Protein profile

PA3640

DNA polymerase III subunit alpha

Genome: NC_002516.2

Gene: PA3640 dnaE Structure source: AlphaFold UniProt Q9HXZ1
Export view
Amino acids 1173
Annotations 7
Features 30
PDB binders 2
Druggability 0.624

Overview

Basic information about this protein and its source genome.

Accession
PA3640
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA3640 dnaE
Status
annotated
Amino acids
1173
Structure source
AlphaFold
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: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: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.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Gut microbiome off-target
hit
Essential (DEG)
Y
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 0.624
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

MTVSFVHLRLHTEFSLVDGLVRVKPLAKAVAGLGMPAVAVTDQSNMCSLVKFYKTAMGAGIKPICGADIWLASREEDGPLSRLSLLAMNAKGYRNLTELISRGWSEGQRNGEIIIERDWVKEAAEGLIALSAAKEGEIGHALLDGEEAKAEALLREWMEVFPERFYVEVQRTSRVNDEEHLHAAVALASRCNAPLVATNDVRFIKQEDFEAHETRVCIGEGRTLDDPRRPRTYSDQQYLKSPAEMAELFSDLPEALENTVEIAKRCNIEVQLGKYFLPDFPTPNGMGIDDYLRHASFEGLEERLEVLLPKDTPDYEAKRQVYVDRLNFELDIIIQMGFPGYFLIVMDFIKWAKNNGVPVGPGRGSGAGSLVAYVLKITDLDPLAYDLLFERFLNPERISMPDFDVDFCMEGRDRVIDYVADAYGRNAVSQIITFGTMAAKAVVRDVARVQGKSYGLADRLSKMIPFEVGMTLDKAYEQEEMLRDFLKSDEEAAEIWEMALKLEGITRGTGKHAGGVVIAPTKLTDFSPIACDEEGGGLVTQFDKDDVEAAGLVKFDFLGLRTLTIIKWAMEIINREQAKKGLEPVNIDFIPLDDKPTYSLLQKAETTAVFQLESRGMKELIKKLKPDCLEDLIALVALFRPGPLQSGMVDDFINRKHGRAELSYPHPDYQYAGLEPVLKPTYGIILYQEQVMQIAQVMAGYTLGGADMLRRAMGKKKPEEMAKQRGGFIEGCKNNGIDADLAGNIFDLVEKFAGYGFNKSHSAAYGLVSYQTAWLKTHFPAPFMAAVLTADMQNTDKVVTLIEECRHMKLRIVAPDVNNSEFRFTVDDDGRIVYGLGAIKGVGEGPVEAITECRAEGGPFNTLFDFCDRVDLKRINKRTLEALIRAGALDRLGPHYHDELKAYQATVDLNRAVLLAAMEEAIQAAEQTARSHDSGHMDLFGGVFAEPEADVYANHRKVKELTLKERLKGEKDTLGLYLTGHPIDEYEGEVRRFARQRIVELKPARDTQTVAGLIVNLRVMKNKKGDKMGFVTLDDRSGRIEASLFSEAFAAAQSLLQTDALVVVEGEVSQDDFSGGLRLRAKRVMSLEEARTGLAESLRMKLHADLLKGDRLRWLGELFNRHRGSCPITLDYTSADAKALLQFGESWRVDPADDLIQALRDQFGRDNVFLNYR

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • 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: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: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.

30 records
Show feature table
Start End DB Term Name
434 511 Gene3D G3DSA:1.10.10.1600 Bacterial DNA polymerase III alpha subunit, thumb domain
434 511 InterPro IPR041931 Bacterial DNA polymerase III alpha subunit, thumb domain
1 269 FunFam G3DSA:3.20.20.140:FF:000028 DNA polymerase III subunit alpha
5 1045 NCBIfam TIGR00594 DNA polymerase III subunit alpha
5 1045 InterPro IPR004805 Error-prone DNA polymerase/DNA polymerase III subunit alpha DnaE/PolC
562 736 Pfam PF17657 Bacterial DNA polymerase III alpha subunit finger domain
562 736 InterPro IPR040982 DNA polymerase III alpha subunit finger domain
434 511 FunFam G3DSA:1.10.10.1600:FF:000001 DNA polymerase III subunit alpha
5 262 SUPERFAMILY SSF89550 PHP domain-like
5 262 InterPro IPR016195 Polymerase/histidinol phosphatase-like
810 895 Pfam PF14579 Helix-hairpin-helix motif
810 895 InterPro IPR029460 DNA polymerase, helix-hairpin-helix motif
1 1168 PANTHER PTHR32294 DNA POLYMERASE III SUBUNIT ALPHA
1 1168 InterPro IPR004805 Error-prone DNA polymerase/DNA polymerase III subunit alpha DnaE/PolC
4 280 CDD cd07433 PHP_PolIIIA_DnaE1
714 887 FunFam G3DSA:1.10.150.870:FF:000001 DNA polymerase III subunit alpha
996 1087 FunFam G3DSA:2.40.50.140:FF:000106 DNA polymerase III subunit alpha
1 268 Gene3D G3DSA:3.20.20.140 -
713 887 Gene3D G3DSA:1.10.150.870 -
291 559 Pfam PF07733 Bacterial DNA polymerase III alpha NTPase domain
291 559 InterPro IPR011708 Bacterial DNA polymerase III, alpha subunit, NTPase domain
1009 1083 Pfam PF01336 OB-fold nucleic acid binding domain
1009 1083 InterPro IPR004365 OB-fold nucleic acid binding domain, AA-tRNA synthetase-type
1009 1091 CDD cd04485 DnaE_OBF
994 1087 Gene3D G3DSA:2.40.50.140 -
994 1087 InterPro IPR012340 Nucleic acid-binding, OB-fold
7 171 Pfam PF02811 PHP domain
7 171 InterPro IPR004013 PHP domain
6 73 SMART SM00481 npolultra
6 73 InterPro IPR003141 Polymerase/histidinol phosphatase, N-terminal

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

Loading 3D structure...

Legend High Medium Low

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 PA3640
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
4 0.565
2 0.499
8 0.332
3 0.28

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.