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Entry version 87 (07 Oct 2020)
Sequence version 1 (06 Feb 2007)
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Protein

DNA ligase 2

Gene

lig2

Organism
Thermofilum pendens (strain DSM 2475 / Hrk 5)
Status
Reviewed-Annotation score:

Annotation score:3 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Protein inferred from homologyi <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair.UniRule annotation

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

  • ATP + (deoxyribonucleotide)(n)-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)(m) = (deoxyribonucleotide)(n+m) + AMP + diphosphate.UniRule annotation EC:6.5.1.1

<p>This subsection of the 'Function' section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

Mg2+UniRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei263ATPUniRule annotation1
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei265N6-AMP-lysine intermediateUniRule annotation1
Binding sitei270ATPUniRule annotation1
Binding sitei285ATPUniRule annotation1
Binding sitei314ATPUniRule annotation1
Binding sitei354ATPUniRule annotation1
Binding sitei432ATPUniRule annotation1
Binding sitei438ATPUniRule annotation1

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionLigase
Biological processCell cycle, Cell division, DNA damage, DNA recombination, DNA repair, DNA replication
LigandATP-binding, Magnesium, Metal-binding, Nucleotide-binding

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
DNA ligase 2UniRule annotation (EC:6.5.1.1UniRule annotation)
Alternative name(s):
Polydeoxyribonucleotide synthase [ATP] 2UniRule annotation
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:lig2UniRule annotation
Ordered Locus Names:Tpen_0750
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiThermofilum pendens (strain DSM 2475 / Hrk 5)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri368408 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiArchaeaCrenarchaeotaThermoproteiThermoprotealesThermofilaceaeThermofilum
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000000641 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00003652661 – 601DNA ligase 2Add BLAST601

Proteomic databases

PRoteomics IDEntifications database

More...
PRIDEi
A1RY72

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
368408.Tpen_0750

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...
SMRi
A1RY72

Database of comparative protein structure models

More...
ModBasei
Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the ATP-dependent DNA ligase family.UniRule annotation

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
arCOG01347, Archaea

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_005138_6_0_2

KEGG Orthology (KO)

More...
KOi
K10747

Identification of Orthologs from Complete Genome Data

More...
OMAi
WLFEESY

Database of Orthologous Groups

More...
OrthoDBi
52275at2157

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
1.10.3260.10, 1 hit

HAMAP database of protein families

More...
HAMAPi
MF_00407, DNA_ligase, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in 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
IPR036599, DNA_ligase_N_sf
IPR012340, NA-bd_OB-fold

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF04679, DNA_ligase_A_C, 1 hit
PF01068, DNA_ligase_A_M, 1 hit
PF04675, DNA_ligase_A_N, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF117018, SSF117018, 1 hit
SSF50249, SSF50249, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR00574, dnl1, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS00697, DNA_LIGASE_A1, 1 hit
PS50160, DNA_LIGASE_A3, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

A1RY72-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MGAAGDLPYS VLADFYERIE STSSRLAMTD YLVALFKKTP PEVIDKVVYL
60 70 80 90 100
TQGQLRPDYE GVELGVAEKL ALRALAKASG RHLKDVEDLY KKTGDIGAVA
110 120 130 140 150
EKLLTAPGGG LLEFFGTPVQ KKELTVSQVY SALMKIAQAS GEGAQETKVN
160 170 180 190 200
TLVALLQDAK PKEARYILRT VLGRLRLGIA DMTILDALAA AFAGSKAARD
210 220 230 240 250
VIERAYTKHP DLGYIAKLLA TKGLDAVASL KIEVGIPVLP MLAERLSDPA
260 270 280 290 300
EILEKLGGKC LAEYKYDGER VQAHKSGDKV LLFSRRLENI THHYPDVVEY
310 320 330 340 350
VKRLKVREAI VEGEIVAYNP DTGEMLPFQE LMHRRRKYDV EKAMKEYPVR
360 370 380 390 400
VYLFDVIYMD GEELIEKPLD QRRLILEKIV PEGDEDILLS TAKVVGDAKD
410 420 430 440 450
LLHFFEQAIS EGCEGVMCKS IGPGSIYQMG ARGWLWIKFK RDYRMEMTDT
460 470 480 490 500
VDLVVVGGFH GRGKRAGTYG ALLMAAYDPE TDTFKTVCKV GTGFTDEDLA
510 520 530 540 550
KLPELLDPYK IPHRHPRVFS KIEADVWFVP AVVLEIIGAE ITLSPLHTCA
560 570 580 590 600
LNKLEEGAGL AIRFPRFTGR YRFDKKPEQA TTESELIEMY KSQKKTALQQ

S
Length:601
Mass (Da):66,943
Last modified:February 6, 2007 - v1
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i8AA565878E7AF78B
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

More...
GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
CP000505 Genomic DNA Translation: ABL78152.1

NCBI Reference Sequences

More...
RefSeqi
WP_011752417.1, NC_008698.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
ABL78152; ABL78152; Tpen_0750

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
4600401

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
tpe:Tpen_0750

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000505 Genomic DNA Translation: ABL78152.1
RefSeqiWP_011752417.1, NC_008698.1

3D structure databases

SMRiA1RY72
ModBaseiSearch...

Protein-protein interaction databases

STRINGi368408.Tpen_0750

Proteomic databases

PRIDEiA1RY72

Genome annotation databases

EnsemblBacteriaiABL78152; ABL78152; Tpen_0750
GeneIDi4600401
KEGGitpe:Tpen_0750

Phylogenomic databases

eggNOGiarCOG01347, Archaea
HOGENOMiCLU_005138_6_0_2
KOiK10747
OMAiWLFEESY
OrthoDBi52275at2157

Family and domain databases

Gene3Di1.10.3260.10, 1 hit
HAMAPiMF_00407, DNA_ligase, 1 hit
InterProiView protein in 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
IPR036599, DNA_ligase_N_sf
IPR012340, NA-bd_OB-fold
PfamiView protein in Pfam
PF04679, DNA_ligase_A_C, 1 hit
PF01068, DNA_ligase_A_M, 1 hit
PF04675, DNA_ligase_A_N, 1 hit
SUPFAMiSSF117018, SSF117018, 1 hit
SSF50249, SSF50249, 1 hit
TIGRFAMsiTIGR00574, dnl1, 1 hit
PROSITEiView protein in PROSITE
PS00697, DNA_LIGASE_A1, 1 hit
PS50160, DNA_LIGASE_A3, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiDNLI2_THEPD
<p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: A1RY72
<p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 3, 2009
Last sequence update: February 6, 2007
Last modified: October 7, 2020
This is version 87 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
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