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Q9ZHI0 (DNLJ_THEFI) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 94. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
DNA ligase

EC=6.5.1.2
Alternative name(s):
Polydeoxyribonucleotide synthase [NAD(+)]
Tfi DNA ligase
Gene names
Name:ligA
OrganismThermus filiformis
Taxonomic identifier276 [NCBI]
Taxonomic lineageBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus

Protein attributes

Sequence length670 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.3

Catalytic activity

NAD+ + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + beta-nicotinamide D-ribonucleotide + (deoxyribonucleotide)(n+m). HAMAP-Rule MF_01588

Cofactor

Magnesium. Ref.3

Sequence similarities

Belongs to the NAD-dependent DNA ligase family. LigA subfamily.

Contains 1 BRCT domain.

Biophysicochemical properties

Temperature dependence:

Optimum temperature is 70 degrees Celsius. Ref.3

Ontologies

Keywords
   Biological processDNA damage
DNA repair
DNA replication
   LigandMagnesium
Metal-binding
NAD
Zinc
   Molecular functionLigase
   Technical term3D-structure
Gene Ontology (GO)
   Biological_processDNA repair

Inferred from electronic annotation. Source: UniProtKB-KW

DNA replication

Inferred from electronic annotation. Source: UniProtKB-KW

   Molecular_functionDNA binding

Inferred from electronic annotation. Source: InterPro

DNA ligase (NAD+) activity

Inferred from electronic annotation. Source: UniProtKB-HAMAP

metal ion binding

Inferred from electronic annotation. Source: UniProtKB-KW

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 670670DNA ligase HAMAP-Rule MF_01588
PRO_0000161769

Regions

Domain586 – 67085BRCT
Nucleotide binding34 – 385NAD By similarity
Nucleotide binding84 – 852NAD By similarity
Nucleotide binding116 – 1194NAD HAMAP-Rule MF_01588

Sites

Active site1181N6-AMP-lysine intermediate Ref.3 Ref.4
Metal binding4091Zinc
Metal binding4121Zinc
Metal binding4251Zinc
Metal binding4301Zinc
Binding site1391NAD By similarity
Binding site1741NAD
Binding site2261NAD
Binding site2911NAD By similarity
Binding site3151NAD

Experimental info

Sequence conflict104 – 1118ALGRKRPF → LAEAPS in AAC68862. Ref.1
Sequence conflict1251Missing in AAC68862. Ref.1
Sequence conflict133 – 1397LVFGATR → WSTGS in AAC68862. Ref.1
Sequence conflict2321L → LGL Ref.1
Sequence conflict2571G → C in AAC68862. Ref.1
Sequence conflict2741F → G in AAC68862. Ref.1
Sequence conflict2901V → L in AAC68862. Ref.1
Sequence conflict2961A → T in AAC68862. Ref.1
Sequence conflict2991R → G in AAC68862. Ref.1
Sequence conflict3991E → K in AAC68862. Ref.1
Sequence conflict4081T → A in AAC68862. Ref.1
Sequence conflict5451L → I in AAC68862. Ref.1

Secondary structure

........................................................................................................ 670
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q9ZHI0 [UniParc].

Last modified May 30, 2000. Version 2.
Checksum: 21F0FCAF9B9515FA

FASTA67076,594
        10         20         30         40         50         60 
MTREEARRRI NELRDLIRYH NYRYYVLADP EISDAEYDRL LRELKELEER FPEFKSPDSP 

        70         80         90        100        110        120 
TEQVGARPLE PTFRPVRHPT RMYSLDNAFT YEEVLAFEER LERALGRKRP FLYTVEHKVD 

       130        140        150        160        170        180 
GLSVNLYYEE GVLVFGATRG DGEVGEEVTQ NLLTIPTIPR RLKGVPDRLE VRGEVYMPIE 

       190        200        210        220        230        240 
AFLRLNEELE ERGEKVFKNP RNAAAGSLRQ KDPRVTAKRG LRATFYALGL GLEESGLKSQ 

       250        260        270        280        290        300 
YELLLWLKEK GFPVEHGYEK ALGAEGVEEV YRRFLAQRHA LPFEADGVVV KLDDLALWRE 

       310        320        330        340        350        360 
LGYTARAPRF ALAYKFPAEE KETRLLDVVF QVGRTGRVTP VGVLEPVFIE GSEVSRVTLH 

       370        380        390        400        410        420 
NESYIEELDI RIGDWVLVHK AGGVIPEVLR VLKERRTGEE RPIRWPETCP ECGHRLVKEG 

       430        440        450        460        470        480 
KVHRCPNPLC PAKRFEAIRH YASRKAMDIE GLGEKLIERL LEKGLVRDVA DLYHLRKEDL 

       490        500        510        520        530        540 
LGLERMGEKS AQNLLRQIEE SKHRGLERLL YALGLPGVGE VLARNLARRF GTMDRLLEAS 

       550        560        570        580        590        600 
LEELLEVEEV GELTARAILE TLKDPAFRDL VRRLKEAGVS MESKEEVSDL LSGLTFVLTG 

       610        620        630        640        650        660 
ELSRPREEVK ALLQRLGAKV TDSVSRKTSY LVVGENPGSK LEKARALGVA VLTEEEFWRF 

       670 
LKEKGAPVPA 

« Hide

References

[1]"Cloning, nucleotide sequence, and expression of the DNA ligase-encoding gene from Thermus filiformis."
Kim H.K., Kwon S.-T.
Mol. Cells 8:438-443(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"Biochemical properties of a high fidelity DNA ligase from Thermus species AK16D."
Tong J., Cao W., Barany F.
Nucleic Acids Res. 27:788-794(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 50-586.
Strain: Tok6A1.
[3]"Mutational analyses of the thermostable NAD+-dependent DNA ligase from Thermus filiformis."
Jeon H.J., Shin H.-J., Choi J.J., Hoe H.-S., Kim H.-K., Suh S.W., Kwon S.-T.
FEMS Microbiol. Lett. 237:111-118(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, ACTIVE SITE, COFACTOR, INTERACTION WITH DNA, BIOPHYSICOCHEMICAL PROPERTIES.
[4]"Crystal structure of NAD(+)-dependent DNA ligase: modular architecture and functional implications."
Lee J.Y., Chang C., Song H.K., Moon J., Yang J.K., Kim H.-K., Kwon S.-T., Suh S.W.
EMBO J. 19:1119-1129(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) IN COMPLEXES WITH AMP AND ZINC IONS, ACTIVE SITE.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AF061572 Genomic DNA. Translation: AAC68862.1.
AF092866 Genomic DNA. Translation: AAD13192.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1DGSX-ray2.90A/B1-670[»]
1V9PX-ray2.90A/B1-584[»]
ProteinModelPortalQ9ZHI0.
SMRQ9ZHI0. Positions 1-664.
ModBaseSearch...
MobiDBSearch...

Chemistry

DrugBankDB00131. Adenosine monophosphate.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Family and domain databases

Gene3D2.40.50.140. 1 hit.
3.40.50.10190. 1 hit.
HAMAPMF_01588. DNA_ligase_A.
InterProIPR001357. BRCT_dom.
IPR018239. DNA_ligase_AS.
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]
PfamPF00533. BRCT. 1 hit.
PF01653. DNA_ligase_aden. 1 hit.
PF03120. DNA_ligase_OB. 1 hit.
PF03119. DNA_ligase_ZBD. 1 hit.
[Graphical view]
PIRSFPIRSF001604. LigA. 1 hit.
SMARTSM00292. BRCT. 1 hit.
SM00278. HhH1. 4 hits.
SM00532. LIGANc. 1 hit.
[Graphical view]
SUPFAMSSF47781. SSF47781. 1 hit.
SSF50249. SSF50249. 1 hit.
SSF52113. SSF52113. 1 hit.
TIGRFAMsTIGR00575. dnlj. 1 hit.
PROSITEPS50172. BRCT. 1 hit.
PS01055. DNA_LIGASE_N1. 1 hit.
PS01056. DNA_LIGASE_N2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceQ9ZHI0.

Entry information

Entry nameDNLJ_THEFI
AccessionPrimary (citable) accession number: Q9ZHI0
Secondary accession number(s): Q9ZFY4
Entry history
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: May 30, 2000
Last modified: June 11, 2014
This is version 94 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references