Protein profile

VK055_1860

DNA polymerase III, delta subunit

Genome: KpATCC43816

Gene: holA AIK80466.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GTY2
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Amino acids 343
Annotations 6
Features 19
PDB binders 0
Druggability 0.622

Overview

Basic information about this protein and its source genome.

Accession
VK055_1860
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
holA AIK80466.1
Status
annotated
Amino acids
343
Structure source
AlphaFold + ColabFold
EC
2.7.7.7
GO
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:0009360 The DNA polymerase III holoenzyme is a complex that contains 10 different types of subunits. These subunits are organized into 3 functionally essential sub-assemblies: the pol III core, the beta sliding clamp processivity factor and the clamp-loading complex. The pol III core carries out the polymerase and the 3'-5' exonuclease proofreading activities. The polymerase is tethered to the template via the sliding clamp processivity factor. The clamp-loading complex assembles the beta processivity factor onto the primer template and plays a central role in the organization and communication at the replication fork. 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:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). GO:0006261 A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
85.131
DEG E-value
0.0
Localization
Unknown
ColabFold pLDDT
90.9

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 0.622
Structure A0A0H3GTY2
Pocket Pocket 4
P2Rank 0.048
Structure A0A0H3GTY2
Pocket Pocket 1
ColabFold model
FPocket 0.127 · Pocket 21
P2Rank 0.071 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 113 / 4744 genomes with a hit
Normalized 0.024

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • 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:0009360 The DNA polymerase III holoenzyme is a complex that contains 10 different types of subunits. These subunits are organized into 3 functionally essential sub-assemblies: the pol III core, the beta sliding clamp processivity factor and the clamp-loading complex. The pol III core carries out the polymerase and the 3'-5' exonuclease proofreading activities. The polymerase is tethered to the template via the sliding clamp processivity factor. The clamp-loading complex assembles the beta processivity factor onto the primer template and plays a central role in the organization and communication at the replication fork.
  • 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:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0006261 A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands.

Sequence Features

Domain/signature hits from InterPro and related databases.

19 records
Show feature table
Start End DB Term Name
1 140 FunFam G3DSA:3.40.50.300:FF:001093 DNA polymerase III subunit delta
143 213 FunFam G3DSA:1.10.8.60:FF:000041 DNA polymerase III subunit delta
18 332 NCBIfam TIGR01128 DNA polymerase III subunit delta
18 332 InterPro IPR005790 DNA polymerase III, delta subunit
142 206 CDD cd18138 HLD_clamp_pol_III_delta
1 335 PANTHER PTHR34388 DNA POLYMERASE III SUBUNIT DELTA
1 210 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
1 210 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
212 334 SUPERFAMILY SSF48019 post-AAA+ oligomerization domain-like
212 334 InterPro IPR008921 DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal
21 190 Pfam PF06144 DNA polymerase III, delta subunit
21 190 InterPro IPR010372 DNA polymerase III delta, N-terminal
214 343 Gene3D G3DSA:1.20.272.10 -
143 213 Gene3D G3DSA:1.10.8.60 -
214 343 FunFam G3DSA:1.20.272.10:FF:000008 DNA polymerase III, delta subunit
1 140 Gene3D G3DSA:3.40.50.300 -
1 140 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
214 338 Pfam PF14840 Processivity clamp loader gamma complex DNA pol III C-term
214 338 InterPro IPR032780 DNA polymerase III subunit delta, C-terminal

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 + 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_A0A0H3GTY2
AlphaFold — — full sequence — Viewing
ColabFold VK055_1860
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
4 0.622
16 0.039
11 0.001
12 0.001

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 2.3 0.048