A5UKX2 (DNLI_METS3) Reviewed, UniProtKB/Swiss-Prot

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:	Msm_0645

Organism

Methanobrevibacter smithii (strain PS / ATCC 35061 / DSM 861) [Complete proteome] [HAMAP]

Taxonomic identifier

420247 [NCBI]

Taxonomic lineage

Archaea › Euryarchaeota › Methanobacteria › Methanobacteriales › Methanobacteriaceae › Methanobrevibacter

Protein attributes

Sequence length	551 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 MF_00407
Catalytic activity	ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m). HAMAP MF_00407
Cofactor	Divalent metal cations By similarity. HAMAP MF_00407
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 ligation involved in DNA repair Inferred from electronic annotation. Source: InterPro DNA recombination Inferred from electronic annotation. Source: UniProtKB-KW DNA replication Inferred from electronic annotation. Source: UniProtKB-KW 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: UniProtKB-KW DNA binding Inferred from electronic annotation. Source: InterPro DNA ligase (ATP) activity Inferred from electronic annotation. Source: EC 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 – 551	551	DNA ligase HAMAP MF_00407		PRO_1000049872
Sites
	Active site	248	1	N6-AMP-lysine intermediate By similarity
	Binding site	246	1	ATP By similarity
	Binding site	253	1	ATP By similarity
	Binding site	268	1	ATP By similarity
	Binding site	298	1	ATP By similarity
	Binding site	337	1	ATP By similarity
	Binding site	414	1	ATP By similarity
	Binding site	420	1	ATP By similarity

Sequences

	Sequence		Length	Mass (Da)
	A5UKX2 [UniParc]. Last modified July 10, 2007. Version 1. Checksum: 5CB10B16F770ACFB	FASTA	551	61,948
	10 20 30 40 50 60 MKYQELVDVY SALENTTKRL EKTQIISNFL LKLDSTTLEQ VGLLILGSIF PAWSDKEIGI 70 80 90 100 110 120 GNKLVMQAVG EAVGVTPDKV EDAVRDQGDI GLACISLYAK KSQTTFFSQP LTIDFVFKSL 130 140 150 160 170 180 RKLSEKSGAR STKRKIDIIL EMLSQASASE AKYLTRTILE ELRIGVGEGV VRDAIAQAFN 190 200 210 220 230 240 IDKSVVERAM MLTNDLGLIA VVAKEKGEGG LKELNLTPGT PVKPMLAQLA PPIPEIINEM 250 260 270 280 290 300 GVAICETKYD GIRLQVHRHS DEIKIFTRRL ENITHALPEI VDLFNEYLPH EDYIVEGEVI 310 320 330 340 350 360 ATRDGNPLSF QNILHRVRRK HNIDEAMEQV PLKVFLFDLL YYIVPMIDEP LLKRRKKLEE 370 380 390 400 410 420 IVNTTPDEIN LSNMVYGTPD TIKEVEDLFE LSIAQHHEGI MIKDAGEPYI PGLRGKKMLK 430 440 450 460 470 480 YKAEPETLDM VVVGGTYGIG KRGDFVGSYL VSLRDEDNNL KTVAYVATGL DDATLEYLTK 490 500 510 520 530 540 KMKEYELSTK GREIVVEPKI VLEVAFSEIV ESPEYETGYS LRFPVVKNIR KDKGVDDIDT 550 VERLISMYET Q

References

[1]

"Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut." Samuel B.S., Hansen E.E., Manchester J.K., Coutinho P.M., Henrissat B., Fulton R., Latreille P., Kim K., Wilson R.K., Gordon J.I. Proc. Natl. Acad. Sci. U.S.A. 104:10643-10648(2007) [PubMed: 17563350] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: PS / ATCC 35061 / DSM 861.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP000678 Genomic DNA. Translation: ABQ86850.1.
RefSeq	YP_001273218.1. NC_009515.1.
3D structure databases
ProteinModelPortal	A5UKX2.
ModBase	Search...
Protein-protein interaction databases
STRING	A5UKX2.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	5216232.
GenomeReviews	Gene locus Msm_0645 in contig CP000678_GR.
KEGG	msi:Msm_0645.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	arNOG04596.
HOGENOM	HBG570821.
OMA	GRPRPFQ.
ProtClustDB	CLSK798208.
Family and domain databases
HAMAP	MF_00407. DNA_ligase. [Tree]
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. IPR016027. NA-bd_OB-fold-like. [Graphical view]
Gene3D	G3DSA:1.10.3260.10. DNA_ligase_ATP-dep_N. 1 hit. G3DSA:2.40.50.140. OB_NA_bd_sub. 1 hit.
KO	K10747.
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. False negative. PS00333. DNA_LIGASE_A2. 1 hit. PS50160. DNA_LIGASE_A3. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

DNLI_METS3

Accession

Primary (citable) accession number: A5UKX2

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 15, 2008
Last sequence update:	July 10, 2007
Last modified:	November 16, 2011
This is version 39 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program