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Protein

DNA ligase

Gene

ligA

Organism
Thermus filiformis
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 annotation1 Publication

Catalytic activityi

NAD+ + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + beta-nicotinamide D-ribonucleotide + (deoxyribonucleotide)(n+m).UniRule annotation

Cofactori

Mg2+1 Publication

Temperature dependencei

Optimum temperature is 70 degrees Celsius.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei118N6-AMP-lysine intermediateUniRule annotation2 Publications1
Binding sitei139NADUniRule annotation1
Binding sitei174NADUniRule annotation1
Binding sitei226NADUniRule annotation1
Binding sitei291NADUniRule annotation1
Binding sitei315NADUniRule annotation1 Publication1
Metal bindingi409ZincUniRule annotation1 Publication1
Metal bindingi412ZincUniRule annotation1 Publication1
Metal bindingi425ZincUniRule annotation1 Publication1
Metal bindingi430ZincUniRule annotation1 Publication1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi34 – 38NADUniRule annotation5
Nucleotide bindingi84 – 85NADUniRule annotation2
Nucleotide bindingi116 – 119NAD1 Publication4

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, Metal-binding, NAD, Zinc

Enzyme and pathway databases

BRENDAi6.5.1.2. 6336.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA ligaseUniRule annotation (EC:6.5.1.2UniRule annotation)
Alternative name(s):
Polydeoxyribonucleotide synthase [NAD(+)]UniRule annotation
Tfi DNA ligase
Gene namesi
Name:ligAUniRule annotation
OrganismiThermus filiformis
Taxonomic identifieri276 [NCBI]
Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001617691 – 670DNA ligaseAdd BLAST670

Structurei

Secondary structure

1670
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi3 – 25Combined sources23
Beta strandi34 – 37Combined sources4
Helixi38 – 47Combined sources10
Helixi52 – 54Combined sources3
Helixi60 – 63Combined sources4
Beta strandi65 – 67Combined sources3
Beta strandi75 – 77Combined sources3
Helixi91 – 100Combined sources10
Beta strandi103 – 105Combined sources3
Beta strandi112 – 117Combined sources6
Beta strandi122 – 124Combined sources3
Beta strandi126 – 129Combined sources4
Beta strandi132 – 137Combined sources6
Beta strandi141 – 147Combined sources7
Helixi150 – 152Combined sources3
Beta strandi167 – 176Combined sources10
Helixi179 – 192Combined sources14
Helixi200 – 208Combined sources9
Helixi213 – 218Combined sources6
Beta strandi222 – 224Combined sources3
Turni230 – 233Combined sources4
Helixi240 – 249Combined sources10
Beta strandi258 – 262Combined sources5
Helixi263 – 276Combined sources14
Turni277 – 280Combined sources4
Beta strandi281 – 283Combined sources3
Beta strandi287 – 294Combined sources8
Helixi296 – 300Combined sources5
Beta strandi308 – 315Combined sources8
Beta strandi321 – 332Combined sources12
Beta strandi336 – 349Combined sources14
Beta strandi352 – 358Combined sources7
Helixi362 – 367Combined sources6
Beta strandi371 – 373Combined sources3
Beta strandi375 – 381Combined sources7
Turni382 – 384Combined sources3
Beta strandi385 – 391Combined sources7
Helixi393 – 395Combined sources3
Turni410 – 412Combined sources3
Beta strandi417 – 419Combined sources3
Beta strandi422 – 424Combined sources3
Helixi431 – 433Combined sources3
Helixi434 – 442Combined sources9
Turni444 – 447Combined sources4
Helixi454 – 462Combined sources9
Helixi469 – 475Combined sources7
Helixi478 – 481Combined sources4
Beta strandi488 – 490Combined sources3
Helixi491 – 500Combined sources10
Helixi501 – 503Combined sources3
Helixi506 – 512Combined sources7
Helixi520 – 528Combined sources9
Helixi533 – 536Combined sources4
Helixi541 – 545Combined sources5
Helixi552 – 563Combined sources12
Helixi565 – 576Combined sources12

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1DGSX-ray2.90A/B1-670[»]
1V9PX-ray2.90A/B1-584[»]
ProteinModelPortaliQ9ZHI0.
SMRiQ9ZHI0.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9ZHI0.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini586 – 670BRCTUniRule annotationAdd BLAST85

Sequence similaritiesi

Belongs to the NAD-dependent DNA ligase family. LigA subfamily.UniRule annotation
Contains 1 BRCT domain.UniRule annotation

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.

Q9ZHI0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTREEARRRI NELRDLIRYH NYRYYVLADP EISDAEYDRL LRELKELEER
60 70 80 90 100
FPEFKSPDSP TEQVGARPLE PTFRPVRHPT RMYSLDNAFT YEEVLAFEER
110 120 130 140 150
LERALGRKRP FLYTVEHKVD GLSVNLYYEE GVLVFGATRG DGEVGEEVTQ
160 170 180 190 200
NLLTIPTIPR RLKGVPDRLE VRGEVYMPIE AFLRLNEELE ERGEKVFKNP
210 220 230 240 250
RNAAAGSLRQ KDPRVTAKRG LRATFYALGL GLEESGLKSQ YELLLWLKEK
260 270 280 290 300
GFPVEHGYEK ALGAEGVEEV YRRFLAQRHA LPFEADGVVV KLDDLALWRE
310 320 330 340 350
LGYTARAPRF ALAYKFPAEE KETRLLDVVF QVGRTGRVTP VGVLEPVFIE
360 370 380 390 400
GSEVSRVTLH NESYIEELDI RIGDWVLVHK AGGVIPEVLR VLKERRTGEE
410 420 430 440 450
RPIRWPETCP ECGHRLVKEG KVHRCPNPLC PAKRFEAIRH YASRKAMDIE
460 470 480 490 500
GLGEKLIERL LEKGLVRDVA DLYHLRKEDL LGLERMGEKS AQNLLRQIEE
510 520 530 540 550
SKHRGLERLL YALGLPGVGE VLARNLARRF GTMDRLLEAS LEELLEVEEV
560 570 580 590 600
GELTARAILE TLKDPAFRDL VRRLKEAGVS MESKEEVSDL LSGLTFVLTG
610 620 630 640 650
ELSRPREEVK ALLQRLGAKV TDSVSRKTSY LVVGENPGSK LEKARALGVA
660 670
VLTEEEFWRF LKEKGAPVPA
Length:670
Mass (Da):76,594
Last modified:May 30, 2000 - v2
Checksum:i21F0FCAF9B9515FA
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti104 – 111ALGRKRPF → LAEAPS in AAC68862 (PubMed:9749531).Curated8
Sequence conflicti125Missing in AAC68862 (PubMed:9749531).Curated1
Sequence conflicti133 – 139LVFGATR → WSTGS in AAC68862 (PubMed:9749531).Curated7
Sequence conflicti232L → LGL (PubMed:9749531).Curated1
Sequence conflicti257G → C in AAC68862 (PubMed:9749531).Curated1
Sequence conflicti274F → G in AAC68862 (PubMed:9749531).Curated1
Sequence conflicti290V → L in AAC68862 (PubMed:9749531).Curated1
Sequence conflicti296A → T in AAC68862 (PubMed:9749531).Curated1
Sequence conflicti299R → G in AAC68862 (PubMed:9749531).Curated1
Sequence conflicti399E → K in AAC68862 (PubMed:9749531).Curated1
Sequence conflicti408T → A in AAC68862 (PubMed:9749531).Curated1
Sequence conflicti545L → I in AAC68862 (PubMed:9749531).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF061572 Genomic DNA. Translation: AAC68862.1.
AF092866 Genomic DNA. Translation: AAD13192.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF061572 Genomic DNA. Translation: AAC68862.1.
AF092866 Genomic DNA. Translation: AAD13192.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1DGSX-ray2.90A/B1-670[»]
1V9PX-ray2.90A/B1-584[»]
ProteinModelPortaliQ9ZHI0.
SMRiQ9ZHI0.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

BRENDAi6.5.1.2. 6336.

Miscellaneous databases

EvolutionaryTraceiQ9ZHI0.

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_THEFI
AccessioniPrimary (citable) accession number: Q9ZHI0
Secondary accession number(s): Q9ZFY4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: May 30, 2000
Last modified: November 30, 2016
This is version 105 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

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.