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Protein

DNA ligase

Gene

lig

Organism
Metallosphaera sedula (strain ATCC 51363 / DSM 5348)
Status
Reviewed-Annotation score: Annotation score: 3 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.UniRule annotation

Catalytic activityi

ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m).UniRule annotation

Cofactori

Mg2+UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei259 – 2591ATPUniRule annotation
Active sitei261 – 2611N6-AMP-lysine intermediateUniRule annotation
Binding sitei266 – 2661ATPUniRule annotation
Binding sitei281 – 2811ATPUniRule annotation
Binding sitei311 – 3111ATPUniRule annotation
Binding sitei351 – 3511ATPUniRule annotation
Binding sitei428 – 4281ATPUniRule annotation
Binding sitei434 – 4341ATPUniRule annotation

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-HAMAP
  2. DNA binding Source: InterPro
  3. DNA ligase (ATP) activity Source: UniProtKB-HAMAP
  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 involved in DNA repair Source: InterPro
  5. DNA recombination Source: UniProtKB-HAMAP
  6. DNA replication Source: UniProtKB-HAMAP
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

BioCyciMSED399549:GH1O-160-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA ligaseUniRule annotation (EC:6.5.1.1UniRule annotation)
Alternative name(s):
Polydeoxyribonucleotide synthase [ATP]UniRule annotation
Gene namesi
Name:ligUniRule annotation
Ordered Locus Names:Msed_0150
OrganismiMetallosphaera sedula (strain ATCC 51363 / DSM 5348)
Taxonomic identifieri399549 [NCBI]
Taxonomic lineageiArchaeaCrenarchaeotaThermoproteiSulfolobalesSulfolobaceaeMetallosphaera
ProteomesiUP000000242 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 598598DNA ligasePRO_1000072271Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi399549.Msed_0150.

Structurei

3D structure databases

ProteinModelPortaliA4YD25.
SMRiA4YD25. Positions 1-588.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the ATP-dependent DNA ligase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG1793.
HOGENOMiHOG000036008.
KOiK10747.
OMAiPQVVIEV.

Family and domain databases

Gene3Di1.10.3260.10. 1 hit.
2.40.50.140. 1 hit.
HAMAPiMF_00407. DNA_ligase.
InterProiIPR022865. DNA_ligae_ATP-dep_bac/arc.
IPR000977. 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]

Sequencei

Sequence statusi: Complete.

A4YD25-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKFKLIAEYF DRLEKISSRI QLTSLLSDLF KNTEREVIDK VVYLIQGRLW
60 70 80 90 100
PDFTGMPEIG MGEKFLIKAI AMAYGNKEEE VEKLYKNIGD LGEVAYSLRS
110 120 130 140 150
KVKGVSILSF VGGNQEAGEL DVMEVYNELV KIATSTGEGS RDIKIRIFAG
160 170 180 190 200
LIKKATPIEA KYLVRFVEGR LRLGIGDATV LDALAITFGG SADYRPIVER
210 220 230 240 250
AYNLRADLGD IARVIATEGI EKLKNISPTP GIPIRPMLAE RLPDPEEIME
260 270 280 290 300
KMNGKALVDY KYDGERAQIH RKGDKVTIFS RRMENITDQY IDVTEYVKQF
310 320 330 340 350
VKGDNFIVEG EIVPVDPESG EMRPFQELMH RRRKNNIAEA IKEYPVNLFL
360 370 380 390 400
FDLMFFEGED YTTKPLPERR AKLEEILASN DKVHIASHII ADRVDKLREY
410 420 430 440 450
FYQAISEGAE GVMVKSIGPD SIYQAGSRGW LWIKLKRDYQ SEMADTVDLV
460 470 480 490 500
VVGAFYGKGK RGGKFSSLLM AAYNPEKDVF ETVCKVASGF SDQELDEMQK
510 520 530 540 550
KINELKREQK HPRVVSDMIP DVWVSPTLVA EVIGAEITIS PLHTCCRGEK
560 570 580 590
GGLSIRFPRF IRWRDDKSPE DATTNQEIME MYSKQLKKIE EKPVDENI
Length:598
Mass (Da):67,922
Last modified:May 29, 2007 - v1
Checksum:iA9C70DF05DA44BB0
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000682 Genomic DNA. Translation: ABP94327.1.
RefSeqiWP_011921295.1. NC_009440.1.
YP_001190251.1. NC_009440.1.

Genome annotation databases

EnsemblBacteriaiABP94327; ABP94327; Msed_0150.
GeneIDi5105003.
KEGGimse:Msed_0150.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000682 Genomic DNA. Translation: ABP94327.1.
RefSeqiWP_011921295.1. NC_009440.1.
YP_001190251.1. NC_009440.1.

3D structure databases

ProteinModelPortaliA4YD25.
SMRiA4YD25. Positions 1-588.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi399549.Msed_0150.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABP94327; ABP94327; Msed_0150.
GeneIDi5105003.
KEGGimse:Msed_0150.

Phylogenomic databases

eggNOGiCOG1793.
HOGENOMiHOG000036008.
KOiK10747.
OMAiPQVVIEV.

Enzyme and pathway databases

BioCyciMSED399549:GH1O-160-MONOMER.

Family and domain databases

Gene3Di1.10.3260.10. 1 hit.
2.40.50.140. 1 hit.
HAMAPiMF_00407. DNA_ligase.
InterProiIPR022865. DNA_ligae_ATP-dep_bac/arc.
IPR000977. 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. "The genome sequence of the metal-mobilizing, extremely thermoacidophilic archaeon Metallosphaera sedula provides insights into bioleaching-associated metabolism."
    Auernik K.S., Maezato Y., Blum P.H., Kelly R.M.
    Appl. Environ. Microbiol. 74:682-692(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 51363 / DSM 5348.

Entry informationi

Entry nameiDNLI_METS5
AccessioniPrimary (citable) accession number: A4YD25
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 26, 2008
Last sequence update: May 29, 2007
Last modified: April 29, 2015
This is version 58 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. 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.