008081 Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group.
  • GO:0006284 In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase.
  • GO:0009372 The cell-cell signaling process in which single-celled organisms carry out coordinated responses by monitoring their own population density, and often also that of other microbes, by producing small, diffusible, signal molecules, detecting the concentration of these molecules, and triggering a signal transduction pathway when a certain threshold is reached. Quorum sensing can occur amongst microbial communities in the environment or within host organisms.
  • GO:0043609 Any process that modulates the frequency, rate, or extent of carbon utilization.
  • GO:1900190 Any process that modulates the frequency, rate or extent of single-species biofilm formation.
  • GO:0004518 Catalysis of the cleavage of ester linkages within nucleic acids.
  • 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:0006281 The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.

Sequence Features

Domain/signature hits from InterPro and related databases.

14 records
Show feature table
Start End DB Term Name
5 233 Pfam PF03372 Endonuclease/Exonuclease/phosphatase family
5 233 InterPro IPR005135 Endonuclease/exonuclease/phosphatase
1 254 PANTHER PTHR43250 -
1 254 InterPro IPR037493 Exodeoxyribonuclease III-like
1 259 FunFam G3DSA:3.60.10.10:FF:000001 Exodeoxyribonuclease III
1 253 CDD cd10281 Nape_like_AP-endo
1 259 Gene3D G3DSA:3.60.10.10 Endonuclease/exonuclease/phosphatase
1 259 InterPro IPR036691 Endonuclease/exonuclease/phosphatase superfamily
1 253 NCBIfam TIGR00633 exodeoxyribonuclease III
1 253 InterPro IPR004808 AP endonuclease 1
1 254 SUPERFAMILY SSF56219 DNase I-like
1 254 InterPro IPR036691 Endonuclease/exonuclease/phosphatase superfamily
1 255 ProSiteProfiles PS51435 AP endonucleases family 1 profile.
1 255 InterPro IPR004808 AP endonuclease 1

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

2 + 1

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

Entry Method Resolution Chain Coverage Links Status
PDB 4JG3
X-ray 1.80 Å A
100.0% 1-259
PDBe RCSB PDBj File
Viewing
PDB 4F1R
X-ray 2.20 Å A
100.0% 1-259
PDBe RCSB PDBj File
Loaded
AlphaFold PA5332
AlphaFold — — 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
3 0.959

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 4.11 0.165
2 2.15 0.05
3 0.74 0.002

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.

151 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
PGA
5WN2
P27695 156.0 Da LogP -0.82 TPSA 104.1 ✓ Ro5 ✓ Clean C(C(=O)O)OP(=O)(O)O

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.