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UniProtKB - P25772 (LIGB_ECOLI)

Entry version 150 (02 Dec 2020)
Sequence version 2 (01 Jul 1993)
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Protein

DNA ligase B

Gene

ligB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score:

Annotation score:4 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>-Experimental evidence at protein leveli <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

Catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction.1 Publication

Miscellaneous

Considerably less active in nick joining than LigA.

<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

  • NAD(+) + (deoxyribonucleotide)(n)-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)(m) = (deoxyribonucleotide)(n+m) + AMP + beta-nicotinamide D-nucleotide. EC:6.5.1.2

<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+1 Publication, Mn2+1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<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 sitei124N6-AMP-lysine intermediateCurated1

<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

  • DNA ligase (NAD+) activity Source: EcoCyc
Complete GO annotation on QuickGO ...

GO - Biological processi

Complete GO annotation on QuickGO ...

<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 processDNA damage, DNA repair, DNA replication
LigandMagnesium, Manganese, NAD

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		EcoCyc:EG11334-MONOMER
MetaCyc:EG11334-MONOMER

<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 B (EC:6.5.1.2)
Alternative name(s):
Polydeoxyribonucleotide synthase [NAD(+)] B
<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:ligB
Synonyms:yicF
Ordered Locus Names:b3647, JW3622
<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>OrganismiEscherichia coli (strain K12)
<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 identifieri83333 [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 lineageiBacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia ›
<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
  • UP000000318 <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
  • UP000000625 Componenti: Chromosome

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

GO - Cellular componenti

Complete GO annotation on QuickGO ...

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology%5Fand%5Fbiotech%5Fsection">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi124K → A: Loss of activity. 1 Publication1

<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_00001617761 – 560DNA ligase BAdd BLAST560

Proteomic databases

PaxDb, a database of protein abundance averages across all three domains of life

More...PaxDbi		P25772

PRoteomics IDEntifications database

More...PRIDEi		P25772

<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

The Biological General Repository for Interaction Datasets (BioGRID)

More...BioGRIDi		4262567, 167 interactors

Protein interaction database and analysis system

More...IntActi		P25772, 3 interactors

STRING: functional protein association networks

More...STRINGi		511145.b3647

<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		P25772

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 NAD-dependent DNA ligase family. LigB subfamily.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		COG0272, Bacteria

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		CLU_489786_0_0_6

Database for complete collections of gene phylogenies

More...PhylomeDBi		P25772

Family and domain databases

HAMAP database of protein families

More...HAMAPi		MF_01587, DNA_ligase_B, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR018239, DNA_ligase_AS
IPR020923, DNA_ligase_B
IPR033136, DNA_ligase_CS
IPR013839, DNAligase_adenylation
IPR013840, DNAligase_N
IPR012340, NA-bd_OB-fold
IPR004150, NAD_DNA_ligase_OB
IPR010994, RuvA_2-like

Pfam protein domain database

More...Pfami		View protein in Pfam
PF01653, DNA_ligase_aden, 1 hit
PF03120, DNA_ligase_OB, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...SMARTi		View protein in SMART
SM00532, LIGANc, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF47781, SSF47781, 1 hit
SSF50249, SSF50249, 1 hit

PROSITE; a protein domain and family database

More...PROSITEi		View protein in PROSITE
PS01055, DNA_LIGASE_N1, 1 hit
PS01056, DNA_LIGASE_N2, 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.

P25772-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MKVWMAILIG ILCWQSSVWA VCPAWSPARA QEEISRLQQQ IKQWDDDYWK 
        60         70         80         90        100
EGKSEVEDGV YDQLSARLTQ WQRCFGSEPR DVMMPPLNGA VMHPVAHTGV 
       110        120        130        140        150
RKMVDKNALS LWMRERSDLW VQPKVDGVAV TLVYRDGKLN KAISRGNGLK 
       160        170        180        190        200
GEDWTQKVSL ISAVPQTVSG PLANSTLQGE IFLQREGHIQ QQMGGINARA 
       210        220        230        240        250
KVAGLMMRQD DSDTLNSLGV FVWAWPDGPQ LMSDRLKELA TAGFTLTQTY 
       260        270        280        290        300
TRAVKNADEV ARVRNEWWKA ELPFVTDGVV VRAAKEPESR HWLPGQAEWL 
       310        320        330        340        350
VAWKYQPVAQ VAEVKAIQFA VGKSGKISVV ASLAPVMLDD KKVQRVNIGS 
       360        370        380        390        400
VRRWQEWDIA PGDQILVSLA GQGIPRIDDV VWRGAERTKP TPPENRFNSL 
       410        420        430        440        450
TCYFASDVCQ EQFISRLVWL GAKQVLGLDG IGEAGWRALH QTHRFEHIFS 
       460        470        480        490        500
WLLLTPEQLQ NTPGIAKSKS AQLWHQFNLA RKQPFTRWVM AMGIPLTRAA 
       510        520        530        540        550
LNASDERSWS QLLFSTEQFW QQLPGTGSGR ARQVIEWKEN AQIKKLGSWL 
       560
AAQQITGFEP
Length:560
Mass (Da):63,179
Last modified:July 1, 1993 - v2
<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:i2C1BA1F9B247A599
GO

<p>This subsection of the 'Sequence' section reports difference(s) between the protein sequence shown in the UniProtKB entry and other available protein sequences derived from the same gene.<p><a href='/help/sequence_caution' target='_top'>More...</a></p>Sequence cautioni

The sequence AAA62000 differs from that shown. Reason: Erroneous initiation. Extended N-terminus.Curated
The sequence AAB88710 differs from that shown. Reason: Erroneous initiation. Extended N-terminus.Curated

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
L10328 Genomic DNA Translation: AAA62000.1 Different initiation.
U00096 Genomic DNA Translation: AAC76671.2
AP009048 Genomic DNA Translation: BAE77646.1
M84400 Genomic DNA Translation: AAB88710.1 Different initiation.

Protein sequence database of the Protein Information Resource

More...PIRi		A65166

NCBI Reference Sequences

More...RefSeqi		NP_418104.2, NC_000913.3
WP_000870036.1, NZ_LN832404.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		AAC76671; AAC76671; b3647
BAE77646; BAE77646; BAE77646

Database of genes from NCBI RefSeq genomes

More...GeneIDi		948164

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		ecj:JW3622
eco:b3647

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|511145.12.peg.3767

<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
L10328 Genomic DNA Translation: AAA62000.1 Different initiation.
U00096 Genomic DNA Translation: AAC76671.2
AP009048 Genomic DNA Translation: BAE77646.1
M84400 Genomic DNA Translation: AAB88710.1 Different initiation.
PIRiA65166
RefSeqiNP_418104.2, NC_000913.3
WP_000870036.1, NZ_LN832404.1

3D structure databases

SMRiP25772
ModBaseiSearch...

Protein-protein interaction databases

BioGRIDi4262567, 167 interactors
IntActiP25772, 3 interactors
STRINGi511145.b3647

Proteomic databases

PaxDbiP25772
PRIDEiP25772

Protocols and materials databases

The DNASU plasmid repository

More...DNASUi		948164

Genome annotation databases

EnsemblBacteriaiAAC76671; AAC76671; b3647
BAE77646; BAE77646; BAE77646
GeneIDi948164
KEGGiecj:JW3622
eco:b3647
PATRICifig|511145.12.peg.3767

Organism-specific databases

EchoBASE - an integrated post-genomic database for E. coli

More...EchoBASEi		EB1310

Phylogenomic databases

eggNOGiCOG0272, Bacteria
HOGENOMiCLU_489786_0_0_6
PhylomeDBiP25772

Enzyme and pathway databases

BioCyciEcoCyc:EG11334-MONOMER
MetaCyc:EG11334-MONOMER

Miscellaneous databases

Protein Ontology

More...PROi		PR:P25772

Family and domain databases

HAMAPiMF_01587, DNA_ligase_B, 1 hit
InterProiView protein in InterPro
IPR018239, DNA_ligase_AS
IPR020923, DNA_ligase_B
IPR033136, DNA_ligase_CS
IPR013839, DNAligase_adenylation
IPR013840, DNAligase_N
IPR012340, NA-bd_OB-fold
IPR004150, NAD_DNA_ligase_OB
IPR010994, RuvA_2-like
PfamiView protein in Pfam
PF01653, DNA_ligase_aden, 1 hit
PF03120, DNA_ligase_OB, 1 hit
SMARTiView protein in SMART
SM00532, LIGANc, 1 hit
SUPFAMiSSF47781, SSF47781, 1 hit
SSF50249, SSF50249, 1 hit
PROSITEiView protein in PROSITE
PS01055, DNA_LIGASE_N1, 1 hit
PS01056, DNA_LIGASE_N2, 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 nameiLIGB_ECOLI
<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: P25772
Secondary accession number(s): P78120, Q2M7W0
<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: May 1, 1992
Last sequence update: July 1, 1993
Last modified: December 2, 2020
This is version 150 of the entry and version 2 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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