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Protein

DNA ligase 1

Gene

lig-1

Organism
Caenorhabditis elegans
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Protein inferred from homologyi

Functioni

DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair.By similarity

Catalytic activityi

ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m).PROSITE-ProRule annotation

Cofactori

Mg2+By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei37 – 371Interaction with target DNABy similarity
Binding sitei287 – 2871ATPBy similarity
Active sitei289 – 2891N6-AMP-lysine intermediatePROSITE-ProRule annotation
Binding sitei294 – 2941ATPBy similarity
Binding sitei310 – 3101ATPBy similarity
Sitei311 – 3111Interaction with target DNABy similarity
Metal bindingi342 – 3421Magnesium 1By similarity
Metal bindingi439 – 4391Magnesium 2By similarity
Binding sitei444 – 4441ATPBy similarity
Binding sitei457 – 4571ATPBy similarity
Binding sitei463 – 4631ATPBy similarity
Sitei489 – 4891Interaction with target DNABy similarity
Sitei514 – 5141Interaction with target DNABy similarity

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. DNA binding Source: InterPro
  3. DNA ligase (ATP) activity Source: GO_Central
  4. metal ion binding Source: UniProtKB-KW

GO - Biological processi

  1. cell cycle Source: UniProtKB-KW
  2. cell division Source: UniProtKB-KW
  3. DNA biosynthetic process Source: InterPro
  4. DNA ligation Source: GO_Central
  5. DNA ligation involved in DNA repair Source: InterPro
  6. DNA recombination Source: UniProtKB-KW
  7. lagging strand elongation Source: GO_Central
Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

Cell cycle, Cell division, DNA damage, DNA recombination, DNA repair, DNA replication

Keywords - Ligandi

ATP-binding, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

ReactomeiREACT_229565. Processive synthesis on the lagging strand.
REACT_231992. Removal of DNA patch containing abasic residue.
REACT_242854. Gap-filling DNA repair synthesis and ligation in TC-NER.
REACT_243554. Gap-filling DNA repair synthesis and ligation in GG-NER.
REACT_243976. Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha).
REACT_245709. Resolution of D-loop structures through Holliday junction intermediates.
REACT_247610. Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta).

Names & Taxonomyi

Protein namesi
Recommended name:
DNA ligase 1 (EC:6.5.1.1)
Alternative name(s):
DNA ligase I
Polydeoxyribonucleotide synthase [ATP] 1
Gene namesi
Name:lig-1
ORF Names:C29A12.3
OrganismiCaenorhabditis elegans
Taxonomic identifieri6239 [NCBI]
Taxonomic lineageiEukaryotaMetazoaEcdysozoaNematodaChromadoreaRhabditidaRhabditoideaRhabditidaePeloderinaeCaenorhabditis
ProteomesiUP000001940: Chromosome V

Organism-specific databases

WormBaseiC29A12.3a; CE37480; WBGene00002985; lig-1.
C29A12.3b; CE37481; WBGene00002985; lig-1.

Subcellular locationi

Nucleus By similarity

GO - Cellular componenti

  1. chromosome Source: GO_Central
  2. mitochondrion Source: GO_Central
  3. nucleus Source: GO_Central
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 773773DNA ligase 1PRO_0000059583Add
BLAST

Proteomic databases

PaxDbiQ27474.
PRIDEiQ27474.

Interactioni

Protein-protein interaction databases

STRINGi6239.C29A12.3a.

Structurei

3D structure databases

ProteinModelPortaliQ27474.
SMRiQ27474. Positions 13-619.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni180 – 18910Interaction with target DNABy similarity
Regioni362 – 3643Interaction with target DNABy similarity

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi638 – 64811Poly-GluAdd
BLAST
Compositional biasi660 – 762103Lys-richAdd
BLAST

Sequence similaritiesi

Belongs to the ATP-dependent DNA ligase family.Curated

Phylogenomic databases

eggNOGiCOG1793.
GeneTreeiENSGT00780000121970.
HOGENOMiHOG000036006.
InParanoidiQ27474.
KOiK10747.
OMAiPQVVIEV.
OrthoDBiEOG7RFTGN.
PhylomeDBiQ27474.

Family and domain databases

Gene3Di1.10.3260.10. 1 hit.
2.40.50.140. 1 hit.
InterProiIPR000977. DNA_ligase_ATP-dep.
IPR012309. DNA_ligase_ATP-dep_C.
IPR012310. DNA_ligase_ATP-dep_cent.
IPR016059. DNA_ligase_ATP-dep_CS.
IPR012308. DNA_ligase_ATP-dep_N.
IPR012340. NA-bd_OB-fold.
[Graphical view]
PfamiPF04679. DNA_ligase_A_C. 1 hit.
PF01068. DNA_ligase_A_M. 1 hit.
PF04675. DNA_ligase_A_N. 1 hit.
[Graphical view]
SUPFAMiSSF117018. SSF117018. 1 hit.
SSF50249. SSF50249. 1 hit.
TIGRFAMsiTIGR00574. dnl1. 1 hit.
PROSITEiPS00697. DNA_LIGASE_A1. 1 hit.
PS00333. DNA_LIGASE_A2. 1 hit.
PS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. Align

Isoform a (identifier: Q27474-1) [UniParc]FASTAAdd to Basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MFFSKAGKAA VEWAKGSKVP YKEFALTLEK IEELSGKKKV DELAQFFTKV
60 70 80 90 100
LDFSPDDLTA CVYMSVNQLG PSYEGLELGV AENSLIKAVA KATGRTEGKI
110 120 130 140 150
KEDLRAKGDL GTVAQQSRSN QKMLAVPKAL TVPTVFNKLT EIAKLSGTSA
160 170 180 190 200
MNKKVDAISA LLIACQGIEA RFLVRMLAGK MRIGLGEQSV LSALGHAFTL
210 220 230 240 250
SKITDQKVRG DKLDSLKDAN VKRVKTAYCE CPNYNRLIEV ALTEGVEALV
260 270 280 290 300
EKCKLSPGIP LKPMLAHPTK GIDEIMRRFR NQTMTCEWKY DGERGQIHKR
310 320 330 340 350
EDGQIFIYSR NQENNTTKYP DIIEKISSCI GDGVTSFIVD AEVVAIDEAG
360 370 380 390 400
LILPFQVLST RKRKNATDDN GVKVVVFLFD LLYFNGEPLV RKPLRKRREL
410 420 430 440 450
LRTNFKKIDG SFYFATSVDT NDTDEINSFF DEAVQNKCEG LMIKTLDTEA
460 470 480 490 500
TYEISRRSHS WLKMKKDYVD GVGDTLDLVV MGAYSGVGKR TGVYGGYLLG
510 520 530 540 550
CYNPTTEEYE SVCKIGTGFT DEDLAEQYKI LQDKKIDKSP SYYQFDHTLK
560 570 580 590 600
PDDTFSPYLV FEVKCADITI SPRHKAASGL TDDGKGISLR FPRFLRIRDD
610 620 630 640 650
KNSDDATSSE QVLEMYKNQE AFANQKIEKA DAVDEDDEFE EKEDEEEELN
660 670 680 690 700
MTNVSEGSSK ENPVKEEIKK ETPKSVSPKK FEKKPPVKSS PVNKSPVKSS
710 720 730 740 750
PIKKEAEKKK GPVASIFSSS TKKNEKDVKV ESPSPIRKKK LPSDSDESDE
760 770
ETSTNKKQPA KKRSRVAIDS DSD

Note: No experimental confirmation available.

Length:773
Mass (Da):86,310
Last modified:May 24, 2005 - v2
Checksum:i458B676F9FCE0BA0
GO
Isoform b (identifier: Q27474-2) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     208-210: VRG → RMP
     211-773: Missing.

Note: No experimental confirmation available.

Show »
Length:210
Mass (Da):22,716
Checksum:i7384B3AB04FDDF68
GO

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei208 – 2103VRG → RMP in isoform b. CuratedVSP_013778
Alternative sequencei211 – 773563Missing in isoform b. CuratedVSP_013779Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z73970 Genomic DNA. Translation: CAA98242.2.
Z73970 Genomic DNA. Translation: CAD44112.2.
PIRiT19544.
RefSeqiNP_741625.2. NM_171537.3. [Q27474-1]
NP_741626.2. NM_171538.3. [Q27474-2]
UniGeneiCel.23475.

Genome annotation databases

EnsemblMetazoaiC29A12.3a; C29A12.3a; WBGene00002985. [Q27474-1]
GeneIDi179502.
KEGGicel:CELE_C29A12.3.
UCSCiC29A12.3a. c. elegans. [Q27474-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z73970 Genomic DNA. Translation: CAA98242.2.
Z73970 Genomic DNA. Translation: CAD44112.2.
PIRiT19544.
RefSeqiNP_741625.2. NM_171537.3. [Q27474-1]
NP_741626.2. NM_171538.3. [Q27474-2]
UniGeneiCel.23475.

3D structure databases

ProteinModelPortaliQ27474.
SMRiQ27474. Positions 13-619.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi6239.C29A12.3a.

Proteomic databases

PaxDbiQ27474.
PRIDEiQ27474.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblMetazoaiC29A12.3a; C29A12.3a; WBGene00002985. [Q27474-1]
GeneIDi179502.
KEGGicel:CELE_C29A12.3.
UCSCiC29A12.3a. c. elegans. [Q27474-1]

Organism-specific databases

CTDi179502.
WormBaseiC29A12.3a; CE37480; WBGene00002985; lig-1.
C29A12.3b; CE37481; WBGene00002985; lig-1.

Phylogenomic databases

eggNOGiCOG1793.
GeneTreeiENSGT00780000121970.
HOGENOMiHOG000036006.
InParanoidiQ27474.
KOiK10747.
OMAiPQVVIEV.
OrthoDBiEOG7RFTGN.
PhylomeDBiQ27474.

Enzyme and pathway databases

ReactomeiREACT_229565. Processive synthesis on the lagging strand.
REACT_231992. Removal of DNA patch containing abasic residue.
REACT_242854. Gap-filling DNA repair synthesis and ligation in TC-NER.
REACT_243554. Gap-filling DNA repair synthesis and ligation in GG-NER.
REACT_243976. Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha).
REACT_245709. Resolution of D-loop structures through Holliday junction intermediates.
REACT_247610. Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta).

Miscellaneous databases

NextBioi905678.
PROiQ27474.

Family and domain databases

Gene3Di1.10.3260.10. 1 hit.
2.40.50.140. 1 hit.
InterProiIPR000977. DNA_ligase_ATP-dep.
IPR012309. DNA_ligase_ATP-dep_C.
IPR012310. DNA_ligase_ATP-dep_cent.
IPR016059. DNA_ligase_ATP-dep_CS.
IPR012308. DNA_ligase_ATP-dep_N.
IPR012340. NA-bd_OB-fold.
[Graphical view]
PfamiPF04679. DNA_ligase_A_C. 1 hit.
PF01068. DNA_ligase_A_M. 1 hit.
PF04675. DNA_ligase_A_N. 1 hit.
[Graphical view]
SUPFAMiSSF117018. SSF117018. 1 hit.
SSF50249. SSF50249. 1 hit.
TIGRFAMsiTIGR00574. dnl1. 1 hit.
PROSITEiPS00697. DNA_LIGASE_A1. 1 hit.
PS00333. DNA_LIGASE_A2. 1 hit.
PS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Genome sequence of the nematode C. elegans: a platform for investigating biology."
    The C. elegans sequencing consortium
    Science 282:2012-2018(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], ALTERNATIVE SPLICING.
    Strain: Bristol N2.

Entry informationi

Entry nameiDNLI1_CAEEL
AccessioniPrimary (citable) accession number: Q27474
Secondary accession number(s): Q8MQB3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: May 24, 2005
Last modified: February 4, 2015
This is version 113 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programCaenorhabditis annotation project

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Caenorhabditis elegans
    Caenorhabditis elegans: entries, gene names and cross-references to WormBase
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.