Protein profile

KP13_03334

DNA polymerase III subunit delta

Genome: KpKP13

Gene: holA AHE45713.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GTY2
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Amino acids 344
Annotations 6
Features 19
PDB binders 0
Druggability 0.622

Overview

Basic information about this protein and its source genome.

Accession
KP13_03334
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
holA AHE45713.1
Status
annotated
Amino acids
344
Structure source
AlphaFold + ColabFold
EC
2.7.7.7
GO
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: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: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
91.14

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 0.3 · Pocket 17
P2Rank 0.045 · 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: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: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: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
22 191 Pfam PF06144 DNA polymerase III, delta subunit
22 191 InterPro IPR010372 DNA polymerase III delta, N-terminal
143 207 CDD cd18138 HLD_clamp_pol_III_delta
2 211 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
2 211 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
215 344 Gene3D G3DSA:1.20.272.10 -
215 344 FunFam G3DSA:1.20.272.10:FF:000008 DNA polymerase III, delta subunit
144 214 FunFam G3DSA:1.10.8.60:FF:000041 DNA polymerase III subunit delta
215 339 Pfam PF14840 Processivity clamp loader gamma complex DNA pol III C-term
215 339 InterPro IPR032780 DNA polymerase III subunit delta, C-terminal
2 336 PANTHER PTHR34388 DNA POLYMERASE III SUBUNIT DELTA
213 335 SUPERFAMILY SSF48019 post-AAA+ oligomerization domain-like
213 335 InterPro IPR008921 DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal
19 333 NCBIfam TIGR01128 DNA polymerase III subunit delta
19 333 InterPro IPR005790 DNA polymerase III, delta subunit
2 141 Gene3D G3DSA:3.40.50.300 -
2 141 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
144 214 Gene3D G3DSA:1.10.8.60 -
2 141 FunFam G3DSA:3.40.50.300:FF:001093 DNA polymerase III subunit delta

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 KP13_03334
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