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Protein

DNA ligase

Gene

ligA

Organism
Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

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.UniRule annotation

Catalytic activityi

NAD+ + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + beta-nicotinamide D-ribonucleotide + (deoxyribonucleotide)(n+m).UniRule annotation

Cofactori

Mg2+UniRule annotation, Mn2+UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei114 – 1141NADUniRule annotation
Active sitei116 – 1161N6-AMP-lysine intermediateUniRule annotation
Binding sitei137 – 1371NADUniRule annotation
Binding sitei174 – 1741NADUniRule annotation
Binding sitei291 – 2911NADUniRule annotation
Binding sitei315 – 3151NADUniRule annotation
Metal bindingi409 – 4091ZincUniRule annotation
Metal bindingi412 – 4121ZincUniRule annotation
Metal bindingi427 – 4271ZincUniRule annotation
Metal bindingi433 – 4331ZincUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi32 – 365NADUniRule annotation
Nucleotide bindingi81 – 822NADUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

DNA damage, DNA repair, DNA replication

Keywords - Ligandi

Magnesium, Manganese, Metal-binding, NAD, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
DNA ligaseUniRule annotation (EC:6.5.1.2UniRule annotation)
Alternative name(s):
Polydeoxyribonucleotide synthase [NAD(+)]UniRule annotation
Gene namesi
Name:ligAUniRule annotation
Synonyms:lig, ligN
Ordered Locus Names:HI_1100
OrganismiHaemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
Taxonomic identifieri71421 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPasteurellalesPasteurellaceaeHaemophilus
Proteomesi
  • UP000000579 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 670670DNA ligasePRO_0000161746Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi71421.HI1100.

Structurei

Secondary structure

1
670
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi4 – 2320Combined sources
Helixi32 – 4817Combined sources
Helixi50 – 523Combined sources
Helixi58 – 603Combined sources
Beta strandi72 – 743Combined sources
Helixi88 – 10114Combined sources
Beta strandi102 – 1043Combined sources
Beta strandi110 – 12718Combined sources
Beta strandi130 – 1367Combined sources
Beta strandi140 – 1456Combined sources
Helixi147 – 1515Combined sources
Beta strandi161 – 1644Combined sources
Beta strandi167 – 17610Combined sources
Helixi179 – 19113Combined sources
Helixi200 – 2089Combined sources
Helixi213 – 2164Combined sources
Beta strandi222 – 23312Combined sources
Helixi240 – 24910Combined sources
Beta strandi259 – 2635Combined sources
Helixi264 – 27613Combined sources
Turni277 – 2815Combined sources
Beta strandi285 – 29410Combined sources
Helixi295 – 3017Combined sources
Beta strandi311 – 3155Combined sources
Helixi319 – 3213Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3BACX-ray3.00A64-327[»]
3PN1X-ray2.00A1-318[»]
3UQ8X-ray1.70A3-324[»]
4UCOX-ray2.50A1-324[»]
4UCRX-ray2.15A1-324[»]
4UCSX-ray1.90A1-324[»]
4UCTX-ray2.10A1-324[»]
4UCUX-ray2.10A1-324[»]
4UCVX-ray2.60A1-324[»]
4UFZX-ray2.33A1-324[»]
ProteinModelPortaliP43813.
SMRiP43813. Positions 1-584.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP43813.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini592 – 67079BRCTUniRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the NAD-dependent DNA ligase family. LigA subfamily.UniRule annotation
Contains 1 BRCT domain.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105C77. Bacteria.
COG0272. LUCA.
KOiK01972.
OMAiFTAKSPR.
PhylomeDBiP43813.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
3.40.50.10190. 1 hit.
HAMAPiMF_01588. DNA_ligase_A. 1 hit.
InterProiIPR001357. BRCT_dom.
IPR018239. DNA_ligase_AS.
IPR033136. DNA_ligase_CS.
IPR001679. DNAligase.
IPR013839. DNAligase_adenylation.
IPR013840. DNAligase_N.
IPR003583. Hlx-hairpin-Hlx_DNA-bd_motif.
IPR012340. NA-bd_OB-fold.
IPR004150. NAD_DNA_ligase_OB.
IPR010994. RuvA_2-like.
IPR004149. Znf_DNAligase_C4.
[Graphical view]
PfamiPF00533. BRCT. 1 hit.
PF01653. DNA_ligase_aden. 1 hit.
PF03120. DNA_ligase_OB. 1 hit.
PF03119. DNA_ligase_ZBD. 1 hit.
[Graphical view]
PIRSFiPIRSF001604. LigA. 1 hit.
SMARTiSM00292. BRCT. 1 hit.
SM00278. HhH1. 4 hits.
SM00532. LIGANc. 1 hit.
[Graphical view]
SUPFAMiSSF47781. SSF47781. 1 hit.
SSF50249. SSF50249. 1 hit.
SSF52113. SSF52113. 1 hit.
TIGRFAMsiTIGR00575. dnlj. 1 hit.
PROSITEiPS50172. BRCT. 1 hit.
PS01055. DNA_LIGASE_N1. 1 hit.
PS01056. DNA_LIGASE_N2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P43813-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTNIQTQLDN LRKTLRQYEY EYHVLDNPSV PDSEYDRLFH QLKALELEHP
60 70 80 90 100
EFLTSDSPTQ RVGAKPLSGF SQIRHEIPML SLDNAFSDAE FNAFVKRIED
110 120 130 140 150
RLILLPKPLT FCCEPKLDGL AVSILYVNGE LTQAATRGDG TTGEDITANI
160 170 180 190 200
RTIRNVPLQL LTDNPPARLE VRGEVFMPHA GFERLNKYAL EHNEKTFANP
210 220 230 240 250
RNAAAGSLRQ LDPNITSKRP LVLNAYGIGI AEGVDLPTTH YARLQWLKSI
260 270 280 290 300
GIPVNPEIRL CNGADEVLGF YRDIQNKRSS LGYDIDGTVL KINDIALQNE
310 320 330 340 350
LGFISKAPRW AIAYKFPAQE ELTLLNDVEF QVGRTGAITP VAKLEPVFVA
360 370 380 390 400
GVTVSNATLH NGDEIERLNI AIGDTVVIRR AGDVIPQIIG VLHERRPDNA
410 420 430 440 450
KPIIFPTNCP VCDSQIIRIE GEAVARCTGG LFCAAQRKEA LKHFVSRKAM
460 470 480 490 500
DIDGVGGKLI EQLVDRELIH TPADLFKLDL TTLTRLERMG AKSAENALNS
510 520 530 540 550
LENAKSTTLA RFIFALGIRE VGEATALNLA NHFKTLDALK DANLEELQQV
560 570 580 590 600
PDVGEVVANR IFIFWREAHN VAVVEDLIAQ GVHWETVEVK EASENLFKDK
610 620 630 640 650
TVVLTGTLTQ MGRNEAKALL QQLGAKVSGS VSSKTDFVIA GDAAGSKLAK
660 670
AQELNITVLT EEEFLAQITR
Length:670
Mass (Da):74,043
Last modified:January 15, 2008 - v2
Checksum:iA4110EE380A76C9C
GO

Sequence cautioni

The sequence AAC22753 differs from that shown. Reason: Erroneous initiation. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L42023 Genomic DNA. Translation: AAC22753.1. Different initiation.
PIRiD64182.
RefSeqiNP_439257.2. NC_000907.1.
WP_005665886.1. NC_000907.1.

Genome annotation databases

EnsemblBacteriaiAAC22753; AAC22753; HI_1100.
GeneIDi950070.
KEGGihin:HI1100.
PATRICi20190867. VBIHaeInf48452_1146.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L42023 Genomic DNA. Translation: AAC22753.1. Different initiation.
PIRiD64182.
RefSeqiNP_439257.2. NC_000907.1.
WP_005665886.1. NC_000907.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3BACX-ray3.00A64-327[»]
3PN1X-ray2.00A1-318[»]
3UQ8X-ray1.70A3-324[»]
4UCOX-ray2.50A1-324[»]
4UCRX-ray2.15A1-324[»]
4UCSX-ray1.90A1-324[»]
4UCTX-ray2.10A1-324[»]
4UCUX-ray2.10A1-324[»]
4UCVX-ray2.60A1-324[»]
4UFZX-ray2.33A1-324[»]
ProteinModelPortaliP43813.
SMRiP43813. Positions 1-584.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi71421.HI1100.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC22753; AAC22753; HI_1100.
GeneIDi950070.
KEGGihin:HI1100.
PATRICi20190867. VBIHaeInf48452_1146.

Phylogenomic databases

eggNOGiENOG4105C77. Bacteria.
COG0272. LUCA.
KOiK01972.
OMAiFTAKSPR.
PhylomeDBiP43813.

Miscellaneous databases

EvolutionaryTraceiP43813.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
3.40.50.10190. 1 hit.
HAMAPiMF_01588. DNA_ligase_A. 1 hit.
InterProiIPR001357. BRCT_dom.
IPR018239. DNA_ligase_AS.
IPR033136. DNA_ligase_CS.
IPR001679. DNAligase.
IPR013839. DNAligase_adenylation.
IPR013840. DNAligase_N.
IPR003583. Hlx-hairpin-Hlx_DNA-bd_motif.
IPR012340. NA-bd_OB-fold.
IPR004150. NAD_DNA_ligase_OB.
IPR010994. RuvA_2-like.
IPR004149. Znf_DNAligase_C4.
[Graphical view]
PfamiPF00533. BRCT. 1 hit.
PF01653. DNA_ligase_aden. 1 hit.
PF03120. DNA_ligase_OB. 1 hit.
PF03119. DNA_ligase_ZBD. 1 hit.
[Graphical view]
PIRSFiPIRSF001604. LigA. 1 hit.
SMARTiSM00292. BRCT. 1 hit.
SM00278. HhH1. 4 hits.
SM00532. LIGANc. 1 hit.
[Graphical view]
SUPFAMiSSF47781. SSF47781. 1 hit.
SSF50249. SSF50249. 1 hit.
SSF52113. SSF52113. 1 hit.
TIGRFAMsiTIGR00575. dnlj. 1 hit.
PROSITEiPS50172. BRCT. 1 hit.
PS01055. DNA_LIGASE_N1. 1 hit.
PS01056. DNA_LIGASE_N2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDNLJ_HAEIN
AccessioniPrimary (citable) accession number: P43813
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: January 15, 2008
Last modified: September 7, 2016
This is version 117 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Haemophilus influenzae
    Haemophilus influenzae (strain Rd): entries and gene names
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.