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Entry version 42 (18 Sep 2019)
Sequence version 1 (16 Apr 2014)
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Protein

Multifunctional non-homologous end joining DNA repair protein LigD

Gene

ligD

Organism
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Status
Reviewed-Annotation score:

Annotation score:5 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

With Ku forms a non-homologous end joining (NHEJ) repair enzyme which repairs DNA double-strand breaks (DSB) with reduced fidelity. Recognizes, processes and reseals DSBs, including repairs on incompatible DSB which require 3'-resection, gap filling and ligation. Anneals the 3' overhanging strands from opposing breaks to form a gapped intermediate, which then can be extended in trans by using the termini as primers for extension of the annealed break. Binds to the recessed 5'-phosphate moiety of the downstream DNA strand forming a stable synaptic complex even when the 3'-protruding ends of the template DNA strands are not complementary. Has numerous activites; gap filling copies the template strand, and prefers a 5'-phosphate in the gap and rNTPS (PubMed:17174332, PubMed:17947582), DNA-directed DNA or RNA polymerase on 5'-overhangs, terminal transferase (extending ssDNA or blunt dsDNA in a non-templated fashion, preferentially with rNTPs), DNA-dependent RNA primase (synthesizes short RNAs on unprimed closed ssDNA) and 3'- to 5'-exonuclease on ssDNA (PubMed:15499016). Isolated Pol domain (and presumably the holoenzyme) is able to form complexes between 2 noncompatible protruding 3'-ends DNA ends via microhomologous DNA strands, in a end-bridging function to which it adds a templated nucleotide (PubMed:17947582). Minimal primer length is 2 nucleotides (PubMed:21255731).4 Publications
The preference of the polymerase domain for rNTPs over dNTPs may be advantageous in dormant cells, where the dNTP pool is limiting.
In conjunction with endogenous or Mycobacterium phage Omega Ku (AC Q853W0) can reconstitute NHEJ in Saccharomyces cerevisiae.

Miscellaneous

LigD has variable architecture; domain order can be permutated, domains can be independently encoded, while some bacteria lack the 3'-phosphoesterase domain entirely.
It is not clear whether there is a 5- to 3'-exonuclease activity associated with the enzyme.

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">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

<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+5 PublicationsNote: Binds 4 Mn2+; 2 Mn2+ for polymerase/primase activity, 1 each for 3-phosphoesterase and ligase.5 Publications

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes regulatory mechanisms for enzymes, transporters or microbial transcription factors, and reports the components which regulate (by activation or inhibition) the reaction.<p><a href='/help/activity_regulation' target='_top'>More...</a></p>Activity regulationi

The polymerase, exonuclease and ligase activities are stimulated by Ku. Polymerase activity is inhibited by EDTA.2 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">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 sitei52Substrate; for polymerase activity1 Publication1
Binding sitei111Substrate; for polymerase activity1 Publication1
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">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 bindingi137Manganese 11 Publication1
Metal bindingi137Manganese 21 Publication1
Metal bindingi139Manganese 11 Publication1
Metal bindingi139Manganese 21 Publication1
Metal bindingi227Manganese 21 Publication1
Binding sitei230Substrate; for polymerase activity1 Publication1
Binding sitei236Substrate; for polymerase activity1 Publication1
Binding sitei244Substrate; for polymerase activity1 Publication1
Metal bindingi331Manganese 3; via pros nitrogen; catalytic; for 3'-phosphoesterase activityBy similarity1
Metal bindingi337Manganese 3; via tele nitrogen; catalytic; for 3'-phosphoesterase activityBy similarity1
Metal bindingi339Manganese 3; catalytic; for 3'-phosphoesterase activityBy similarity1
<p>This subsection describes interesting single amino acid sites on the sequence that are not defined in any other subsection. This subsection can be displayed in different sections (‘Function’, ‘PTM / Processing’, ‘Pathology and Biotech’) according to its content.<p><a href='/help/site' target='_top'>More...</a></p>Sitei373Transition state stabilizer; for 3'-phosphoesterase activityBy similarity1
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">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 sitei481N6-AMP-lysine intermediate; for ligase activity2 Publications1
Metal bindingi483Manganese 41 Publication1
Metal bindingi613Manganese 41 Publication1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section specifies the position and type of each DNA-binding domain present within the protein.<p><a href='/help/dna_bind' target='_top'>More...</a></p>DNA bindingi13 – 16Interaction with target DNA4
DNA bindingi26Interaction with target DNA1
DNA bindingi53 – 55Interaction with target DNA3
DNA bindingi63 – 67Interaction with target DNA5
DNA bindingi71Interaction with target DNA1
DNA bindingi83 – 88Interaction with target DNA6
DNA bindingi104Interaction with target DNA1
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">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 bindingi137 – 139Substrate; for polymerase activity1 Publication3
DNA bindingi137Interaction with target DNA1
Nucleotide bindingi172 – 178Substrate; for polymerase activity1 Publication7
DNA bindingi215 – 220Interaction with target DNA6
DNA bindingi227 – 235Interaction with target DNA9

<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-binding, DNA-directed DNA polymerase, Exonuclease, Hydrolase, Ligase, Multifunctional enzyme, Nuclease, Nucleotidyltransferase, Transferase
Biological processDNA damage, DNA recombination, DNA repair, Host-virus interaction
LigandATP-binding, Manganese, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
MTBH37RV:G185E-5093-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_and_taxonomy_section">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:
Multifunctional non-homologous end joining DNA repair protein LigD
Short name:
NHEJ DNA repair protein D
Alternative name(s):
Mt-Lig
NHEJ DNA polymerase
Including the following 3 domains:
DNA repair polymerase
Short name:
Pol
Alternative name(s):
Polymerase/primase
3'-phosphoesterase
Short name:
3'-ribonuclease/3'-phosphatase
Short name:
PE
DNA ligase (EC:6.5.1.13 Publications)
Short name:
Lig
Alternative name(s):
Polydeoxyribonucleotide synthase [ATP]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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:ligD
Ordered Locus Names:Rv0938
ORF Names:MTCY08D9.01c, MTCY10D7.36c
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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>OrganismiMycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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 identifieri83332 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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 lineageiBacteriaActinobacteriaCorynebacterialesMycobacteriaceaeMycobacteriumMycobacterium tuberculosis complex
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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
  • UP000001584 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">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

Organism-specific databases

Mycobacterium tuberculosis strain H37Rv genome database

More...
TubercuListi
Rv0938

<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

<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

<p>This subsection of the ‘Pathology and Biotech’ section describes the in vivo effects caused by ablation of the gene (or one or more transcripts) coding for the protein described in the entry. This includes gene knockout and knockdown, provided experiments have been performed in the context of a whole organism or a specific tissue, and not at the single-cell level.<p><a href='/help/disruption_phenotype' target='_top'>More...</a></p>Disruption phenotypei

Not essential for growth, 80% reduction in NHEJ (in strain Erdman).1 Publication

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology_and_biotech_section">'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>Mutagenesisi16K → A: Loss of DNA-binding, no polymerase activity, no effect of gap-filling (in Pol domain). 1 Publication1
Mutagenesisi53R → A: On substrate with 5'-phosphate, 1 base pair (bp) complementarity and 1 nucleotide (nt) gap, greatly reduced DNA-binding and gap-filling. Barely detectable activity on substrate with high complementarity and 3'-overhang (in Pol domain). 1 Publication1
Mutagenesisi63F → A: On substrate with 5'-phosphate, 1 bp complementarity and 1 nt gap, greatly reduced DNA-binding and gap-filling. No activity on substrate with high complementarity and 3'-overhang (in Pol domain). 1 Publication1
Mutagenesisi64F → A: On substrate with 5'-phosphate, 1 bp complementarity and 1 nt gap, greatly reduced DNA-binding and gap-filling. Barely detectable activity on substrate with high complementarity and 3'-overhang (in Pol domain). 1 Publication1
Mutagenesisi83 – 85HRS → AAA: Binds DNA, no formation of DNA end-bridging complex, no polymerase activity. Significantly decreased ability to fill in 2 nt gaps (in Pol domain). 2 Publications3
Mutagenesisi137 – 139DLD → ALA: Loss of polymerase activities, no DNA repair (in Pol domain). 2 Publications3
Mutagenesisi217K → A: Better than wild-type DNA-binding and filling on single nt gaps, impaired gap filling on more complicated templates (in Pol domain). 1 Publication1
Mutagenesisi220R → A: Binds DNA, no gap-filling (in Pol domain). 1 Publication1
Mutagenesisi230Q → A: Wild-type filling on single nt gaps, impaired gap filling on more complicated templates (in Pol domain). 1 Publication1
Mutagenesisi235K → A: Wild-type filling on single nt gaps, impaired gap filling on more complicated templates (in Pol domain). 1 Publication1
Mutagenesisi373H → A: Loss of exonuclease, no DNA repair. 1 Publication1
Mutagenesisi481K → A: Loss of adenyltransferase activity, no N6-AMP-lysine formation and loss of ligase activity. No effect on phosphodiester bond formation on pre-adenylated nicked DNA, or on DNA polymerase. 3 Publications1
Mutagenesisi483D → A: No ligase of singly nicked dsDNA activity, no N6-AMP-lysine intermediate formed, decreased phosphodiester bond formation on pre-adenylated nicked DNA, no effect on DNA polymerase. 1 Publication1
Mutagenesisi530E → A: No ligase of singly nicked dsDNA activity, no N6-AMP-lysine intermediate formed, no phosphodiester bond formation on pre-adenylated nicked DNA, no effect on DNA polymerase. 1 Publication1
Mutagenesisi613E → A: No ligase of singly nicked dsDNA activity, no N6-AMP-lysine intermediate formed, decreased phosphodiester bond formation on pre-adenylated nicked DNA, no effect on DNA polymerase. 1 Publication1
Mutagenesisi635K → A: 20% ligase activity for singly nicked dsDNA, normal N6-AMP-lysine intermediate formed, no effect on phosphodiester bond formation, no effect on DNA polymerase. 1 Publication1
Mutagenesisi637K → A: No ligase of singly nicked dsDNA activity, 25% N6-AMP-lysine intermediate formed, decreased phosphodiester bond formation, no effect on DNA polymerase. 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.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00000596271 – 759Multifunctional non-homologous end joining DNA repair protein LigDAdd BLAST759

Proteomic databases

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

More...
PaxDbi
P9WNV3

<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

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Monomer.

Component of the NHEJ repair enzyme with mKu.

Interacts with Ku in the absence of DSB via the Pol domain. In structures of the Pol domain with template DNA 2 Pol domains are bound to microhomologous DNA complexes to form an end-bridging complex. Probably interacts with Mycobacterium phage Omega and Corndog Ku homologs (AC Q853W0, AC Q856K7).

Interacts with Sir2; may form a trimeric complex with LigD during NHEJ.

10 Publications

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
83332.Rv0938

<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

Secondary structure

1759
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

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

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SMRi
P9WNV3

Database of comparative protein structure models

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ModBasei
Search...

Protein Data Bank in Europe - Knowledge Base

More...
PDBe-KBi
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

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni1 – 411Not required for ligase activityAdd BLAST411
Regioni9 – 261DNA repair polymerase domain (Pol); interacts with KuAdd BLAST253
Regioni297 – 4463-phosphoesterase domain (PE)Add BLAST150
Regioni460 – 757Ligase domain (Lig)Add BLAST298

<p>This subsection of the ‘Family and domains’ section provides general information on the biological role of a domain. The term ‘domain’ is intended here in its wide acceptation, it may be a structural domain, a transmembrane region or a functional domain. Several domains are described in this subsection.<p><a href='/help/domain_cc' target='_top'>More...</a></p>Domaini

The N-terminal Mn2+-dependent polymerase/primase domain (Pol) functions as an independent domain, binds DNA, is sufficient for DNA-directed and non-DNA-directed DNA synthesis (PubMed:15778718) and interacts with Ku (PubMed:16023671).2 Publications
The central 3'-phosphoesterase domain (PE) has exonuclease activity probably constituted of 3'-ribonuclease and 3'-phosphatase activity (PubMed:15499016). It does not function as an independent domain (PubMed:16023671).2 Publications
The C-terminal ligase domain (Lig) binds dsDNA and functions as an independent domain (PubMed:14985346, PubMed:16023671).2 Publications

<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

In the N-terminal section; belongs to the LigD polymerase family.Curated
In the central section; belongs to the LigD 3'-phosphoesterase family.Curated
In the C-terminal section; belongs to the ATP-dependent DNA ligase family.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

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eggNOGi
ENOG4105DQE Bacteria
COG1793 LUCA
COG3285 LUCA

KEGG Orthology (KO)

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KOi
K01971

Identification of Orthologs from Complete Genome Data

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OMAi
AAPRTWD

Database for complete collections of gene phylogenies

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PhylomeDBi
P9WNV3

Family and domain databases

Conserved Domains Database

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CDDi
cd04863 MtLigD_Pol_like, 1 hit

Integrated resource of protein families, domains and functional sites

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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

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SUPFAMi
SSF50249 SSF50249, 1 hit

TIGRFAMs; a protein family database

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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

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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_length">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_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">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.

P9WNV3-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MGSASEQRVT LTNADKVLYP ATGTTKSDIF DYYAGVAEVM LGHIAGRPAT
60 70 80 90 100
RKRWPNGVDQ PAFFEKQLAL SAPPWLSRAT VAHRSGTTTY PIIDSATGLA
110 120 130 140 150
WIAQQAALEV HVPQWRFVAE PGSGELNPGP ATRLVFDLDP GEGVMMAQLA
160 170 180 190 200
EVARAVRDLL ADIGLVTFPV TSGSKGLHLY TPLDEPVSSR GATVLAKRVA
210 220 230 240 250
QRLEQAMPAL VTSTMTKSLR AGKVFVDWSQ NSGSKTTIAP YSLRGRTHPT
260 270 280 290 300
VAAPRTWAEL DDPALRQLSY DEVLTRIARD GDLLERLDAD APVADRLTRY
310 320 330 340 350
RRMRDASKTP EPIPTAKPVT GDGNTFVIQE HHARRPHYDF RLECDGVLVS
360 370 380 390 400
WAVPKNLPDN TSVNHLAIHT EDHPLEYATF EGAIPSGEYG AGKVIIWDSG
410 420 430 440 450
TYDTEKFHDD PHTGEVIVNL HGGRISGRYA LIRTNGDRWL AHRLKNQKDQ
460 470 480 490 500
KVFEFDNLAP MLATHGTVAG LKASQWAFEG KWDGYRLLVE ADHGAVRLRS
510 520 530 540 550
RSGRDVTAEY PQLRALAEDL ADHHVVLDGE AVVLDSSGVP SFSQMQNRGR
560 570 580 590 600
DTRVEFWAFD LLYLDGRALL GTRYQDRRKL LETLANATSL TVPELLPGDG
610 620 630 640 650
AQAFACSRKH GWEGVIAKRR DSRYQPGRRC ASWVKDKHWN TQEVVIGGWR
660 670 680 690 700
AGEGGRSSGV GSLLMGIPGP GGLQFAGRVG TGLSERELAN LKEMLAPLHT
710 720 730 740 750
DESPFDVPLP ARDAKGITYV KPALVAEVRY SEWTPEGRLR QSSWRGLRPD

KKPSEVVRE
Length:759
Mass (Da):83,572
Last modified:April 16, 2014 - 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:i81BD49222EE09E36
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

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EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

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DDBJi
Links Updated
AL123456 Genomic DNA Translation: CCP43686.1

Protein sequence database of the Protein Information Resource

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PIRi
B70585

NCBI Reference Sequences

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RefSeqi
NP_215453.1, NC_000962.3
WP_003911307.1, NZ_NVQJ01000001.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

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EnsemblBacteriai
CCP43686; CCP43686; Rv0938

Database of genes from NCBI RefSeq genomes

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GeneIDi
885561

KEGG: Kyoto Encyclopedia of Genes and Genomes

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KEGGi
mtu:Rv0938
mtv:RVBD_0938

<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
AL123456 Genomic DNA Translation: CCP43686.1
PIRiB70585
RefSeqiNP_215453.1, NC_000962.3
WP_003911307.1, NZ_NVQJ01000001.1

3D structure databases

Select the link destinations:

Protein Data Bank Europe

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PDBei

Protein Data Bank RCSB

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RCSB PDBi

Protein Data Bank Japan

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PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1VS0X-ray2.40A/B452-759[»]
2IRUX-ray1.65A/B1-300[»]
2IRXX-ray1.80A1-300[»]
2IRYX-ray1.78A/B1-300[»]
2R9LX-ray2.40A/B1-300[»]
3PKYX-ray3.10A/B1-300[»]
4MKYX-ray2.40A/B/C/D1-300[»]
SMRiP9WNV3
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

STRINGi83332.Rv0938

Proteomic databases

PaxDbiP9WNV3

Genome annotation databases

EnsemblBacteriaiCCP43686; CCP43686; Rv0938
GeneIDi885561
KEGGimtu:Rv0938
mtv:RVBD_0938

Organism-specific databases

TubercuListiRv0938

Phylogenomic databases

eggNOGiENOG4105DQE Bacteria
COG1793 LUCA
COG3285 LUCA
KOiK01971
OMAiAAPRTWD
PhylomeDBiP9WNV3

Enzyme and pathway databases

BioCyciMTBH37RV:G185E-5093-MONOMER

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

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ProtoNeti
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MobiDB: a database of protein disorder and mobility annotations

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MobiDBi
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<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 nameiLIGD_MYCTU
<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: P9WNV3
Secondary accession number(s): L0T5C5, O05865, P71571
<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_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 16, 2014
Last sequence update: April 16, 2014
Last modified: September 18, 2019
This is version 42 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Mycobacterium tuberculosis strains ATCC 25618 / H37Rv and CDC 1551 / Oshkosh
    Mycobacterium tuberculosis strains ATCC 25618 / H37Rv and CDC 1551 / Oshkosh: entries and gene names
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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