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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 PublicationUniRule annotation

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)LengthDescriptionGraphical viewFeature identifierActions
Active sitei118 – 1181N6-AMP-lysine intermediate2 PublicationsUniRule annotation
Binding sitei139 – 1391NADUniRule annotation
Binding sitei174 – 1741NAD
Binding sitei226 – 2261NAD
Binding sitei291 – 2911NADUniRule annotation
Binding sitei315 – 3151NAD
Metal bindingi409 – 4091Zinc
Metal bindingi412 – 4121Zinc
Metal bindingi425 – 4251Zinc
Metal bindingi430 – 4301Zinc

Regions

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

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 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)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 670670DNA ligasePRO_0000161769Add
BLAST

Structurei

Secondary structure

1
670
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi3 – 2523Combined sources
Beta strandi34 – 374Combined sources
Helixi38 – 4710Combined sources
Helixi52 – 543Combined sources
Helixi60 – 634Combined sources
Beta strandi65 – 673Combined sources
Beta strandi75 – 773Combined sources
Helixi91 – 10010Combined sources
Beta strandi103 – 1053Combined sources
Beta strandi112 – 1176Combined sources
Beta strandi122 – 1243Combined sources
Beta strandi126 – 1294Combined sources
Beta strandi132 – 1376Combined sources
Beta strandi141 – 1477Combined sources
Helixi150 – 1523Combined sources
Beta strandi167 – 17610Combined sources
Helixi179 – 19214Combined sources
Helixi200 – 2089Combined sources
Helixi213 – 2186Combined sources
Beta strandi222 – 2243Combined sources
Turni230 – 2334Combined sources
Helixi240 – 24910Combined sources
Beta strandi258 – 2625Combined sources
Helixi263 – 27614Combined sources
Turni277 – 2804Combined sources
Beta strandi281 – 2833Combined sources
Beta strandi287 – 2948Combined sources
Helixi296 – 3005Combined sources
Beta strandi308 – 3158Combined sources
Beta strandi321 – 33212Combined sources
Beta strandi336 – 34914Combined sources
Beta strandi352 – 3587Combined sources
Helixi362 – 3676Combined sources
Beta strandi371 – 3733Combined sources
Beta strandi375 – 3817Combined sources
Turni382 – 3843Combined sources
Beta strandi385 – 3917Combined sources
Helixi393 – 3953Combined sources
Turni410 – 4123Combined sources
Beta strandi417 – 4193Combined sources
Beta strandi422 – 4243Combined sources
Helixi431 – 4333Combined sources
Helixi434 – 4429Combined sources
Turni444 – 4474Combined sources
Helixi454 – 4629Combined sources
Helixi469 – 4757Combined sources
Helixi478 – 4814Combined sources
Beta strandi488 – 4903Combined sources
Helixi491 – 50010Combined sources
Helixi501 – 5033Combined sources
Helixi506 – 5127Combined sources
Helixi520 – 5289Combined sources
Helixi533 – 5364Combined sources
Helixi541 – 5455Combined sources
Helixi552 – 56312Combined sources
Helixi565 – 57612Combined sources

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiQ9ZHI0.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini586 – 67085BRCTUniRule annotationAdd
BLAST

Sequence similaritiesi

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

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

        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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti104 – 1118ALGRKRPF → LAEAPS in AAC68862. (PubMed:9749531)Curated
Sequence conflicti125 – 1251Missing in AAC68862. (PubMed:9749531)Curated
Sequence conflicti133 – 1397LVFGATR → WSTGS in AAC68862. (PubMed:9749531)Curated
Sequence conflicti232 – 2321L → LGL(PubMed:9749531)Curated
Sequence conflicti257 – 2571G → C in AAC68862. (PubMed:9749531)Curated
Sequence conflicti274 – 2741F → G in AAC68862. (PubMed:9749531)Curated
Sequence conflicti290 – 2901V → L in AAC68862. (PubMed:9749531)Curated
Sequence conflicti296 – 2961A → T in AAC68862. (PubMed:9749531)Curated
Sequence conflicti299 – 2991R → G in AAC68862. (PubMed:9749531)Curated
Sequence conflicti399 – 3991E → K in AAC68862. (PubMed:9749531)Curated
Sequence conflicti408 – 4081T → A in AAC68862. (PubMed:9749531)Curated
Sequence conflicti545 – 5451L → I in AAC68862. (PubMed:9749531)Curated

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
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...

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: November 26, 2014
This is version 97 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