Reviewed, UniProtKB/Swiss-Prot Q12X08 (DNLI_METBU)

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:	Mbur_1088

Organism

Methanococcoides burtonii (strain DSM 6242) [Complete proteome] [HAMAP]

Taxonomic identifier

259564 [NCBI]

Taxonomic lineage

Archaea › Euryarchaeota › Methanomicrobia › Methanosarcinales › Methanosarcinaceae › Methanococcoides

Protein attributes

Sequence length	567 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
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.
Catalytic activity	ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m). HAMAP MF_00407
Cofactor	Divalent metal cations By similarity.
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 Metal-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 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 – 567	567	DNA ligase HAMAP MF_00407		PRO_1000049869
Sites
	Active site	262	1	N6-AMP-lysine intermediate By similarity
	Binding site	260	1	ATP By similarity
	Binding site	267	1	ATP By similarity
	Binding site	282	1	ATP By similarity
	Binding site	312	1	ATP By similarity
	Binding site	352	1	ATP By similarity
	Binding site	427	1	ATP By similarity
	Binding site	433	1	ATP By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q12X08-1 [UniParc]. Last modified August 22, 2006. Version 1. Checksum: 3942FDE27D6C32F0	FASTA	567	62,743
	10 20 30 40 50 60 MTDFKEFADV CKQIEHISSS LEMTDVVSDM LKSISTEELP VVTHFVMGDV FPAWSVEQLG 70 80 90 100 110 120 VGTSLLYSAL SESSGLSLKE IEDLVRSTGD IGETAVAALG KKKKNKKKNQ ASLSFFSEDA 130 140 150 160 170 180 ASVSISIMDV FERFLDISRY SGAGSQSSKM RNLQFLFNSS SSEEARYLAR LTIEDLRIGV 190 200 210 220 230 240 GEGIVRDAIS KAFDVPAGDI ERGFMLTNDL GLVAVAAKEG GIEEISKLRM ELDRPIKMML 250 260 270 280 290 300 AQVTPSIEAA IKDLGMLAVE WKFDGARVQI HKKGDSINIF SRRLENVTLS LPDIVEAVKL 310 320 330 340 350 360 HVKADSAILE GEAVAVDENG APRAFQDILK RFRRKYDVET MVREIPLTLN LFDILYLNGD 370 380 390 400 410 420 VLMDQSLLRR REQLVACVEN CDSIKVDEQV LTDDVNVVND IYAAALNGGH EGVMLKNPEA 430 440 450 460 470 480 SYSPGKRGKN WLKKKPIMET LDLVVIAAEW GYGKRANLIG SYALACFDPE DGKFLPIGKV 490 500 510 520 530 540 ATGFSDEQLA ELTEVFSELI IGESGREIEL KPDVVFEIAF EEIQKSTNYG SGYALRFPRL 550 560 VNVREDKSPE EAETIDRIES IYLSQRG

References

[1]

"Complete sequence of Methanococcoides burtonii DSM 6242." Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Kadner K., Aerts A., Dehal P., Pitluck S., Martinez M., Schmutz J., Larimer F., Land M. , Hauser L., Kyrpides N., Anderson I., Franzmann P., Thomas T., Saunders N., Cavicchioli R., Sowers K., Richardson P. Submitted (MAR-2006) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

Cross-references

Sequence databases
EMBLGenBankDDBJ	CP000300 Genomic DNA. Translation: ABE52018.1.
RefSeq	YP_565768.1.
3D structure databases
ModBase	Search...
Genome annotation databases
GeneID	3998025.
GenomeReviews	Gene locus Mbur_1088 in contig CP000300_GR.
KEGG	mbu:Mbur_1088.
NMPDR	fig|259564.8.peg.1034.
Organism-specific databases
CMR	Search...
Phylogenomic databases
HOGENOM	Q12X08.
OMA	Q12X08. SNLHLGA.
Enzyme and pathway databases
BioCyc	MBUR259564:MBUR_1088-MON.
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_METBU

Accession

Primary (citable) accession number: Q12X08

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 15, 2008
Last sequence update:	August 22, 2006
Last modified:	June 16, 2009
This is version 25 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)