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Protein

DNA ligase

Gene

lig

Organism
Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

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 sitei247 – 2471ATPUniRule annotation
Active sitei249 – 2491N6-AMP-lysine intermediateUniRule annotation
Binding sitei254 – 2541ATPUniRule annotation
Binding sitei269 – 2691ATPUniRule annotation
Binding sitei298 – 2981ATPUniRule annotation
Binding sitei337 – 3371ATPUniRule annotation
Binding sitei411 – 4111ATPUniRule annotation
Binding sitei417 – 4171ATPUniRule 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

BioCyciAFUL224325:GJBC-638-MONOMER.
BRENDAi6.5.1.1. 414.

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:AF_0623
OrganismiArchaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
Taxonomic identifieri224325 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaArchaeoglobiArchaeoglobalesArchaeoglobaceaeArchaeoglobus
ProteomesiUP000002199 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 555555DNA ligasePRO_0000059601Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi224325.AF0623.

Structurei

Secondary structure

1
555
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi3 – 1311Combined sources
Helixi19 – 3113Combined sources
Helixi36 – 4611Combined sources
Helixi63 – 7412Combined sources
Helixi78 – 8811Combined sources
Helixi91 – 10515Combined sources
Helixi114 – 12613Combined sources
Helixi132 – 14615Combined sources
Helixi149 – 15911Combined sources
Helixi169 – 17911Combined sources
Helixi184 – 19411Combined sources
Helixi197 – 21317Combined sources
Beta strandi227 – 2304Combined sources
Helixi234 – 2407Combined sources
Beta strandi241 – 2499Combined sources
Beta strandi251 – 2599Combined sources
Beta strandi265 – 2684Combined sources
Helixi275 – 2773Combined sources
Helixi279 – 28810Combined sources
Beta strandi291 – 30313Combined sources
Beta strandi306 – 3083Combined sources
Helixi310 – 3189Combined sources
Helixi324 – 3296Combined sources
Beta strandi332 – 34514Combined sources
Helixi351 – 36111Combined sources
Beta strandi366 – 3705Combined sources
Beta strandi373 – 3775Combined sources
Helixi379 – 39113Combined sources
Beta strandi396 – 4005Combined sources
Beta strandi411 – 42111Combined sources
Beta strandi425 – 43410Combined sources
Helixi439 – 4413Combined sources
Beta strandi442 – 45110Combined sources
Turni453 – 4553Combined sources
Beta strandi458 – 4647Combined sources
Helixi470 – 48011Combined sources
Helixi481 – 4833Combined sources
Beta strandi484 – 4885Combined sources
Beta strandi491 – 4944Combined sources
Beta strandi499 – 5035Combined sources
Beta strandi505 – 5095Combined sources
Beta strandi511 – 5133Combined sources
Beta strandi516 – 5216Combined sources
Beta strandi523 – 5275Combined sources
Helixi533 – 5353Combined sources
Helixi539 – 5479Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3GDEX-ray2.30A1-555[»]
ProteinModelPortaliO29632.
SMRiO29632. Positions 1-554.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO29632.

Family & Domainsi

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG1793.
KOiK10747.
OMAiGRPRPFQ.

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.

O29632-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLFAEFAEFC ERLEKISSTL ELTARIAAFL QKIEDERDLY DVVLFITGKV
60 70 80 90 100
YPPWDERELG VGIGLLYEAL ENVSGVKRSE IESMIREYGD LGLVAEQLIK
110 120 130 140 150
KKKMTTLAFE ELTVRKVRET FDEIASLTGE GSMKRKIMLL TGLYGLATPL
160 170 180 190 200
EARYLTRLIL NEMRLGVGEG IMRDAIARAF RADPETVERA YMITNDLGRV
210 220 230 240 250
AVVAKKEGEE GLRKMKIEIH IPVRMMLAQV AESLESAVRE MRTAAVEWKF
260 270 280 290 300
DGSRVQVHWD GSRVTIYSRR LENVTNALPD IVEEIKKSVK PGVILDGEVI
310 320 330 340 350
AVKEGKPMPF QHVLRRFRRK HDVAKMVEKI PLEAHFFDIL YHDGECIDLP
360 370 380 390 400
LRERRKLLES AVNESEKIKL AKQIVTDSVD EVRKMYDEAI SAGHEGVMIK
410 420 430 440 450
LPSSPYIPGK RGKNWLKVKA IMETLDLVVV GGEWGEGKRS HWLSSFELAC
460 470 480 490 500
LDPVTGKLLK VGRVATGFTE EDLEELTEMF RPLIVSQQGK KVEFIPKYVF
510 520 530 540 550
EVAYQEIQKS PKYESGYALR FPRFVRLRDD KDVDEADTIE RVENLYKLQF

EVKRQ
Length:555
Mass (Da):63,553
Last modified:June 20, 2001 - v2
Checksum:iD050FE80B2341EDB
GO

Sequence cautioni

The sequence AAB90616.1 differs from that shown. Reason: Erroneous initiation. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000782 Genomic DNA. Translation: AAB90616.1. Different initiation.
PIRiG69327.
RefSeqiNP_069457.1. NC_000917.1.

Genome annotation databases

EnsemblBacteriaiAAB90616; AAB90616; AF_0623.
GeneIDi1483841.
KEGGiafu:AF0623.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000782 Genomic DNA. Translation: AAB90616.1. Different initiation.
PIRiG69327.
RefSeqiNP_069457.1. NC_000917.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3GDEX-ray2.30A1-555[»]
ProteinModelPortaliO29632.
SMRiO29632. Positions 1-554.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224325.AF0623.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAB90616; AAB90616; AF_0623.
GeneIDi1483841.
KEGGiafu:AF0623.

Phylogenomic databases

eggNOGiCOG1793.
KOiK10747.
OMAiGRPRPFQ.

Enzyme and pathway databases

BioCyciAFUL224325:GJBC-638-MONOMER.
BRENDAi6.5.1.1. 414.

Miscellaneous databases

EvolutionaryTraceiO29632.

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 complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus."
    Klenk H.-P., Clayton R.A., Tomb J.-F., White O., Nelson K.E., Ketchum K.A., Dodson R.J., Gwinn M.L., Hickey E.K., Peterson J.D., Richardson D.L., Kerlavage A.R., Graham D.E., Kyrpides N.C., Fleischmann R.D., Quackenbush J., Lee N.H., Sutton G.G.
    , Gill S.R., Kirkness E.F., Dougherty B.A., McKenney K., Adams M.D., Loftus B.J., Peterson S.N., Reich C.I., McNeil L.K., Badger J.H., Glodek A., Zhou L., Overbeek R., Gocayne J.D., Weidman J.F., McDonald L.A., Utterback T.R., Cotton M.D., Spriggs T., Artiach P., Kaine B.P., Sykes S.M., Sadow P.W., D'Andrea K.P., Bowman C., Fujii C., Garland S.A., Mason T.M., Olsen G.J., Fraser C.M., Smith H.O., Woese C.R., Venter J.C.
    Nature 390:364-370(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126.

Entry informationi

Entry nameiDNLI_ARCFU
AccessioniPrimary (citable) accession number: O29632
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1999
Last sequence update: June 20, 2001
Last modified: April 1, 2015
This is version 101 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  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.