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Entry version 72 (12 Aug 2020)
Sequence version 1 (26 May 2009)
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Protein

3'-phosphoesterase

Gene

ligD

Organism
Rhodococcus opacus (strain B4)
Status
Unreviewed-Annotation score:

Annotation score:2 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 predictedi <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

<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.ARBA 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

Mn2+ARBA annotation

<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 functionDNA-bindingARBA annotation, DNA-directed DNA polymeraseARBA annotation, ExonucleaseARBA annotation, Hydrolase, LigaseImportedARBA annotation, Multifunctional enzymeARBA annotation, Nuclease, Nucleotidyltransferase, Transferase
LigandManganeseARBA annotation

<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:
3'-phosphoesteraseARBA annotation (EC:6.5.1.1ARBA annotation)
Alternative name(s):
DNA repair polymeraseARBA annotation
NHEJ DNA polymeraseARBA annotation
Polydeoxyribonucleotide synthase [ATP]ARBA annotation
Polymerase/primaseARBA 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:ligDImported
Ordered Locus Names:ROP_51120Imported
<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>OrganismiRhodococcus opacus (strain B4)Imported
<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 identifieri632772 [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 lineageiBacteriaActinobacteriaCorynebacterialesNocardiaceaeRhodococcus
<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
  • UP000002212 <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 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>Domaini543 – 666DNA_LIGASE_A3InterPro annotationAdd BLAST124

Phylogenomic databases

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_008325_2_1_11

KEGG Orthology (KO)

More...
KOi
K01971

Identification of Orthologs from Complete Genome Data

More...
OMAi
QWLAHRM

Family and domain databases

Conserved Domains Database

More...
CDDi
cd04863, MtLigD_Pol_like, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR012309, DNA_ligase_ATP-dep_C
IPR012310, DNA_ligase_ATP-dep_cent
IPR014146, LigD_ligase_dom
IPR014144, LigD_PE_domain
IPR014145, LigD_pol_dom
IPR033649, MtLigD_Pol-like
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
PF13298, LigD_N, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF50249, SSF50249, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR02777, LigD_PE_dom, 1 hit
TIGR02778, ligD_pol, 1 hit
TIGR02779, NHEJ_ligase_lig, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
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.

C1ATU5-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MATAGTRQLT VDGHRLSLTN LGKVLYPESG TVKGEVIDYY SRIAPAMLPH
60 70 80 90 100
VVDRPATRKR WPNGVDSEPF FEKNLAASAP GWLERRALEH SDRSVHYPLL
110 120 130 140 150
NSVAALVWAG QQAALELHVP QWRFDGSHRG PATRIVFDLD PGPGVGLVEC
160 170 180 190 200
AEVARAVRDL VANLGWTAYP VTSGSKGIHL YVPLDRKLDG SGASTVAKQV
210 220 230 240 250
ATGLEKLRPE LVTATMAKSV RAGKVFVDWS QNNPSKTTIA PYSLRGRSEP
260 270 280 290 300
YVAAPRSWDE LDDPGLRQLR FEEVLERWES DGDLLAGLDP PIEDDTALAE
310 320 330 340 350
YRRKRDPGRT PEPMPHTVQP GAGNSFVIQE HHARRLHYDL RLERDGVLVS
360 370 380 390 400
WAVPKNVPTT TGENRLAVHT EDHPLEYLTF SGSIPKGEYG GGQMTIWDTG
410 420 430 440 450
TYDTEKWRDD EVIVQLHGEQ VEGRFALIRT KGDQWLMHLM KDQSPGGSRS
460 470 480 490 500
SELPRGLSPM LASPGTLDGL GADEWAFEGK WDGIRVIAEI SGGELKMTSR
510 520 530 540 550
AGNDKTRDYA QLGWLADSLE DHEVVLDGEV VAFDERGVAN FGLLQQGNEP
560 570 580 590 600
HFLAFDVLYL DGVSLLRKKY TDRRRVLEAL AAKVDDLVVP PQLHGSAQEA
610 620 630 640 650
LDESRRKGWE GVVAKRRESV YLPGKRGSSW IKVKNWRTQE AVIGGWRRGQ
660 670 680 690 700
GGRSSGIGSV LLGVPEDEGL RYIGRVGTGF TERDLQELAA TLGPLETDTS
710 720 730 740 750
PFVEDLPTAD RKGAVWVTPT LVAEVRFMDW TGSRRLRHPS WRGLRNDKAP

EDVEVESS
Length:758
Mass (Da):83,891
Last modified:May 26, 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:i2593A15C98DF93C5
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
AP011115 Genomic DNA Translation: BAH53359.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
BAH53359; BAH53359; ROP_51120

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
rop:ROP_51120

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|632772.20.peg.5338

<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
AP011115 Genomic DNA Translation: BAH53359.1

3D structure databases

Database of comparative protein structure models

More...
ModBasei
Search...

SWISS-MODEL Interactive Workspace

More...
SWISS-MODEL-Workspacei
Submit a new modelling project...

Genome annotation databases

EnsemblBacteriaiBAH53359; BAH53359; ROP_51120
KEGGirop:ROP_51120
PATRICifig|632772.20.peg.5338

Phylogenomic databases

HOGENOMiCLU_008325_2_1_11
KOiK01971
OMAiQWLAHRM

Family and domain databases

CDDicd04863, MtLigD_Pol_like, 1 hit
InterProiView protein in InterPro
IPR012309, DNA_ligase_ATP-dep_C
IPR012310, DNA_ligase_ATP-dep_cent
IPR014146, LigD_ligase_dom
IPR014144, LigD_PE_domain
IPR014145, LigD_pol_dom
IPR033649, MtLigD_Pol-like
IPR012340, NA-bd_OB-fold
PfamiView protein in Pfam
PF04679, DNA_ligase_A_C, 1 hit
PF01068, DNA_ligase_A_M, 1 hit
PF13298, LigD_N, 1 hit
SUPFAMiSSF50249, SSF50249, 1 hit
TIGRFAMsiTIGR02777, LigD_PE_dom, 1 hit
TIGR02778, ligD_pol, 1 hit
TIGR02779, NHEJ_ligase_lig, 1 hit
PROSITEiView protein in PROSITE
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 nameiC1ATU5_RHOOB
<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: C1ATU5
<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/TrEMBL: May 26, 2009
Last sequence update: May 26, 2009
Last modified: August 12, 2020
This is version 72 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 statusiUnreviewed (UniProtKB/TrEMBL)

<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 proteomeImported
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