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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)-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)(m) = (deoxyribonucleotide)(n+m) + AMP + diphosphate.UniRule annotation

Cofactori

Mg2+UniRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei247ATPUniRule annotation1
Active sitei249N6-AMP-lysine intermediateUniRule annotation1
Binding sitei254ATPUniRule annotation1
Binding sitei269ATPUniRule annotation1
Binding sitei298ATPUniRule annotation1
Binding sitei337ATPUniRule annotation1
Binding sitei411ATPUniRule annotation1
Binding sitei417ATPUniRule annotation1

GO - Molecular functioni

GO - Biological processi

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

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
Proteomesi
  • UP000002199 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000596011 – 555DNA ligaseAdd BLAST555

Interactioni

Protein-protein interaction databases

STRINGi224325.AF0623.

Structurei

Secondary structure

1555
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi3 – 13Combined sources11
Helixi19 – 31Combined sources13
Helixi36 – 46Combined sources11
Helixi63 – 74Combined sources12
Helixi78 – 88Combined sources11
Helixi91 – 105Combined sources15
Helixi114 – 126Combined sources13
Helixi132 – 146Combined sources15
Helixi149 – 159Combined sources11
Helixi169 – 179Combined sources11
Helixi184 – 194Combined sources11
Helixi197 – 213Combined sources17
Beta strandi227 – 230Combined sources4
Helixi234 – 240Combined sources7
Beta strandi241 – 249Combined sources9
Beta strandi251 – 259Combined sources9
Beta strandi265 – 268Combined sources4
Helixi275 – 277Combined sources3
Helixi279 – 288Combined sources10
Beta strandi291 – 303Combined sources13
Beta strandi306 – 308Combined sources3
Helixi310 – 318Combined sources9
Helixi324 – 329Combined sources6
Beta strandi332 – 345Combined sources14
Helixi351 – 361Combined sources11
Beta strandi366 – 370Combined sources5
Beta strandi373 – 377Combined sources5
Helixi379 – 391Combined sources13
Beta strandi396 – 400Combined sources5
Beta strandi411 – 421Combined sources11
Beta strandi425 – 434Combined sources10
Helixi439 – 441Combined sources3
Beta strandi442 – 451Combined sources10
Turni453 – 455Combined sources3
Beta strandi458 – 464Combined sources7
Helixi470 – 480Combined sources11
Helixi481 – 483Combined sources3
Beta strandi484 – 488Combined sources5
Beta strandi491 – 494Combined sources4
Beta strandi499 – 503Combined sources5
Beta strandi505 – 509Combined sources5
Beta strandi511 – 513Combined sources3
Beta strandi516 – 521Combined sources6
Beta strandi523 – 527Combined sources5
Helixi533 – 535Combined sources3
Helixi539 – 547Combined sources9

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiO29632.

Family & Domainsi

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiarCOG01347. Archaea.
COG1793. LUCA.
KOiK10747.
OMAiDVETLDC.

Family and domain databases

Gene3Di1.10.3260.10. 1 hit.
HAMAPiMF_00407. DNA_ligase. 1 hit.
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 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.
RefSeqiWP_048064635.1. NC_000917.1.

Genome annotation databases

EnsemblBacteriaiAAB90616; AAB90616; AF_0623.
GeneIDi24794226.
KEGGiafu:AF_0623.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000782 Genomic DNA. Translation: AAB90616.1. Different initiation.
PIRiG69327.
RefSeqiWP_048064635.1. NC_000917.1.

3D structure databases

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

Protein-protein interaction databases

STRINGi224325.AF0623.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAB90616; AAB90616; AF_0623.
GeneIDi24794226.
KEGGiafu:AF_0623.

Phylogenomic databases

eggNOGiarCOG01347. Archaea.
COG1793. LUCA.
KOiK10747.
OMAiDVETLDC.

Enzyme and pathway databases

BRENDAi6.5.1.1. 414.

Miscellaneous databases

EvolutionaryTraceiO29632.

Family and domain databases

Gene3Di1.10.3260.10. 1 hit.
HAMAPiMF_00407. DNA_ligase. 1 hit.
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...

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: November 30, 2016
This is version 109 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

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.