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Protein

DNA ligase

Gene

1.3

Organism
Enterobacteria phage T7 (Bacteriophage T7)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair in an ATP-dependent reaction. Binds specifically to DNA nicks containing a 3'-OH and a 5'-phosphate group.1 Publication

Catalytic activityi

ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m).PROSITE-ProRule annotation1 Publication

Cofactori

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei34 – 341N6-AMP-lysine intermediatePROSITE-ProRule annotation
Binding sitei39 – 391ATP1 Publication
Binding sitei93 – 931ATP1 Publication
Metal bindingi217 – 2171Divalent metal cationBy similarity
Binding sitei232 – 2321ATP1 Publication
Binding sitei238 – 2381ATP1 Publication

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi32 – 354ATP1 Publication
Nucleotide bindingi55 – 573ATP1 Publication

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

DNA damage, DNA recombination, DNA repair, DNA replication

Keywords - Ligandi

ATP-binding, DNA-binding, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BRENDAi6.5.1.1. 736.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA ligase (EC:6.5.1.1)
Alternative name(s):
DNA ligase gp1.3
Gene product 1.3
Short name:
Gp1.3
Gene namesi
Ordered Locus Names:1.3
OrganismiEnterobacteria phage T7 (Bacteriophage T7)
Taxonomic identifieri10760 [NCBI]
Taxonomic lineageiVirusesdsDNA viruses, no RNA stageCaudoviralesPodoviridaeAutographivirinaeT7likevirus
Virus hostiEscherichia coli [TaxID: 562]
ProteomesiUP000000840 Componenti: Genome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi238 – 2381K → A: Complete loss of transadenylation activity. 1 Publication
Mutagenesisi240 – 2401K → A: About 99% loss of transadenylation activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 359359DNA ligasePRO_0000059598Add
BLAST

Interactioni

Protein-protein interaction databases

MINTiMINT-1513817.

Structurei

Secondary structure

1
359
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi9 – 135Combined sources
Helixi16 – 2611Combined sources
Beta strandi27 – 337Combined sources
Beta strandi37 – 459Combined sources
Beta strandi48 – 536Combined sources
Helixi61 – 666Combined sources
Helixi71 – 788Combined sources
Beta strandi87 – 9913Combined sources
Turni101 – 1033Combined sources
Helixi104 – 1096Combined sources
Beta strandi115 – 1195Combined sources
Turni141 – 1433Combined sources
Beta strandi144 – 15310Combined sources
Helixi154 – 1596Combined sources
Beta strandi163 – 1664Combined sources
Helixi167 – 18418Combined sources
Beta strandi188 – 1925Combined sources
Beta strandi195 – 2006Combined sources
Helixi201 – 21212Combined sources
Turni213 – 2153Combined sources
Beta strandi219 – 2224Combined sources
Beta strandi230 – 24011Combined sources
Beta strandi243 – 25311Combined sources
Turni257 – 2593Combined sources
Beta strandi267 – 2715Combined sources
Beta strandi277 – 2815Combined sources
Helixi286 – 29914Combined sources
Turni300 – 3023Combined sources
Turni321 – 3244Combined sources
Beta strandi326 – 3349Combined sources
Beta strandi340 – 3423Combined sources
Beta strandi344 – 3485Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1A0IX-ray2.60A3-349[»]
ProteinModelPortaliP00969.
SMRiP00969. Positions 2-349.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP00969.

Family & Domainsi

Sequence similaritiesi

Belongs to the ATP-dependent DNA ligase family.Curated

Phylogenomic databases

KOiK18951.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
InterProiIPR012310. DNA_ligase_ATP-dep_cent.
IPR016059. DNA_ligase_ATP-dep_CS.
IPR016306. DNA_ligase_ATP-dep_T3.
IPR012340. NA-bd_OB-fold.
[Graphical view]
PfamiPF01068. DNA_ligase_A_M. 1 hit.
[Graphical view]
PIRSFiPIRSF001600. DNA_ligase_phage_T3. 1 hit.
SUPFAMiSSF50249. SSF50249. 1 hit.
PROSITEiPS00697. DNA_LIGASE_A1. 1 hit.
PS00333. DNA_LIGASE_A2. 1 hit.
PS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P00969-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MMNIKTNPFK AVSFVESAIK KALDNAGYLI AEIKYDGVRG NICVDNTANS
60 70 80 90 100
YWLSRVSKTI PALEHLNGFD VRWKRLLNDD RCFYKDGFML DGELMVKGVD
110 120 130 140 150
FNTGSGLLRT KWTDTKNQEF HEELFVEPIR KKDKVPFKLH TGHLHIKLYA
160 170 180 190 200
ILPLHIVESG EDCDVMTLLM QEHVKNMLPL LQEYFPEIEW QAAESYEVYD
210 220 230 240 250
MVELQQLYEQ KRAEGHEGLI VKDPMCIYKR GKKSGWWKMK PENEADGIIQ
260 270 280 290 300
GLVWGTKGLA NEGKVIGFEV LLESGRLVNA TNISRALMDE FTETVKEATL
310 320 330 340 350
SQWGFFSPYG IGDNDACTIN PYDGWACQIS YMEETPDGSL RHPSFVMFRG

TEDNPQEKM
Length:359
Mass (Da):41,133
Last modified:July 21, 1986 - v1
Checksum:i43DA453B71BDF8DC
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
V01124 Genomic DNA. Translation: CAA24322.1.
V01126 Genomic DNA. Translation: CAA24326.1.
V01127 Genomic DNA. Translation: CAA24336.1.
V01146 Genomic DNA. Translation: CAA24393.1.
PIRiE94615. LQBP37.
RefSeqiNP_041963.1. NC_001604.1.

Genome annotation databases

GeneIDi1261055.
KEGGivg:1261055.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
V01124 Genomic DNA. Translation: CAA24322.1.
V01126 Genomic DNA. Translation: CAA24326.1.
V01127 Genomic DNA. Translation: CAA24336.1.
V01146 Genomic DNA. Translation: CAA24393.1.
PIRiE94615. LQBP37.
RefSeqiNP_041963.1. NC_001604.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1A0IX-ray2.60A3-349[»]
ProteinModelPortaliP00969.
SMRiP00969. Positions 2-349.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

MINTiMINT-1513817.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi1261055.
KEGGivg:1261055.

Phylogenomic databases

KOiK18951.

Enzyme and pathway databases

BRENDAi6.5.1.1. 736.

Miscellaneous databases

EvolutionaryTraceiP00969.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
InterProiIPR012310. DNA_ligase_ATP-dep_cent.
IPR016059. DNA_ligase_ATP-dep_CS.
IPR016306. DNA_ligase_ATP-dep_T3.
IPR012340. NA-bd_OB-fold.
[Graphical view]
PfamiPF01068. DNA_ligase_A_M. 1 hit.
[Graphical view]
PIRSFiPIRSF001600. DNA_ligase_phage_T3. 1 hit.
SUPFAMiSSF50249. SSF50249. 1 hit.
PROSITEiPS00697. DNA_LIGASE_A1. 1 hit.
PS00333. DNA_LIGASE_A2. 1 hit.
PS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements."
    Dunn J.J., Studier F.W.
    J. Mol. Biol. 166:477-535(1983) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  2. "Nucleotide sequence from the genetic left end of bacteriophage T7 DNA to the beginning of gene 4."
    Dunn J.J., Studier F.W.
    J. Mol. Biol. 148:303-330(1981) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. "The transcription termination site at the end of the early region of bacteriophage T7 DNA."
    Dunn J.J., Studier F.W.
    Nucleic Acids Res. 8:2119-2132(1980) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 278-359.
  4. "Nucleotide sequence of the primary origin of bacteriophage T7 DNA replication: relationship to adjacent genes and regulatory elements."
    Saito H., Tabor S., Tamanoi F., Richardson C.C.
    Proc. Natl. Acad. Sci. U.S.A. 77:3917-3921(1980) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-5.
  5. Cited for: FUNCTION, MUTAGENESIS OF LYS-238 AND LYS-240.
  6. "Crystal structure of an ATP-dependent DNA ligase from bacteriophage T7."
    Subramanya H.S., Doherty A.J., Ashford S.R., Wigley D.B.
    Cell 85:607-615(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) IN COMPLEX WITH ATP, CATALYTIC ACTIVITY, DNA-BINDING.

Entry informationi

Entry nameiDNLI_BPT7
AccessioniPrimary (citable) accession number: P00969
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: July 21, 1986
Last modified: May 27, 2015
This is version 108 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

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

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 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.