DNA ligase - Thermococcus sibiricus (strain MM 739 / DSM 12597)

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C6A2U9 (C6A2U9_THESM) Unreviewed, UniProtKB/TrEMBL

Last modified May 1, 2013. Version 31. History...

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

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

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

Names and origin

Protein names

Recommended name:
DNA ligase HAMAP-Rule MF_00407 RuleBase RU000617
EC=6.5.1.1 HAMAP-Rule MF_00407 RuleBase RU000617

Alternative name(s):
Polydeoxyribonucleotide synthase [ATP] HAMAP-Rule MF_00407

Gene names

Name:	lig HAMAP-Rule MF_00407
Ordered Locus Names:	TSIB_0885 EMBL ACS89944.1

Organism

Thermococcus sibiricus (strain MM 739 / DSM 12597) [Complete proteome] [HAMAP] EMBL ACS89944.1

Taxonomic identifier

Taxonomic lineage

Archaea › Euryarchaeota › Thermococci › Thermococcales › Thermococcaceae › Thermococcus ›

Protein attributes

Sequence length	560 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

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 RuleBase RU000617
Cofactor	Divalent metal cations By similarity. HAMAP-Rule MF_00407
Sequence similarities	Belongs to the ATP-dependent DNA ligase family. HAMAP-Rule MF_00407 RuleBase RU004196

Ontologies

Keywords
Biological process	Cell cycle Cell division HAMAP-Rule MF_00407 DNA damage DNA recombination HAMAP-Rule MF_00407 RuleBase RU000617 DNA repair HAMAP-Rule MF_00407 RuleBase RU000617 DNA replication HAMAP-Rule MF_00407 RuleBase RU000617
Ligand	ATP-binding HAMAP-Rule MF_00407 RuleBase RU000617 Metal-binding HAMAP-Rule MF_00407 Nucleotide-binding
Molecular function	Ligase HAMAP-Rule MF_00407 RuleBase RU000617 EMBL ACS89944.1
Technical term	3D-structure PDB 4EQ5 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

Sites

Active site

1

N6-AMP-lysine intermediate By similarity HAMAP-Rule MF_00407

Binding site

1

ATP By similarity HAMAP-Rule MF_00407

Binding site

1

ATP By similarity HAMAP-Rule MF_00407

Binding site

1

ATP By similarity HAMAP-Rule MF_00407

Binding site

1

ATP By similarity HAMAP-Rule MF_00407

Binding site

1

ATP By similarity HAMAP-Rule MF_00407

Binding site

1

ATP By similarity HAMAP-Rule MF_00407

Binding site

1

ATP By similarity HAMAP-Rule MF_00407

Sequences

Sequence

Length

Mass (Da)

Tools

C6A2U9 [UniParc].

Last modified September 1, 2009. Version 1.
Checksum: 3B20F1C68A04EDA8
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560

63,448

        10         20         30         40         50         60 
MLYKELVELY KRLEKTTLKT LKTKFVSDFL KSVEKPELLE VIPYLILGKV FPDWDERELG 

        70         80         90        100        110        120 
IGEKLLIKAV SMATGINSEE IENSVRDTGD LGESIALALN KRKQKSFFSQ PLTIERVYNT 

       130        140        150        160        170        180 
LVKIAEASGA GSQDRKLKYL ANLFMDASPD EGKYLARTVL GIMRTGVAEG LLRDALADAF 

       190        200        210        220        230        240 
KVRVELVERA YMLTSDFGFV AKVAKLEGDE GLAKVKIQVG KPIKPMLAQM AANVREALVE 

       250        260        270        280        290        300 
MGGEAEFEIK YDGARVQVHK NGNKVLIYSR RLENVTKSIP EVVERVKEAL KPEKVIVEGE 

       310        320        330        340        350        360 
LVAVEETGRP RPFQYVLRRF RRKYNIEEMI EKIPLELNLF DILYVDGQNM IDTPFMERRK 

       370        380        390        400        410        420 
VLESVVNSNE WIKSAENLIT KSPEEAEAFY HKALDLGHEG LMAKRLDSTY EPGNRGKKWL 

       430        440        450        460        470        480 
KIKPTMENLD LVVLGAEWGE GRRSGVLSSF LLGAYDPVKG DFVPVGKVGS GFTDEDLVEF 

       490        500        510        520        530        540 
TKMLKPLIKK EHGKEVELEP KVVIEVAYQE IQKSPKYESG FALRFPRYIA LREDKGPEDA 

       550        560 
DTVQRLAELY QFQERLKGGR

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Metabolic versatility and indigenous origin of the archaeon Thermococcus sibiricus, isolated from a siberian oil reservoir, as revealed by genome analysis." Mardanov A.V., Ravin N.V., Svetlitchnyi V.A., Beletsky A.V., Miroshnichenko M.L., Bonch-Osmolovskaya E.A., Skryabin K.G. Appl. Environ. Microbiol. 75:4580-4588(2009) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: MM 739 / DSM 12597.
[2]	"Expression, purification, crystallization and preliminary crystallographic analysis of a thermostable DNA ligase from the archaeon Thermococcus sibiricus." Petrova T.E., Bezsudnova E.Y., Dorokhov B.D., Slutskaya E.S., Polyakov K.M., Dorovatovskiy P.V., Ravin N.V., Skryabin K.G., Kovalchuk M.V., Popov V.O. Acta Crystallogr. F 68:163-165(2012) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.85 ANGSTROMS) OF 2-560.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

CP001463 Genomic DNA. Translation: ACS89944.1.

RefSeq

YP_002994293.1. NC_012883.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
4EQ5	X-ray	2.85	A	2-560	[»]

ProteinModelPortal

ModBase

Protein-protein interaction databases

STRING

604354.TSIB_0885.

Protocols and materials databases

StructuralBiologyKnowledgebase

Genome annotation databases

EnsemblBacteria

ACS89944; ACS89944; TSIB_0885.

GeneID

KEGG

Organism-specific databases

CMR

Phylogenomic databases

eggNOG

HOGENOM

KO

OMA

ProtClustDB

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

Entry information

Entry name

C6A2U9_THESM

Accession

Primary (citable) accession number: C6A2U9

Entry history

Integrated into UniProtKB/TrEMBL:	September 1, 2009
Last sequence update:	September 1, 2009
Last modified:	May 1, 2013
This is version 31 of the entry and version 1 of the sequence. [Complete history]

Entry status

Unreviewed (UniProtKB/TrEMBL)

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