Reviewed, UniProtKB/Swiss-Prot A3MS62 (DNLI_PYRCJ)

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:	Pcal_0039

Organism

Pyrobaculum calidifontis (strain JCM 11548 / VA1) [Complete proteome] [HAMAP]

Taxonomic identifier

410359 [NCBI]

Taxonomic lineage

Archaea › Crenarchaeota › Thermoprotei › Thermoproteales › Thermoproteaceae › Pyrobaculum

Protein attributes

Sequence length	583 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Inferred from homology.

General annotation (Comments)

Function	This protein seals, during DNA replication, DNA recombination and DNA repair, nicks in double-stranded DNA By similarity.
Catalytic activity	ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m).
Sequence similarities	Belongs to the ATP-dependent DNA ligase family.

Ontologies

Keywords
Biological process	Cell cycle Cell division DNA damage DNA recombination DNA repair DNA replication
Ligand	ATP-binding Nucleotide-binding
Molecular function	Ligase
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	DNA recombination Inferred from electronic annotation. Source: HAMAP DNA repair 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
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 583	583	DNA ligase		PRO_1000049876
Sites
	Active site	251	1	N6-AMP-lysine intermediate By similarity

Sequences

	Sequence		Length	Mass (Da)
	A3MS62-1 [UniParc]. Last modified April 3, 2007. Version 1. Checksum: 3B3B4E318FC2C215	FASTA	583	64,840
	10 20 30 40 50 60 MQFGELAKVL AAVESTTQRT TMVKLLTSLF KKAKPEEIDK IVYFILGDLR PPWEGVELGV 70 80 90 100 110 120 AEKLCIRAIS KATGLSAAEL EGWYKKSGDV GEVARRALAA GKRPTLLAFA QQKPLEVAEV 130 140 150 160 170 180 YDTLLKVAKA AGEGAQDLKV SLLSSLFSRA SPEEAKYIAR FVVGKLRLGV ADMTLIEALS 190 200 210 220 230 240 EAFGVSKEGL ERAYHVYPDL GRLARHVAEG RPLEEIKITP GVPVLPMLAQ RLSSASEILA 250 260 270 280 290 300 KLGGTAICEY KYDGERAQIH LREGSVKIFS RRLEDITHAY PDVAKAVKEA VKAREAILEG 310 320 330 340 350 360 EIVAVDPDTG EMLPFQELMH RKRKHDVAEA MEAYPAVLYL FDLLYVDGED LTTQPLIYRR 370 380 390 400 410 420 LRLSEVVEEG GDVYIAKWGM FDGAEDVDLF FHEAVSLGTE GLICKSPTST YEMGARGWNW 430 440 450 460 470 480 IKYKRDYRSE MIDTVDLVVV GAFHGRGKRA GLYGAFLLAA YDPSTDMFYT VCKVGSGFTD 490 500 510 520 530 540 ADLRRMYDML QPLKIPHRHP RVVSKMQPDV WFVPQVVIEV IGAEITLSPL HTCCIGAVKP 550 560 570 580 GVGLAIRFPR FTGRYRTDKR PEDATTTKEL VEMYQRQKKV PTT

References

[1]

"Complete sequence of Pyrobaculum calidifontis JCM 11548." Copeland A., Lucas S., Lapidus A., Barry K., Glavina del Rio T., Dalin E., Tice H., Pitluck S., Chain P., Malfatti S., Shin M., Vergez L., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N., Mikhailova N. , Cozen A.E., Fitz-Gibbon S.T., House C.H., Saltikov C., Lowe T.M., Richardson P. Submitted (FEB-2007) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

Cross-references

Sequence databases
EMBLGenBankDDBJ	CP000561 Genomic DNA. Translation: ABO07479.1.
RefSeq	YP_001054945.1.
3D structure databases
ModBase	Search...
Genome annotation databases
GeneID	4908550.
GenomeReviews	Gene locus Pcal_0039 in contig CP000561_GR.
KEGG	pcl:Pcal_0039.
Organism-specific databases
CMR	Search...
Family and domain databases
HAMAP	MF_00407. [Tree]
InterPro	IPR000977. DNA_ligase. IPR012309. DNA_ligase_A_C. IPR012310. DNA_ligase_A_M. IPR012308. DNA_ligase_A_N. IPR016059. DNA_ligase_CS. IPR012340. NA-bd_OB-fold. [Graphical view]
Gene3D	G3DSA:2.40.50.140. OB_NA_bd_sub. 1 hit.
Pfam	PF04679. DNA_ligase_A_C. 1 hit. PF01068. DNA_ligase_A_M. 1 hit. PF04675. DNA_ligase_A_N. 1 hit. [Graphical view]
TIGRFAMs	TIGR00574. dnl1. 1 hit.
PROSITE	PS00697. DNA_LIGASE_A1. 1 hit. PS00333. DNA_LIGASE_A2. False negative. PS50160. DNA_LIGASE_A3. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

DNLI_PYRCJ

Accession

Primary (citable) accession number: A3MS62

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 15, 2008
Last sequence update:	April 3, 2007
Last modified:	November 25, 2008
This is version 14 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)