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Protein

Multifunctional non-homologous end joining protein LigD

Gene

ligD

Organism
Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

With Ku probably forms a non-homologous end joining (NHEJ) repair enzyme, which repairs dsDNA breaks (DSB) with reduced fidelity. Acts as a DNA ligase on singly nicked dsDNA, fills dsDNA gaps (3- or 4- nucleotide gaps, prefers a 5'-phosphate at the gap distal end, prefers dNTPs over rNTPs) (PubMed:20018881), has DNA-directed DNA polymerase activity (templated primer extension) and DNA-directed RNA polymerase activity (PubMed:15897197), adds 1 or 2 non-templated rNTP (or less well dNTP) to ssDNA or blunt-end dsDNA (primer extension). Has 3' resection activity, removing 3'-rNMPs from DNA using its 3'-ribonuclease and 3'-phosphatase activities sequentially. Resection requires a 2'-OH in the penultimate nucleoside position (i.e. a ribo- not deoxyribonucleoside) (PubMed:15897197), although the 3'-phosphatase activity does not, and its specific activity is 16-fold higher on a DNA substrate (PubMed:16046407). On appropriate substrates will extend a DNA primer to the end of the template strand and then incorporate a non-templated nucleotide.3 Publications
The preference of the polymerase domain for rNTPs over dNTPs may be advantageous in quiescent cells where the dNTP pool may be limiting.

Catalytic activityi

ATP + (deoxyribonucleotide)(n)-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)(m) = (deoxyribonucleotide)(n+m) + AMP + diphosphate.

Cofactori

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

Enzyme regulationi

rNTP addition and end joining activities are stimulated by Ku homodimer.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi42Manganese 1; via pros nitrogen; catalytic; for 3'-phosphoesterase activity2 Publications1
Metal bindingi48Manganese 1; via tele nitrogen; catalytic; for 3'-phosphoesterase activity2 Publications1
Metal bindingi50Manganese 1; catalytic; for 3'-phosphoesterase activity2 Publications1
Sitei84Transition state stabilizer; for 3'-phosphoesterase activityCurated1
Active sitei238N6-AMP-lysine intermediateCurated1
Metal bindingi240Manganese 2By similarity1
Metal bindingi376Manganese 2By similarity1
Binding sitei604ATP1 Publication1
Binding sitei651ATP1 Publication1
Metal bindingi669Manganese 32 Publications1
Metal bindingi669Manganese 42 Publications1
Metal bindingi671Manganese 32 Publications1
Binding sitei671ATP1 Publication1
Metal bindingi759Manganese 42 Publications1
Binding sitei768ATP1 Publication1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi704 – 710ATP1 Publication7
Nucleotide bindingi776 – 778ATP1 Publication3

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • DNA binding Source: UniProtKB-KW
  • DNA-directed DNA polymerase activity Source: UniProtKB
  • DNA ligase (ATP) activity Source: UniProtKB
  • exoribonuclease activity Source: UniProtKB
  • metal ion binding Source: UniProtKB-KW
  • nucleotidyltransferase activity Source: UniProtKB

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

DNA-directed DNA polymerase, Exonuclease, Hydrolase, Ligase, Nuclease, Nucleotidyltransferase, Transferase

Keywords - Biological processi

DNA damage, DNA recombination, DNA repair

Keywords - Ligandi

ATP-binding, DNA-binding, Manganese, Metal-binding, Nucleotide-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Multifunctional non-homologous end joining protein LigD
Alternative name(s):
NHEJ DNA polymerase
Including the following 3 domains:
3'-phosphoesterase
Short name:
3'-ribonuclease/3'-phosphatase
DNA ligase D (EC:6.5.1.1)
Short name:
LigD
Alternative name(s):
Polydeoxyribonucleotide synthase [ATP]
DNA repair polymerase
Short name:
Pol
Alternative name(s):
Polymerase/primase
Gene namesi
Name:ligD
Ordered Locus Names:PA2138
OrganismiPseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
Taxonomic identifieri208964 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas
Proteomesi
  • UP000002438 Componenti: Chromosome

Organism-specific databases

PseudoCAPiPA2138.

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi14R → A: 77% ribonuclease activity, loss of 3'-phosphatase activity (in PE domain). 1 Publication1
Mutagenesisi15D → A: 3% 3'-phosphatase activity (in PE domain). 1 Publication1
Mutagenesisi21E → A: Loss of 3'-phosphatase activity (in PE domain). 1 Publication1
Mutagenesisi40Q → A: 41% ribonuclease activity, 7% 3'-phosphatase activity (in PE domain). 1 Publication1
Mutagenesisi42H → A: Loss of ribonuclease and 3'-phosphatase activity (in PE domain). 1 Publication1
Mutagenesisi46R → A: 16% ribonuclease activity, 20% 3'-phosphatase activity (in PE domain). 1 Publication1
Mutagenesisi48H → A: Loss of ribonuclease and 3'-phosphatase activity (in PE domain). 1 Publication1
Mutagenesisi50D → A: Loss of nuclease and 3'-phosphatase activity (in PE domain). 1 Publication1
Mutagenesisi52R → A: Loss of nuclease and 3'-phosphatase activity (in PE domain). 1 Publication1
Mutagenesisi54E → A: Nearly wild-type nuclease and 3'-phosphatase activity (in PE domain). 1 Publication1
Mutagenesisi66K → A: 3% ribonuclease activity, 28% 3'-phosphatase activity (in PE domain). 1 Publication1
Mutagenesisi76R → A: 1% ribonuclease activity, 16% 3'-phosphatase activity (in PE domain). 1 Publication1
Mutagenesisi82E → A: Selective loss of 3'-phosphatase activity (in PE domain). 1 Publication1
Mutagenesisi83D → A: 57% ribonuclease activity, 50% 3'-phosphatase activity (in PE domain). 1 Publication1
Mutagenesisi84H → A: Loss of nuclease and 3'-phosphatase activity (in PE domain). 1 Publication1
Mutagenesisi88Y → A: 7% ribonuclease activity, loss of 3'-phosphatase activity (in PE domain). 1 Publication1
Mutagenesisi553 – 566HPQRL…IQASK → APQALIDPSIQASA: 5'-phosphate at distal end of gap no longer advantageous for rNTP or dNTP addition (in Pol domain). 1 PublicationAdd BLAST14
Mutagenesisi553 – 566HPQRL…IQASK → APQRLIDPSIQASA: Addition of rNTP to gapped molecule decreases to 1 or 2 nucleotides, dNTP addition decreased, 5'-phosphate at distal end of gap no longer advantageous (in Pol domain). 1 PublicationAdd BLAST14
Mutagenesisi553H → A: Wild-type gap closing by rNTP or dNTP addition (in Pol domain). 1 Publication1
Mutagenesisi556R → A: Decreases gap closing efficiency by rNTP, wild-type by dNTP (in Pol domain). 1 Publication1
Mutagenesisi566K → A: No change in dNTP addition to gapped molecule, 5'-phosphate at distal of the gap no longer advantageous for rNTP addition (in Pol domain). 1 Publication1
Mutagenesisi603F → A: Last nucleotide rarely added during gap closing for dNTP or rNTP addition, (in Pol domain). Stacks a DNA template base. 1 Publication1
Mutagenesisi604F → A: Nearly complete loss of templated dNTP or rNTP addition (in Pol domain). 1 Publication1
Mutagenesisi669 – 671DLD → ALA: Loss of templated and non-templated DNA synthesis (in Pol domain). 1 Publication3
Mutagenesisi669D → A or N: Loss of templated DNA synthesis (in Pol domain). 1 Publication1
Mutagenesisi669D → E: Partial loss of templated DNA synthesis (in Pol domain). 1 Publication1
Mutagenesisi671D → A, E or N: Loss of templated DNA synthesis (in Pol domain). 1 Publication1
Mutagenesisi710H → A: Loss of templated DNA synthesis (in Pol domain). 1 Publication1
Mutagenesisi710H → N: Partial loss of templated DNA synthesis (in Pol domain). 1 Publication1
Mutagenesisi710H → Q: Nearly wild-type templated DNA synthesis (in Pol domain). 1 Publication1
Mutagenesisi752R → A or Q: Loss of templated DNA synthesis (in Pol domain). 1 Publication1
Mutagenesisi752R → K: Partial loss of templated DNA synthesis (in Pol domain). 1 Publication1
Mutagenesisi759D → A or N: Loss of templated DNA synthesis (in Pol domain). 1 Publication1
Mutagenesisi759D → E: Partial loss of templated DNA synthesis (in Pol domain). 1 Publication1
Mutagenesisi776R → A: Loss of templated DNA synthesis (in Pol domain). 1 Publication1
Mutagenesisi776R → K: Nearly wild-type templated DNA synthesis (in Pol domain). 1 Publication1
Mutagenesisi776R → Q: Partial loss of templated DNA synthesis (in Pol domain). 1 Publication1
Mutagenesisi778R → A: Nearly wild-type templated dNTP or rNTP addition (in Pol domain). 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004259501 – 840Multifunctional non-homologous end joining protein LigDAdd BLAST840

Proteomic databases

PaxDbiQ9I1X7.

Interactioni

Subunit structurei

Monomer. Interacts with Ku (By similarity).By similarity

Protein-protein interaction databases

STRINGi208964.PA2138.

Structurei

Secondary structure

1840
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi35 – 55Combined sources21
Beta strandi58 – 64Combined sources7
Beta strandi72 – 74Combined sources3
Beta strandi76 – 84Combined sources9
Helixi86 – 90Combined sources5
Beta strandi91 – 95Combined sources5
Turni97 – 100Combined sources4
Beta strandi104 – 117Combined sources14
Helixi119 – 125Combined sources7
Beta strandi127 – 136Combined sources10
Beta strandi138 – 145Combined sources8
Beta strandi148 – 153Combined sources6
Beta strandi154 – 159Combined sources6
Turni168 – 170Combined sources3
Helixi173 – 176Combined sources4
Turni181 – 183Combined sources3
Turni544 – 548Combined sources5
Beta strandi556 – 559Combined sources4
Helixi560 – 562Combined sources3
Helixi566 – 575Combined sources10
Helixi577 – 584Combined sources8
Beta strandi587 – 593Combined sources7
Beta strandi603 – 605Combined sources3
Helixi621 – 623Combined sources3
Beta strandi630 – 632Combined sources3
Helixi636 – 644Combined sources9
Beta strandi647 – 652Combined sources6
Beta strandi664 – 672Combined sources9
Helixi678 – 695Combined sources18
Beta strandi700 – 703Combined sources4
Beta strandi705 – 714Combined sources10
Helixi721 – 738Combined sources18
Turni740 – 742Combined sources3
Helixi749 – 751Combined sources3
Beta strandi755 – 759Combined sources5
Helixi761 – 763Combined sources3
Helixi789 – 794Combined sources6
Turni803 – 805Combined sources3
Helixi806 – 813Combined sources8
Turni818 – 824Combined sources7
Helixi831 – 836Combined sources6

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2FAOX-ray1.50A/B533-840[»]
2FAQX-ray1.90A/B533-840[»]
2FARX-ray1.90A/B533-840[»]
2LJ6NMR-A1-177[»]
3N9BX-ray1.92A/B17-187[»]
3N9DX-ray2.30A17-187[»]
ProteinModelPortaliQ9I1X7.
SMRiQ9I1X7.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9I1X7.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni7 – 1623'-phosphoesterase domain (PE)Add BLAST156
Regioni219 – 521Ligase domain (Lig)Add BLAST303
Regioni549 – 793DNA repair polymerase domain (Pol)Add BLAST245

Domaini

The N-terminal 3'-phosphoesterase domain (PE) has 3'-ribonuclease and 3'-phosphatase activities.1 Publication
The central ATP-dependent ligase domain (Lig) functions as an independent domain.1 Publication
The C-terminal polymerase/primase domain (Pol) (PubMed:15520014) adds up to 4 rNTPs in a DNA template-directed fashion (PubMed:15897197).2 Publications

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105DQE. Bacteria.
COG1793. LUCA.
COG3285. LUCA.
HOGENOMiHOG000222509.
InParanoidiQ9I1X7.
KOiK01971.
OMAiYARKRDF.
PhylomeDBiQ9I1X7.

Family and domain databases

CDDicd04862. PaeLigD_Pol_like. 1 hit.
InterProiIPR012309. DNA_ligase_ATP-dep_C.
IPR012310. DNA_ligase_ATP-dep_cent.
IPR014146. LigD_ligase_dom.
IPR014144. LigD_PE_domain.
IPR014145. LigD_pol_dom.
IPR012340. NA-bd_OB-fold.
IPR014143. NHEJ_ligase_prk.
IPR033651. PaeLigD_Pol-like.
[Graphical view]
PfamiPF04679. DNA_ligase_A_C. 1 hit.
PF01068. DNA_ligase_A_M. 1 hit.
PF13298. LigD_N. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 1 hit.
TIGRFAMsiTIGR02777. LigD_PE_dom. 1 hit.
TIGR02778. ligD_pol. 1 hit.
TIGR02779. NHEJ_ligase_lig. 1 hit.
TIGR02776. NHEJ_ligase_prk. 1 hit.
PROSITEiPS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9I1X7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPSSKPLAEY ARKRDFRQTP EPSGRKPRKD STGLLRYCVQ KHDASRLHYD
60 70 80 90 100
FRLELDGTLK SWAVPKGPCL DPAVKRLAVQ VEDHPLDYAD FEGSIPQGHY
110 120 130 140 150
GAGDVIVWDR GAWTPLDDPR EGLEKGHLSF ALDGEKLSGR WHLIRTNLRG
160 170 180 190 200
KQSQWFLVKA KDGEARSLDR FDVLKERPDS VLSERTLLPR HGEAATPAAR
210 220 230 240 250
PARRGKSGGK TPMPEWIAPE LASLVEQPPR GEWAYELKLD GYRLMSRIED
260 270 280 290 300
GHVRLLTRNG HDWTERLPHL EKALAGLGLQ RSWLDGELVV LDEEGRPDFQ
310 320 330 340 350
ALQNAFEEGR GENILYVLFD LPYHEGEDLR DVALEERRAR LEALLEGRDE
360 370 380 390 400
DPLRFSATLA EDPRDLLASA CKLGLEGVIG KRLGSAYRSR RSNDWIKLKC
410 420 430 440 450
QLRQEFVIVG YTEPKGSRRH IGALLLGLYS PDEERRLRYA GKVGSGFTAA
460 470 480 490 500
SLKKVRERLE PLAVRSSPLA KVPPARETGS VQWVRPQQLC EVSYAQMTRG
510 520 530 540 550
GIIRQAVFHG LREDKPAREV TGERPAGPPP LRGARKASAG ASRAATAGVR
560 570 580 590 600
ISHPQRLIDP SIQASKLELA EFHARYADLL LRDLRERPVS LVRGPDGIGG
610 620 630 640 650
ELFFQKHAAR LKIPGIVQLD PALDPGHPPL LQIRSAEALV GAVQMGSIEF
660 670 680 690 700
HTWNASLANL ERPDRFVLDL DPDPALPWKR MLEATQLSLT LLDELGLRAF
710 720 730 740 750
LKTSGGKGMH LLVPLERRHG WDEVKDFAQA ISQHLARLMP ERFSAVSGPR
760 770 780 790 800
NRVGKIFVDY LRNSRGASTV AAYSVRAREG LPVSVPVFRE ELDSLQGANQ
810 820 830 840
WNLRSLPQRL DELAGDDPWA DYAGTRQRIS AAMRRQLGRG
Length:840
Mass (Da):94,030
Last modified:March 1, 2001 - v1
Checksum:i5CAE7929CC5F29C7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE004091 Genomic DNA. Translation: AAG05526.1.
PIRiC83378.
RefSeqiNP_250828.1. NC_002516.2.
WP_003113639.1. NC_002516.2.

Genome annotation databases

EnsemblBacteriaiAAG05526; AAG05526; PA2138.
GeneIDi880451.
KEGGipae:PA2138.
PATRICi19838710. VBIPseAer58763_2235.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE004091 Genomic DNA. Translation: AAG05526.1.
PIRiC83378.
RefSeqiNP_250828.1. NC_002516.2.
WP_003113639.1. NC_002516.2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2FAOX-ray1.50A/B533-840[»]
2FAQX-ray1.90A/B533-840[»]
2FARX-ray1.90A/B533-840[»]
2LJ6NMR-A1-177[»]
3N9BX-ray1.92A/B17-187[»]
3N9DX-ray2.30A17-187[»]
ProteinModelPortaliQ9I1X7.
SMRiQ9I1X7.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi208964.PA2138.

Proteomic databases

PaxDbiQ9I1X7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAG05526; AAG05526; PA2138.
GeneIDi880451.
KEGGipae:PA2138.
PATRICi19838710. VBIPseAer58763_2235.

Organism-specific databases

PseudoCAPiPA2138.

Phylogenomic databases

eggNOGiENOG4105DQE. Bacteria.
COG1793. LUCA.
COG3285. LUCA.
HOGENOMiHOG000222509.
InParanoidiQ9I1X7.
KOiK01971.
OMAiYARKRDF.
PhylomeDBiQ9I1X7.

Miscellaneous databases

EvolutionaryTraceiQ9I1X7.

Family and domain databases

CDDicd04862. PaeLigD_Pol_like. 1 hit.
InterProiIPR012309. DNA_ligase_ATP-dep_C.
IPR012310. DNA_ligase_ATP-dep_cent.
IPR014146. LigD_ligase_dom.
IPR014144. LigD_PE_domain.
IPR014145. LigD_pol_dom.
IPR012340. NA-bd_OB-fold.
IPR014143. NHEJ_ligase_prk.
IPR033651. PaeLigD_Pol-like.
[Graphical view]
PfamiPF04679. DNA_ligase_A_C. 1 hit.
PF01068. DNA_ligase_A_M. 1 hit.
PF13298. LigD_N. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 1 hit.
TIGRFAMsiTIGR02777. LigD_PE_dom. 1 hit.
TIGR02778. ligD_pol. 1 hit.
TIGR02779. NHEJ_ligase_lig. 1 hit.
TIGR02776. NHEJ_ligase_prk. 1 hit.
PROSITEiPS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiLIGD_PSEAE
AccessioniPrimary (citable) accession number: Q9I1X7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 19, 2014
Last sequence update: March 1, 2001
Last modified: November 30, 2016
This is version 107 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

LigD has variable architecture; domain order can be permutated, domains can be independently encoded, while some bacteria lack the 3'-phosphoesterase domain entirely.

Keywords - Technical termi

3D-structure, Complete proteome, Multifunctional enzyme, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.