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D3SYT3 (D3SYT3_NATMM) Unreviewed, UniProtKB/TrEMBL

Last modified February 19, 2014. Version 24. Feed History...

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

Names and origin

Protein namesRecommended name:
DNA ligase RuleBase RU000617 HAMAP-Rule MF_00407

EC=6.5.1.1 RuleBase RU000617 HAMAP-Rule MF_00407
Alternative name(s):
Polydeoxyribonucleotide synthase [ATP] HAMAP-Rule MF_00407
Gene names
Name:lig HAMAP-Rule MF_00407
Ordered Locus Names:Nmag_0608 EMBL ADD04194.1
ORF Names:C500_15590 EMBL ELY26599.1
OrganismNatrialba magadii (strain ATCC 43099 / DSM 3394 / NCIMB 2190 / MS3) (Natronobacterium magadii) [Complete proteome] [HAMAP] EMBL ADD04194.1
Taxonomic identifier547559 [NCBI]
Taxonomic lineageArchaeaEuryarchaeotaHalobacteriaHalobacterialesHalobacteriaceaeNatrialba

Protein attributes

Sequence length610 AA.
Sequence statusComplete.
Protein existenceInferred from homology

General annotation (Comments)

Function

DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair By similarity. HAMAP-Rule MF_00407

Catalytic activity

ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m). RuleBase RU000617 HAMAP-Rule MF_00407

Cofactor

Divalent metal cations By similarity. HAMAP-Rule MF_00407

Sequence similarities

Belongs to the ATP-dependent DNA ligase family. RuleBase RU004196 HAMAP-Rule MF_00407

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Sites

Active site2941N6-AMP-lysine intermediate By similarity HAMAP-Rule MF_00407
Binding site2921ATP By similarity HAMAP-Rule MF_00407
Binding site2991ATP By similarity HAMAP-Rule MF_00407
Binding site3251ATP By similarity HAMAP-Rule MF_00407
Binding site3541ATP By similarity HAMAP-Rule MF_00407
Binding site3941ATP By similarity HAMAP-Rule MF_00407
Binding site4751ATP By similarity HAMAP-Rule MF_00407
Binding site4811ATP By similarity HAMAP-Rule MF_00407

Sequences

Sequence LengthMass (Da)Tools
D3SYT3 [UniParc].

Last modified April 20, 2010. Version 1.
Checksum: AAB053AF4CC701D6

FASTA61065,823
        10         20         30         40         50         60 
MEFATFADRA ATIEAESADL EIVAHVRDLL AEAGDDLPIV ARFVQGRVFP AWDSTTLDIG 

        70         80         90        100        110        120 
PNTCYEAIAR AAGTNVDADD VEERLADRGE IGAVAASYDF GGQQGLGAFM SGGGSGAGGA 

       130        140        150        160        170        180 
VDNNDDQDDR NNGGNGSNSG NDSNSSNDSN SSNGTGDLTV REINDTLTDL AAAEGSGSQD 

       190        200        210        220        230        240 
RKVDLLFGLF NRCSSDEARY LARLVLSEMR IGVGEGTVRD AIAEAFEVPQ EPVERALQVS 

       250        260        270        280        290        300 
NDYGQVAETA REDGVDGLDE IDLEIGRPVQ AMLAQAGTVT DALEEWDEAA VEWKYDGARI 

       310        320        330        340        350        360 
QLHYDPAGPG GPDGDSNGET HVFSRNMEAV TDALPEVVEF ADEHLDGPAI LDGEVVAIDD 

       370        380        390        400        410        420 
DGNPLPFQEV LKRFRRKHDV AKARENVSVR PVFFDCLHAD GDDLLEEPLV ERHNQLESVL 

       430        440        450        460        470        480 
AMGPQQEPEE IDGFSLLWVT DNPDEIEAVD ADALEAGHEG IMLKNPDSAY SPGRRGKNWQ 

       490        500        510        520        530        540 
KRKPDVETLD CVVTGAEWGE GRRATFLGTF ELSVRDGDDL ETVGKVATGI TDEKLEELTE 

       550        560        570        580        590        600 
LLEPHIVAED GTAVELEPAV VFEVGYEEIQ TSPTYSSGYA LRFPRFLGVR YDKDTAGAET 

       610 
LERLETLFES 

« Hide

References

« Hide 'large scale' references
[1]"Complete sequence of chromosome of Natrialba magadii ATCC 43099."
US DOE Joint Genome Institute
Lucas S., Copeland A., Lapidus A., Cheng J.-F., Bruce D., Goodwin L., Pitluck S., Davenport K., Saunders E., Detter J.C., Han C., Tapia R., Land M., Hauser L., Kyrpides N., Mikhailova N., De Castro R.E., Maupin-Furlow J.A., Woyke T.
Submitted (FEB-2010) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 43099 / DSM 3394 / NCIMB 2190 / MS3.
[2]"A comparative genomics perspective on the genetic content of the alkaliphilic haloarchaeon Natrialba magadii ATCC 43099T."
Siddaramappa S., Challacombe J.F., Decastro R.E., Pfeiffer F., Sastre D.E., Gimenez M.I., Paggi R.A., Detter J.C., Davenport K.W., Goodwin L.A., Kyrpides N., Tapia R., Pitluck S., Lucas S., Woyke T., Maupin-Furlow J.A.
BMC Genomics 13:165-165(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE.
Strain: ATCC 43099 EMBL ADD04194.1.
[3]Becker E.A., Seitzer P., Tritt A., Larsen D., Yao A., Wu D., Darling A., Eisen J.A., Facciotti M.T.
Submitted (NOV-2012) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE.
Strain: MS-3 EMBL ELY26599.1.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
CP001932 Genomic DNA. Translation: ADD04194.1.
AOHS01000051 Genomic DNA. Translation: ELY26599.1.
RefSeqYP_003478756.1. NC_013922.1.

3D structure databases

ModBaseSearch...
MobiDBSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaADD04194; ADD04194; Nmag_0608.
ELY26599; ELY26599; C500_15590.
GeneID8823435.
KEGGnmg:Nmag_0608.

Organism-specific databases

CMRSearch...

Phylogenomic databases

HOGENOMHOG000036008.
KOK10747.
OMAGRPRPFQ.

Enzyme and pathway databases

BioCycNMAG547559:GJAP-621-MONOMER.

Family and domain databases

Gene3D1.10.3260.10. 2 hits.
2.40.50.140. 1 hit.
HAMAPMF_00407. DNA_ligase.
InterProIPR022865. DNA_ligae_ATP-dep_bac/arc.
IPR000977. DNA_ligase_ATP-dep.
IPR012309. DNA_ligase_ATP-dep_C.
IPR012310. DNA_ligase_ATP-dep_cent.
IPR016059. DNA_ligase_ATP-dep_CS.
IPR012308. DNA_ligase_ATP-dep_N.
IPR012340. NA-bd_OB-fold.
[Graphical view]
PfamPF04679. DNA_ligase_A_C. 1 hit.
PF01068. DNA_ligase_A_M. 1 hit.
PF04675. DNA_ligase_A_N. 2 hits.
[Graphical view]
SUPFAMSSF117018. SSF117018. 2 hits.
SSF50249. SSF50249. 1 hit.
TIGRFAMsTIGR00574. dnl1. 1 hit.
PROSITEPS00697. DNA_LIGASE_A1. 1 hit.
PS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameD3SYT3_NATMM
AccessionPrimary (citable) accession number: D3SYT3
Entry history
Integrated into UniProtKB/TrEMBL: April 20, 2010
Last sequence update: April 20, 2010
Last modified: February 19, 2014
This is version 24 of the entry and version 1 of the sequence. [Complete history]
Entry statusUnreviewed (UniProtKB/TrEMBL)