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Q9ZHI0

- DNLJ_THEFI

UniProt

Q9ZHI0 - DNLJ_THEFI

Protein

DNA ligase

Gene

ligA

Organism
Thermus filiformis
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 95 (01 Oct 2014)
      Sequence version 2 (30 May 2000)
      Previous versions | rss
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    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

    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 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

    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

    Pathology & Biotechi

    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 – 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.
    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

    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

    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:
    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: October 1, 2014
    This is version 95 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