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UniProtKB - B7J653 (DNLJ_ACIF2)

Entry version 73 (02 Dec 2020)
Sequence version 1 (10 Feb 2009)
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Protein

DNA ligase

Gene

ligA

Organism
Acidithiobacillus ferrooxidans (strain ATCC 23270 / DSM 14882 / CIP 104768 / NCIMB 8455) (Ferrobacillus ferrooxidans (strain ATCC 23270))
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 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. It is essential for DNA replication and repair of damaged DNA.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

  • NAD(+) + (deoxyribonucleotide)(n)-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)(m) = (deoxyribonucleotide)(n+m) + AMP + beta-nicotinamide D-nucleotide.UniRule annotation 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+UniRule annotation, Mn2+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 sitei116NADUniRule 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 sitei118N6-AMP-lysine intermediateUniRule annotation1
Binding sitei139NADUniRule annotation1
Binding sitei176NADUniRule annotation1
Binding sitei292NADUniRule annotation1
Binding sitei316NADUniRule annotation1
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the 'Description' field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi410ZincUniRule annotation1
Metal bindingi413ZincUniRule annotation1
Metal bindingi428ZincUniRule annotation1
Metal bindingi434ZincUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes a region in the protein which binds nucleotide phosphates. It always involves more than one amino acid and includes all residues involved in nucleotide-binding.<p><a href='/help/np_bind' target='_top'>More...</a></p>Nucleotide bindingi36 – 40NADUniRule annotation5
Nucleotide bindingi85 – 86NADUniRule annotation2

<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

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, Metal-binding, NAD, Zinc

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		AFER243159:G1GU1-727-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 ligaseUniRule annotation (EC:6.5.1.2UniRule annotation)
Alternative name(s):
Polydeoxyribonucleotide synthase [NAD(+)]UniRule 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:ligAUniRule annotation
Ordered Locus Names:AFE_0757
<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>OrganismiAcidithiobacillus ferrooxidans (strain ATCC 23270 / DSM 14882 / CIP 104768 / NCIMB 8455) (Ferrobacillus ferrooxidans (strain ATCC 23270))
<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 identifieri243159 [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 › Acidithiobacillia › Acidithiobacillales › Acidithiobacillaceae › Acidithiobacillus ›
<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
  • UP000001362 <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_00003802801 – 671DNA ligaseAdd BLAST671

Proteomic databases

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

More...PaxDbi		B7J653

<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		243159.AFE_0757

<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		B7J653

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

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family%5Fand%5Fdomains%5Fsection">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini591 – 671BRCTUniRule annotationAdd BLAST81

<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. LigA subfamily.UniRule annotation

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_007764_2_1_6

Identification of Orthologs from Complete Genome Data

More...OMAi		HDVEHEI

Database of Orthologous Groups

More...OrthoDBi		241401at2

Family and domain databases

Conserved Domains Database

More...CDDi		cd00114, LIGANc, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...Gene3Di		3.40.50.10190, 1 hit

HAMAP database of protein families

More...HAMAPi		MF_01588, DNA_ligase_A, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR001357, BRCT_dom
IPR036420, BRCT_dom_sf
IPR041663, DisA/LigA_HHH
IPR018239, DNA_ligase_AS
IPR033136, DNA_ligase_CS
IPR001679, DNAligase
IPR013839, DNAligase_adenylation
IPR013840, DNAligase_N
IPR003583, Hlx-hairpin-Hlx_DNA-bd_motif
IPR012340, NA-bd_OB-fold
IPR004150, NAD_DNA_ligase_OB
IPR010994, RuvA_2-like
IPR004149, Znf_DNAligase_C4

Pfam protein domain database

More...Pfami		View protein in Pfam
PF00533, BRCT, 1 hit
PF01653, DNA_ligase_aden, 1 hit
PF03120, DNA_ligase_OB, 1 hit
PF03119, DNA_ligase_ZBD, 1 hit
PF12826, HHH_2, 1 hit

PIRSF; a whole-protein classification database

More...PIRSFi		PIRSF001604, LigA, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...SMARTi		View protein in SMART
SM00292, BRCT, 1 hit
SM00278, HhH1, 4 hits
SM00532, LIGANc, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF47781, SSF47781, 1 hit
SSF50249, SSF50249, 1 hit
SSF52113, SSF52113, 1 hit

TIGRFAMs; a protein family database

More...TIGRFAMsi		TIGR00575, dnlj, 1 hit

PROSITE; a protein domain and family database

More...PROSITEi		View protein in PROSITE
PS50172, BRCT, 1 hit
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.

B7J653-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MERVNHTDFE RIQQLRAELV AANNAYYRED SPTLSDAEYD ARLRELRTLE 
        60         70         80         90        100
DRNPQWQSAD SPTQRVGAAP VEVFGEVHYA IPLTSLDNVF DQDGFSDWLA 
       110        120        130        140        150
RVQKGLGRED VPLSAEPKFD GLSVNIRYIE GKLVQAGTRG DGQTGEDVTA 
       160        170        180        190        200
NVRTIRNVPL QLTGKDWPEL LEVRGEVVIP VAAFRRLNGE RLRAGDNPFA 
       210        220        230        240        250
NPRNAAAGSL RQLDSSVTAK RPLAYFPWGW GESSVPLGKS HIAVMERLSA 
       260        270        280        290        300
WGFEVTSYLR GVHELTECQR YFSEMQKIRE GMPFEIDGLV FKVDDLLARE 
       310        320        330        340        350
QLGFTARAPR WAIAYKFPAH EERTVVEDIL ASVGRTGVIT PVAVLKPVQV 
       360        370        380        390        400
GGVTVSRASL HNQDEVDRKD IRVGDTVLVR RAGDVIPEVV MVIKEERPPA 
       410        420        430        440        450
TQPWHMPQRC PVCGSEVLRL ANESAHRCMG GLYCPAQRMG AIRHFASRRA 
       460        470        480        490        500
MDIRGLGEKL VEQLVGHGLV HTVADIYHLD EAALCGLERM ASRSAQKLLA 
       510        520        530        540        550
EIDRSRHTSL PRFLYALGIR QVGEGTAKSL AIYFGDLDPL MAATPELLQN 
       560        570        580        590        600
IPDVGPIVAE SVAHFFAQPH NRDVIAALRA AGVQWAVVQP QKGGRFQGMT 
       610        620        630        640        650
LVLTGALDNM TREEAKTAIE NAGGKVSGSV SAKTSYVVVG KDPGSKAEKA 
       660        670 
AKLGVKQLTE AQFLAMFSEK E
Length:671
Mass (Da):73,917
Last modified:February 10, 2009 - 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:i5AFBDACB0D148DFF
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
CP001219 Genomic DNA Translation: ACK79541.1

NCBI Reference Sequences

More...RefSeqi		WP_012536336.1, NC_011761.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		ACK79541; ACK79541; AFE_0757

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		afr:AFE_0757

<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
CP001219 Genomic DNA Translation: ACK79541.1
RefSeqiWP_012536336.1, NC_011761.1

3D structure databases

SMRiB7J653
ModBaseiSearch...

Protein-protein interaction databases

STRINGi243159.AFE_0757

Proteomic databases

PaxDbiB7J653

Genome annotation databases

EnsemblBacteriaiACK79541; ACK79541; AFE_0757
KEGGiafr:AFE_0757

Phylogenomic databases

eggNOGiCOG0272, Bacteria
HOGENOMiCLU_007764_2_1_6
OMAiHDVEHEI
OrthoDBi241401at2

Enzyme and pathway databases

BioCyciAFER243159:G1GU1-727-MONOMER

Family and domain databases

CDDicd00114, LIGANc, 1 hit
Gene3Di3.40.50.10190, 1 hit
HAMAPiMF_01588, DNA_ligase_A, 1 hit
InterProiView protein in InterPro
IPR001357, BRCT_dom
IPR036420, BRCT_dom_sf
IPR041663, DisA/LigA_HHH
IPR018239, DNA_ligase_AS
IPR033136, DNA_ligase_CS
IPR001679, DNAligase
IPR013839, DNAligase_adenylation
IPR013840, DNAligase_N
IPR003583, Hlx-hairpin-Hlx_DNA-bd_motif
IPR012340, NA-bd_OB-fold
IPR004150, NAD_DNA_ligase_OB
IPR010994, RuvA_2-like
IPR004149, Znf_DNAligase_C4
PfamiView protein in Pfam
PF00533, BRCT, 1 hit
PF01653, DNA_ligase_aden, 1 hit
PF03120, DNA_ligase_OB, 1 hit
PF03119, DNA_ligase_ZBD, 1 hit
PF12826, HHH_2, 1 hit
PIRSFiPIRSF001604, LigA, 1 hit
SMARTiView protein in SMART
SM00292, BRCT, 1 hit
SM00278, HhH1, 4 hits
SM00532, LIGANc, 1 hit
SUPFAMiSSF47781, SSF47781, 1 hit
SSF50249, SSF50249, 1 hit
SSF52113, SSF52113, 1 hit
TIGRFAMsiTIGR00575, dnlj, 1 hit
PROSITEiView protein in PROSITE
PS50172, BRCT, 1 hit
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 nameiDNLJ_ACIF2
<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: B7J653
<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: July 28, 2009
Last sequence update: February 10, 2009
Last modified: December 2, 2020
This is version 73 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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