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Q9ZHI0

- DNLJ_THEFI

UniProt

Q9ZHI0 - DNLJ_THEFI

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Protein
DNA ligase
Gene
ligA
Organism
Thermus filiformis
Status
Reviewed - Annotation score: 5 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.1 Publication

Catalytic activityi

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

Cofactori

Magnesium.1 Publication

Temperature dependencei

Optimum temperature is 70 degrees Celsius.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei118 – 1181N6-AMP-lysine intermediate2 Publications
Binding sitei139 – 1391NAD By similarity
Binding sitei174 – 1741NAD
Binding sitei226 – 2261NAD
Binding sitei291 – 2911NAD By similarity
Binding sitei315 – 3151NAD
Metal bindingi409 – 4091Zinc
Metal bindingi412 – 4121Zinc
Metal bindingi425 – 4251Zinc
Metal bindingi430 – 4301Zinc

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi34 – 385NAD By similarity
Nucleotide bindingi84 – 852NAD By similarity
Nucleotide bindingi116 – 1194NADUniRule annotation

GO - Molecular functioni

  1. DNA binding Source: InterPro
  2. DNA ligase (NAD+) activity Source: UniProtKB-HAMAP
  3. metal ion binding Source: UniProtKB-KW

GO - Biological processi

  1. DNA repair Source: UniProtKB-KW
  2. DNA replication Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

DNA damage, DNA repair, DNA replication

Keywords - Ligandi

Magnesium, Metal-binding, NAD, Zinc

Names & Taxonomyi

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

Pathology & Biotechi

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 670670DNA ligaseUniRule annotation
PRO_0000161769Add
BLAST

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi3 – 2523
Beta strandi34 – 374
Helixi38 – 4710
Helixi52 – 543
Helixi60 – 634
Beta strandi65 – 673
Beta strandi75 – 773
Helixi91 – 10010
Beta strandi103 – 1053
Beta strandi112 – 1176
Beta strandi122 – 1243
Beta strandi126 – 1294
Beta strandi132 – 1376
Beta strandi141 – 1477
Helixi150 – 1523
Beta strandi167 – 17610
Helixi179 – 19214
Helixi200 – 2089
Helixi213 – 2186
Beta strandi222 – 2243
Turni230 – 2334
Helixi240 – 24910
Beta strandi258 – 2625
Helixi263 – 27614
Turni277 – 2804
Beta strandi281 – 2833
Beta strandi287 – 2948
Helixi296 – 3005
Beta strandi308 – 3158
Beta strandi321 – 33212
Beta strandi336 – 34914
Beta strandi352 – 3587
Helixi362 – 3676
Beta strandi371 – 3733
Beta strandi375 – 3817
Turni382 – 3843
Beta strandi385 – 3917
Helixi393 – 3953
Turni410 – 4123
Beta strandi417 – 4193
Beta strandi422 – 4243
Helixi431 – 4333
Helixi434 – 4429
Turni444 – 4474
Helixi454 – 4629
Helixi469 – 4757
Helixi478 – 4814
Beta strandi488 – 4903
Helixi491 – 50010
Helixi501 – 5033
Helixi506 – 5127
Helixi520 – 5289
Helixi533 – 5364
Helixi541 – 5455
Helixi552 – 56312
Helixi565 – 57612

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1DGSX-ray2.90A/B1-670[»]
1V9PX-ray2.90A/B1-584[»]
ProteinModelPortaliQ9ZHI0.
SMRiQ9ZHI0. Positions 1-664.

Miscellaneous databases

EvolutionaryTraceiQ9ZHI0.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini586 – 67085BRCT
Add
BLAST

Sequence similaritiesi

Contains 1 BRCT domain.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
3.40.50.10190. 1 hit.
HAMAPiMF_01588. DNA_ligase_A.
InterProiIPR001357. 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]
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

MTREEARRRI NELRDLIRYH NYRYYVLADP EISDAEYDRL LRELKELEER    50
FPEFKSPDSP TEQVGARPLE PTFRPVRHPT RMYSLDNAFT YEEVLAFEER 100
LERALGRKRP FLYTVEHKVD GLSVNLYYEE GVLVFGATRG DGEVGEEVTQ 150
NLLTIPTIPR RLKGVPDRLE VRGEVYMPIE AFLRLNEELE ERGEKVFKNP 200
RNAAAGSLRQ KDPRVTAKRG LRATFYALGL GLEESGLKSQ YELLLWLKEK 250
GFPVEHGYEK ALGAEGVEEV YRRFLAQRHA LPFEADGVVV KLDDLALWRE 300
LGYTARAPRF ALAYKFPAEE KETRLLDVVF QVGRTGRVTP VGVLEPVFIE 350
GSEVSRVTLH NESYIEELDI RIGDWVLVHK AGGVIPEVLR VLKERRTGEE 400
RPIRWPETCP ECGHRLVKEG KVHRCPNPLC PAKRFEAIRH YASRKAMDIE 450
GLGEKLIERL LEKGLVRDVA DLYHLRKEDL LGLERMGEKS AQNLLRQIEE 500
SKHRGLERLL YALGLPGVGE VLARNLARRF GTMDRLLEAS LEELLEVEEV 550
GELTARAILE TLKDPAFRDL VRRLKEAGVS MESKEEVSDL LSGLTFVLTG 600
ELSRPREEVK ALLQRLGAKV TDSVSRKTSY LVVGENPGSK LEKARALGVA 650
VLTEEEFWRF LKEKGAPVPA 670
Length:670
Mass (Da):76,594
Last modified:May 30, 2000 - v2
Checksum:i21F0FCAF9B9515FA
GO

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti104 – 1118ALGRKRPF → LAEAPS in AAC68862. 1 Publication
Sequence conflicti125 – 1251Missing in AAC68862. 1 Publication
Sequence conflicti133 – 1397LVFGATR → WSTGS in AAC68862. 1 Publication
Sequence conflicti232 – 2321L → LGL1 Publication
Sequence conflicti257 – 2571G → C in AAC68862. 1 Publication
Sequence conflicti274 – 2741F → G in AAC68862. 1 Publication
Sequence conflicti290 – 2901V → L in AAC68862. 1 Publication
Sequence conflicti296 – 2961A → T in AAC68862. 1 Publication
Sequence conflicti299 – 2991R → G in AAC68862. 1 Publication
Sequence conflicti399 – 3991E → K in AAC68862. 1 Publication
Sequence conflicti408 – 4081T → A in AAC68862. 1 Publication
Sequence conflicti545 – 5451L → I in AAC68862. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AF061572 Genomic DNA. Translation: AAC68862.1.
AF092866 Genomic DNA. Translation: AAD13192.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AF061572 Genomic DNA. Translation: AAC68862.1 .
AF092866 Genomic DNA. Translation: AAD13192.1 .

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1DGS X-ray 2.90 A/B 1-670 [» ]
1V9P X-ray 2.90 A/B 1-584 [» ]
ProteinModelPortali Q9ZHI0.
SMRi Q9ZHI0. Positions 1-664.
ModBasei Search...
MobiDBi Search...

Chemistry

DrugBanki DB00131. Adenosine monophosphate.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Miscellaneous databases

EvolutionaryTracei Q9ZHI0.

Family and domain databases

Gene3Di 2.40.50.140. 1 hit.
3.40.50.10190. 1 hit.
HAMAPi MF_01588. DNA_ligase_A.
InterProi IPR001357. 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 ]
Pfami PF00533. BRCT. 1 hit.
PF01653. DNA_ligase_aden. 1 hit.
PF03120. DNA_ligase_OB. 1 hit.
PF03119. DNA_ligase_ZBD. 1 hit.
[Graphical view ]
PIRSFi PIRSF001604. LigA. 1 hit.
SMARTi SM00292. BRCT. 1 hit.
SM00278. HhH1. 4 hits.
SM00532. LIGANc. 1 hit.
[Graphical view ]
SUPFAMi SSF47781. SSF47781. 1 hit.
SSF50249. SSF50249. 1 hit.
SSF52113. SSF52113. 1 hit.
TIGRFAMsi TIGR00575. dnlj. 1 hit.
PROSITEi PS50172. BRCT. 1 hit.
PS01055. DNA_LIGASE_N1. 1 hit.
PS01056. DNA_LIGASE_N2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  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.

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: June 11, 2014
This is version 94 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

External Data

Dasty 3

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