Reviewed,
UniProtKB/Swiss-Prot Q1IHJ4 (DNLJ_ACIBL)
Last modified
February 9, 2010.
Version 33.
History...
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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents
Names and origin
| Protein names | Recommended name: DNA ligase EC=6.5.1.2 Alternative name(s): Polydeoxyribonucleotide synthase [NAD+] | ||||
| Gene names |
| ||||
| Organism | Acidobacteria bacterium (strain Ellin345) [Complete proteome] [HAMAP] | ||||
| Taxonomic identifier | 204669 [NCBI] | ||||
| Taxonomic lineage | Bacteria › Acidobacteria › Candidatus Koribacter |
Protein attributes
| Sequence length | 673 AA. |
| Sequence status | Complete. |
| Protein existence | Inferred from homology. |
General annotation (Comments)
| Function | DNA ligase that catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA By similarity. HAMAP MF_01588 |
| Catalytic activity | NAD+ + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + nicotinamide nucleotide + (deoxyribonucleotide)(n+m). HAMAP MF_01588 |
| Cofactor | Magnesium or manganese By similarity. HAMAP MF_01588 |
| Sequence similarities | Belongs to the NAD-dependent DNA ligase family. LigA subfamily. Contains 1 BRCT domain. |
Ontologies
| Keywords | |
|---|---|
| Biological process | DNA damage DNA repair DNA replication |
| Ligand | Magnesium Manganese Metal-binding NAD Zinc |
| Molecular function | Ligase |
| Technical term | Complete proteome |
| Gene Ontology (GO) | |
| Biological process | DNA repair Inferred from electronic annotation. Source: UniProtKB-KW DNA replicationInferred from electronic annotation. Source: UniProtKB-KW |
| Cellular component | intracellular Inferred from electronic annotation. Source: InterPro |
| Molecular function | DNA binding Inferred from electronic annotation. Source: InterPro DNA ligase (NAD+) activityInferred from electronic annotation. Source: HAMAP magnesium ion bindingInferred from electronic annotation. Source: UniProtKB-KW manganese ion bindingInferred from electronic annotation. Source: UniProtKB-KW zinc ion bindingInferred from electronic annotation. Source: UniProtKB-KW |
| Complete GO annotation... | |
Sequence annotation (Features)
| Feature key | Position(s) | Length | Description | Graphical view | Feature identifier | ||||
Molecule processing | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Chain | 1 – 673 | 673 | DNA ligase HAMAP MF_01588 | PRO_0000313097 | |||||
Regions | |||||||||
| Domain | 595 – 673 | 79 | BRCT | ||||||
| Nucleotide binding | 35 – 39 | 5 | NAD By similarity | ||||||
| Nucleotide binding | 84 – 85 | 2 | NAD By similarity | ||||||
Sites | |||||||||
| Active site | 117 | 1 | N6-AMP-lysine intermediate By similarity | ||||||
| Metal binding | 415 | 1 | Zinc By similarity | ||||||
| Metal binding | 418 | 1 | Zinc By similarity | ||||||
| Metal binding | 433 | 1 | Zinc By similarity | ||||||
| Metal binding | 438 | 1 | Zinc By similarity | ||||||
| Binding site | 115 | 1 | NAD By similarity | ||||||
| Binding site | 138 | 1 | NAD By similarity | ||||||
| Binding site | 180 | 1 | NAD By similarity | ||||||
| Binding site | 296 | 1 | NAD By similarity | ||||||
| Binding site | 320 | 1 | NAD By similarity | ||||||
Sequences
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References
| [1] | "Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils." Ward N.L., Challacombe J.F., Janssen P.H., Henrissat B., Coutinho P.M., Wu M., Xie G., Haft D.H., Sait M., Badger J., Barabote R.D., Bradley B., Brettin T.S., Brinkac L.M., Bruce D., Creasy T., Daugherty S.C., Davidsen T.M.  Kuske C.R.Appl. Environ. Microbiol. 75:2046-2056(2009) [PubMed: 19201974] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. |
Cross-references
Sequence databases | |
|---|---|
| EMBL GenBank DDBJ | CP000360 Genomic DNA. Translation: ABF43656.1. |
| RefSeq | YP_593730.1. |
3D structure databases | |
| SMR | Q1IHJ4. Positions 6-323, 8-590, 596-671. |
| ModBase | Search... |
Protein-protein interaction databases | |
| STRING | Q1IHJ4. |
Genome annotation databases | |
| GeneID | 4070813. |
| GenomeReviews | Gene locus Acid345_4656 in contig CP000360_GR. |
| KEGG | aba:Acid345_4656. |
| NMPDR | fig|204669.6.peg.4633. |
Organism-specific databases | |
| CMR | Search... |
Phylogenomic databases | |
| eggNOG | COG0272. |
| HOGENOM | HBG620317. |
| OMA | IKHFASR. |
| PhylomeDB | Q1IHJ4. |
Enzyme and pathway databases | |
| BioCyc | ABAC204669:ACID345_4656-MONOMER. |
Family and domain databases | |
| HAMAP | MF_01588. DNA_ligase_A. [Tree] |
| InterPro | IPR001357. BRCT. IPR018239. DNA_ligase_AS. IPR004150. DNA_ligase_OB. IPR001679. DNAligase. IPR013839. DNAligase_adenylation. IPR013840. DNAligase_N. IPR003583. Hlx-hairpin-Hlx_DNA-bd_motif. IPR012340. NA-bd_OB-fold. IPR016027. NA-bd_OB-fold-like. IPR010994. RuvA_2-like. IPR004149. Znf_DNAligase_C4. [Graphical view] |
| Gene3D | G3DSA:2.40.50.140. OB_NA_bd_sub. 1 hit. |
| Pfam | PF00533. BRCT. 1 hit. PF01653. DNA_ligase_aden. 1 hit. PF03120. DNA_ligase_OB. 1 hit. PF03119. DNA_ligase_ZBD. 1 hit. [Graphical view] |
| PIRSF | PIRSF001604. LigA. 1 hit. |
| SMART | SM00292. BRCT. 1 hit. SM00278. HhH1. 3 hits. SM00532. LIGANc. 1 hit. [Graphical view] |
| TIGRFAMs | TIGR00575. dnlj. 1 hit. |
| PROSITE | PS50172. BRCT. 1 hit. PS01055. DNA_LIGASE_N1. False negative. PS01056. DNA_LIGASE_N2. 1 hit. [Graphical view] |
| ProtoNet | Search... |
Entry information
| Entry name | DNLJ_ACIBL | ||||||||
| Accession | Primary (citable) accession number: Q1IHJ4 | ||||||||
| Entry history |
| ||||||||
| Entry status | Reviewed (UniProtKB/Swiss-Prot) | ||||||||
| Annotation project | HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes) | ||||||||
