Pseudomonas aeruginosa PAO1, PA2138 (ligD)

Cytoplasmic
Cytoplasmic Membrane
Periplasmic
Outer Membrane
Extracellular
Unknown
View in JBrowse PseudoCyc / Metabolic Pathways

Gene Feature Overview

Strain Pseudomonas aeruginosa PAO1 (Stover et al., 2000)
GCF_000006765.1|latest
Locus Tag
PA2138
Name
ligD
Replicon chromosome
Genomic location 2353086 - 2355608 (+ strand)
Transposon Mutants 2 transposon mutants in PAO1
Transposon Mutants in orthologs 1 transposon mutants in orthologs

Cross-References

RefSeq NP_250828.1
GI 15597334
Affymetrix PA2138_at
Entrez 880451
GenBank AAG05526.1
INSDC AAG05526.1
NCBI Locus Tag PA2138
protein_id(GenBank) gb|AAG05526.1|AE004641_5|gnl|PseudoCAP|PA2138
TIGR NTL03PA02138
UniParc UPI00000C55C8
UniProtKB Acc Q9I1X7
UniProtKB ID LIGD_PSEAE
UniRef100 UniRef100_Q9I1X7
UniRef50 UniRef50_Q9I1X7
UniRef90 UniRef90_Q9I1X7

Product

Feature Type CDS
Coding Frame 1
Product Name
Multifunctional non-homologous end joining protein LigD
Product Name Confidence: Class 1
Synonyms probable ATP-dependent DNA ligase
Evidence for Translation
Charge (pH 7) 18.97
Kyte-Doolittle Hydrophobicity Value -0.530
Molecular Weight (kDa) 94.0
Isoelectric Point (pI) 9.72

Subcellular localization

Individual Mappings
Localization Confidence PMID
Cytoplasmic Class 3
Additional evidence for subcellular localization

AlphaFold 2 Protein Structure Predictions

Protein structure predictions using a neural network model developed by DeepMind. If a UniProtKB accession is associated with this protein, a search link will be provided below.

Look for predicted 3D structure in AlphaFold DB: Search

PDB 3D Structures

Accession Header Accession Date Compound Source Resolution Method Percent Identity
2FAQ HYDROLASE/TRANSFERASE 12/07/05 Crystal Structure of Pseudomonas aeruginosa LigD polymerase domain with ATP and Manganese Pseudomonas aeruginosa 1.9 X-RAY DIFFRACTION 100.0
2LJ6 DNA BINDING PROTEIN 09/06/11 Solution Structure and DNA-binding Properties of the Phosphoesterase Domain of DNA Ligase D Pseudomonas aeruginosa NOT SOLUTION NMR 100.0
2FAO HYDROLASE/TRANSFERASE 12/07/05 Crystal Structure of Pseudomonas aeruginosa LigD polymerase domain Pseudomonas aeruginosa 1.5 X-RAY DIFFRACTION 100.0
3N9D LIGASE 05/28/10 Monoclinic Structure of P. aeruginosa LigD phosphoesterase domain Pseudomonas aeruginosa 2.3 X-RAY DIFFRACTION 100.0
2FAR Hydrolase/Transferase 12/07/05 Crystal Structure of Pseudomonas aeruginosa LigD polymerase domain with dATP and Manganese Pseudomonas aeruginosa 1.9 X-RAY DIFFRACTION 100.0
3N9B LIGASE 05/28/10 Crystal Structure of the P. aeruginosa LigD phosphoesterase domain Pseudomonas aeruginosa 1.92 X-RAY DIFFRACTION 100.0

Pathogen Association Analysis

Results
Common
Found in both pathogen and nonpathogenic strains
Hits to this gene were found in 290 genera

Orthologs/Comparative Genomics

Pseudomonas Ortholog Database View orthologs at Pseudomonas Ortholog Database
Pseudomonas Ortholog Group POG003336 (490 members)
Putative Inparalogs None Found

Interactions

STRING database Search for predicted protein-protein interactions using:
Search term: PA2138
Search term: ligD

Human Homologs

References

Characterization of an ATP-dependent DNA ligase encoded by Haemophilus influenzae.
Cheng C, Shuman S
Nucleic Acids Res 1997 Apr 1;25(7):1369-74
PubMed ID: 9060431
Gap filling activities of Pseudomonas DNA ligase D (LigD) polymerase and functional interactions of LigD with the DNA end-binding Ku protein.
Zhu H, Shuman S
J Biol Chem 2010 Feb 12;285(7):4815-25
PubMed ID: 20018881