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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)DescriptionActionsGraphical viewLength
Binding sitei114NADUniRule annotation1
Active sitei116N6-AMP-lysine intermediateUniRule annotation1
Binding sitei137NADUniRule annotation1
Binding sitei174NADUniRule annotation1
Binding sitei291NADUniRule annotation1
Binding sitei315NADUniRule annotation1
Metal bindingi409ZincUniRule annotation1
Metal bindingi412ZincUniRule annotation1
Metal bindingi427ZincUniRule annotation1
Metal bindingi433ZincUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi32 – 36NADUniRule annotation5
Nucleotide bindingi81 – 82NADUniRule annotation2

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)DescriptionActionsGraphical viewLength
ChainiPRO_00001617461 – 670DNA ligaseAdd BLAST670

Interactioni

Protein-protein interaction databases

STRINGi71421.HI1100.

Structurei

Secondary structure

1670
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi4 – 23Combined sources20
Helixi32 – 48Combined sources17
Helixi50 – 52Combined sources3
Helixi58 – 60Combined sources3
Beta strandi72 – 74Combined sources3
Helixi88 – 101Combined sources14
Beta strandi102 – 104Combined sources3
Beta strandi110 – 127Combined sources18
Beta strandi130 – 136Combined sources7
Beta strandi140 – 145Combined sources6
Helixi147 – 151Combined sources5
Beta strandi161 – 164Combined sources4
Beta strandi167 – 176Combined sources10
Helixi179 – 191Combined sources13
Helixi200 – 208Combined sources9
Helixi213 – 216Combined sources4
Beta strandi222 – 233Combined sources12
Helixi240 – 249Combined sources10
Beta strandi259 – 263Combined sources5
Helixi264 – 276Combined sources13
Turni277 – 281Combined sources5
Beta strandi285 – 294Combined sources10
Helixi295 – 301Combined sources7
Beta strandi311 – 315Combined sources5
Helixi319 – 321Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP43813.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini592 – 670BRCTUniRule annotationAdd BLAST79

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

CDDicd00027. BRCT. 1 hit.
Gene3Di3.40.50.10190. 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
PDB 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.
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

CDDicd00027. BRCT. 1 hit.
Gene3Di3.40.50.10190. 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: November 30, 2016
This is version 120 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.