DNA ligase - Staphylothermus marinus (strain ATCC 43588 / DSM 3639 / F1)

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A3DP49 (DNLI_STAMF) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 54. History...

Clusters with 100%, 90%, 50% identity |

Documents (1) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
DNA ligase
EC=6.5.1.1

Alternative name(s):
Polydeoxyribonucleotide synthase [ATP]

Gene names

Name:	lig
Ordered Locus Names:	Smar_1318

Organism

Staphylothermus marinus (strain ATCC 43588 / DSM 3639 / F1) [Complete proteome] [HAMAP]

Taxonomic identifier

399550 [NCBI]

Taxonomic lineage

Archaea › Crenarchaeota › Thermoprotei › Desulfurococcales › Desulfurococcaceae › Staphylothermus ›

Protein attributes

Sequence length	597 AA.
Sequence status	Complete.
Protein existence	Inferred 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). HAMAP-Rule MF_00407
Cofactor	Divalent metal cations By similarity.
Sequence similarities	Belongs to the ATP-dependent DNA ligase family.
Sequence caution	The sequence ABN70409.1 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
Biological process	Cell cycle Cell division DNA damage DNA recombination DNA repair DNA replication
Ligand	ATP-binding Metal-binding Nucleotide-binding
Molecular function	Ligase
Technical term	Complete proteome
Gene Ontology (GO)
Biological_process	DNA ligation involved in DNA repair Inferred from electronic annotation. Source: InterPro DNA recombination Inferred from electronic annotation. Source: HAMAP DNA replication Inferred from electronic annotation. Source: HAMAP cell cycle Inferred from electronic annotation. Source: UniProtKB-KW cell division Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	ATP binding Inferred from electronic annotation. Source: HAMAP DNA binding Inferred from electronic annotation. Source: InterPro DNA ligase (ATP) activity Inferred from electronic annotation. Source: HAMAP metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 597

597

DNA ligase HAMAP-Rule MF_00407

PRO_0000365264

Sites

Active site

264

N6-AMP-lysine intermediate By similarity

Binding site

262

ATP By similarity

Binding site

269

ATP By similarity

Binding site

284

ATP By similarity

Binding site

314

ATP By similarity

Binding site

354

ATP By similarity

Binding site

431

ATP By similarity

Binding site

437

ATP By similarity

Sequences

Sequence

Length

Mass (Da)

Tools

A3DP49 [UniParc].

Last modified March 3, 2009. Version 2.
Checksum: CA4E62C8890515D6
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FASTA

597

67,627

        10         20         30         40         50         60 
MPFRELADTF ERIEIITSRT QMTVLLVNLF KKTPPEIIDK VVYLLQGRLW PDWKGLPELG 

        70         80         90        100        110        120 
VGEKMLIKAI ALATQSTESE VESLYKSLGD LGKAAEKLKA IYEEKLKKGA MSILAFVPVK 

       130        140        150        160        170        180 
RELTVSQVYE TLSRVALATG EGSRDIKLKL LAGLLSDASP KEAKYIIRFV EGRLRLGIGD 

       190        200        210        220        230        240 
ATIMDALAIV YGGGAHARPI VERAYNLRAD LGHIAKILAT QGLNALKGIK PQVGIPIRPM 

       250        260        270        280        290        300 
LAERLNNPVE ILKKVGGIAF VEYKYDGERA QIHKLGDKIW IYSRRLENIT HQYPDVVDYA 

       310        320        330        340        350        360 
RKYIKANEAI VEGEIVAYDP DTGELRPFQE LMHRKRKHDI HIAIKEVPVK VYLFDLLYVD 

       370        380        390        400        410        420 
GEDYTLKPLP ERRAKLVEII EQTETFQIAE YIRTNNPDEL EKFFLKAIED GAEGVMIKAL 

       430        440        450        460        470        480 
HKNAIYQAGT RGWLWIKYKR DYKSEMIDTV DLVVIGAFYG RGRRGGKYGA LLMASYNPDK 

       490        500        510        520        530        540 
DVFESVCKVG SGFKDEDIDK LPEMLKPYII EHKHPRVVAR MKPDVWVTPA LVAEIIGAEL 

       550        560        570        580        590 
TLSPLHTCCL DIIKPGVGIS IRFPRFIRWR PDKGPEDATT SQELLEMYKR QLKKLSE

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References

[1]

"The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic Crenarchaeota."
Anderson I.J., Dharmarajan L., Rodriguez J., Hooper S., Porat I., Ulrich L.E., Elkins J.G., Mavromatis K., Sun H., Land M., Lapidus A., Lucas S., Barry K., Huber H., Zhulin I.B., Whitman W.B., Mukhopadhyay B., Woese C., Bristow J., Kyrpides N.
BMC Genomics 10:145-145(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 43588 / DSM 3639 / F1.

[2]

"Complete genome sequence of Staphylothermus marinus Stetter and Fiala 1986 type strain F1."
Anderson I.J., Sun H., Lapidus A., Copeland A., Glavina Del Rio T., Tice H., Dalin E., Lucas S., Barry K., Land M., Richardson P., Huber H., Kyrpides N.C.
Stand. Genomic Sci. 1:183-188(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 43588 / DSM 3639 / F1.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP000575 Genomic DNA. Translation: ABN70409.1. Different initiation.
RefSeq	YP_001041317.1. NC_009033.1.
3D structure databases
ModBase	Search...
Protein-protein interaction databases
STRING	399550.Smar_1318.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	ABN70409; ABN70409; Smar_1318.
GeneID	4906593.
KEGG	smr:Smar_1318.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG1793.
HOGENOM	HOG000036008.
KO	K10747.
ProtClustDB	PRK01109.
Enzyme and pathway databases
BioCyc	SMAR399550:GHK2-1363-MONOMER.
Family and domain databases
Gene3D	1.10.3260.10. 1 hit. 2.40.50.140. 1 hit.
HAMAP	MF_00407. DNA_ligase.
InterPro	IPR022865. 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]
Pfam	PF04679. DNA_ligase_A_C. 1 hit. PF01068. DNA_ligase_A_M. 1 hit. PF04675. DNA_ligase_A_N. 1 hit. [Graphical view]
SUPFAM	SSF50249. Nucleic_acid_OB. 1 hit. SSF117018. SSF117018. 1 hit.
TIGRFAMs	TIGR00574. dnl1. 1 hit.
PROSITE	PS00697. DNA_LIGASE_A1. 1 hit. PS00333. DNA_LIGASE_A2. 1 hit. PS50160. DNA_LIGASE_A3. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

DNLI_STAMF

Accession

Primary (citable) accession number: A3DP49

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 3, 2009
Last sequence update:	March 3, 2009
Last modified:	May 1, 2013
This is version 54 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Sites

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Entry information

Relevant documents