Protein profile

PA0669

error-prone DNA polymerase

Genome: NC_002516.2

Gene: PA0669 dnaE2 Structure source: ColabFold UniProt Q9I5Q2
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Amino acids 1031
Annotations 9
Features 23
PDB binders 2
Druggability 0.756

Overview

Basic information about this protein and its source genome.

Accession
PA0669
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA0669 dnaE2
Status
annotated
Amino acids
1031
Structure source
ColabFold
EC
2.7.7.7
GO
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0008408 Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end. GO:0003887 Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); DNA-template-directed extension of the 3'-end of a DNA strand by one nucleotide at a time. GO:0003676 Binding to a nucleic acid. 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. GO:0006260 The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by the origin recognition complex, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
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 0.756
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

MAAWLVRMSAYAELHCLSNFSFQRGASSATELFARAARLGYRALAITDECSLAGIVRAWQAAREHQVQLIVGSEIRLEQGPKLVLLAEDLEGYQNLCRLITRGRRQADKGHYRLLREDLQQPLAGLLAIWLPNDHGDEQAAWLRERFPQRLWLGVELHRGADDDARLDKLLALASHLRLPPVACGDVHMHARGRRALQDCMTAIRNHLPVSEAGAYLFPNGERHLRTLEALQGIYPQALLAETLKIAERCRFDLEQLKYQYPRELVPAGHDPASWLRHLTEQGIARRWPNGASAKVRKQIERELELIAELGYESYFLTVQDIVAFARGRKILCQGRGSAANSAVCFALGITELDPDRTNLLFERFLSRERNEPPDIDVDFEHERREEVIQYVFTRYGRQRAALTAVVSTYHGAGAVRDVAKALGLPPEQVDVLANCCGRWSDQAPSAERLEEAGFDPQSPILRRVLALTDELIGFPRHLSQHPGGFVISEQPLDTLVPVENASMAERTVIQWDKDDLDAVGLLKVDVLALGMLSALRRSFDLIHALRGGKRLSIASIPSEDPATYEMISRADTIGVFQIESRAQMAMLPRLRPQKFYDLVIQVAIVRPGPIQGDMVHPYLRRRNGEEPVAYPSAELEEVFERTLGVPLFQEQVMELAIVAADYTPGEADELRRSMAAWKRHGGLEHHRERLTRGMLAKGYEADFAARIFEQIKGFGSYGFPESHAASFALLTYASSWLKRHEPAAFACALINSWPMGFYSPDQLLQDARRHALQTRPVDVRHSGWDCSLESFGQAQPAIRLGLRMIRGFREEDARRIEQVREAEPFLDVHDLGRRARLDARALELLADAGALRGLAGHRHKARWAVASVEPQLPLFAEGTAIEESTVSLPLPSRGEELLSDYALLGTTLGPHPLKLLRGQLKARRCRDSRELAKLGHGRPIRVAGLVVGRQRPQTASGITFITLEDEFGMVNVVVRHDLAERQRRPFLESRLLQVEGILESSGEVRHVIAGRLHDLTPLLTGLDVRSRDFH

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

8
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0008408 Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end.
  • GO:0003887 Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); DNA-template-directed extension of the 3'-end of a DNA strand by one nucleotide at a time.
  • GO:0003676 Binding to a nucleic acid.
  • 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.
  • GO:0006260 The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by the origin recognition complex, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
  • GO:0009432 An error-prone process for repairing damaged microbial DNA.
  • 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.

Sequence Features

Domain/signature hits from InterPro and related databases.

23 records
Show feature table
Start End DB Term Name
275 529 Pfam PF07733 Bacterial DNA polymerase III alpha NTPase domain
275 529 InterPro IPR011708 Bacterial DNA polymerase III, alpha subunit, NTPase domain
532 698 Pfam PF17657 Bacterial DNA polymerase III alpha subunit finger domain
532 698 InterPro IPR040982 DNA polymerase III alpha subunit finger domain
11 192 SUPERFAMILY SSF89550 PHP domain-like
11 192 InterPro IPR016195 Polymerase/histidinol phosphatase-like
758 850 FunFam G3DSA:1.10.150.870:FF:000002 Error-prone DNA polymerase
762 850 Gene3D G3DSA:1.10.150.870 -
11 262 CDD cd07434 PHP_PolIIIA_DnaE2
11 1031 Hamap MF_01902 Error-prone DNA polymerase [dnaE2].
11 1031 InterPro IPR023073 DNA polymerase, error-prone
5 252 Gene3D G3DSA:3.20.20.140 -
13 130 Pfam PF02811 PHP domain
13 130 InterPro IPR004013 PHP domain
12 79 SMART SM00481 npolultra
12 79 InterPro IPR003141 Polymerase/histidinol phosphatase, N-terminal
774 862 Pfam PF14579 Helix-hairpin-helix motif
774 862 InterPro IPR029460 DNA polymerase, helix-hairpin-helix motif
942 1029 CDD cd04485 DnaE_OBF
12 975 NCBIfam TIGR00594 DNA polymerase III subunit alpha
12 975 InterPro IPR004805 Error-prone DNA polymerase/DNA polymerase III subunit alpha DnaE/PolC
8 1019 PANTHER PTHR32294 DNA POLYMERASE III SUBUNIT ALPHA
8 1019 InterPro IPR004805 Error-prone DNA polymerase/DNA polymerase III subunit alpha DnaE/PolC

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
ColabFold PA0669
ColabFold — — 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
4 0.756
3 0.288
1 0.231

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.

52 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
3PO
2HPM
Q9XDH5 258.0 Da LogP -0.69 TPSA 170.8 ✓ Ro5 ✓ Clean OP(=O)(O)OP(=O)(O)OP(=O)(O)O
DTP
3E0D
Q9XDH5 491.2 Da LogP -0.60 TPSA 258.9 2 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)CO[P@]…

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.