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Q9I1X7 (LIGD_PSEAE) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 88. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Multifunctional non-homologous end joining protein LigD
Alternative name(s):
NHEJ DNA polymerase

Including the following 3 domains:

  1. 3'-phosphoesterase
    Short name=3'-ribonuclease/3'-phosphatase
  2. DNA ligase D
    Short name=LigD
    EC=6.5.1.1
    Alternative name(s):
    Polydeoxyribonucleotide synthase [ATP]
  3. DNA repair polymerase
    Short name=Pol
    Alternative name(s):
    Polymerase/primase
Gene names
Name:ligD
Ordered Locus Names:PA2138
OrganismPseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) [Reference proteome] [HAMAP]
Taxonomic identifier208964 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas

Protein attributes

Sequence length840 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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) (Ref.5), has DNA-directed DNA polymerase activity (templated primer extension) and DNA-directed RNA polymerase activity (Ref.3), 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) (Ref.3), although the 3'-phosphatase activity does not, and its specific activity is 16-fold higher on a DNA substrate (Ref.4). On appropriate substrates will extend a DNA primer to the end of the template strand and then incorporate a non-templated nucleotide. Ref.2 Ref.3 Ref.4 Ref.5 Ref.7

The preference of the polymerase domain for rNTPs over dNTPs may be advantageous in quiescent cells where the dNTP pool may be limiting. Ref.2 Ref.3 Ref.4 Ref.5 Ref.7

Catalytic activity

ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m).

Cofactor

Binds 4 Mn2+; 2 Mn2+ for polymerase/primase activity, 1 each for 3-phosphoesterase and ligase Probable. Ref.2 Ref.3 Ref.4 Ref.6

Enzyme regulation

rNTP addition and end joining activities are stimulated by Ku homodimer. Ref.5

Subunit structure

Monomer. Interacts with Ku By similarity. Ref.2

Domain

The N-terminal 3'-phosphoesterase domain (PE) has 3'-ribonuclease and 3'-phosphatase activities (Ref.3). Ref.2 Ref.3 Ref.4

The central ATP-dependent ligase domain (Lig) functions as an independent domain (Ref.2). Ref.2 Ref.3 Ref.4

The C-terminal polymerase/primase domain (Pol) (Ref.2) adds up to 4 rNTPs in a DNA template-directed fashion (Ref.3). Ref.2 Ref.3 Ref.4

Miscellaneous

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

Sequence similarities

In the N-terminal section; belongs to the LigD 3'-phosphoesterase family.

In the central section; belongs to the ATP-dependent DNA ligase family.

In the C-terminal section; belongs to the LigD polymerase family.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 840840Multifunctional non-homologous end joining protein LigD
PRO_0000425950

Regions

Nucleotide binding704 – 7107ATP
Nucleotide binding776 – 7783ATP
Region7 – 1621563'-phosphoesterase domain (PE)
Region219 – 521303Ligase domain (Lig)
Region549 – 793245DNA repair polymerase domain (Pol)

Sites

Active site2381N6-AMP-lysine intermediate Probable
Metal binding421Manganese 1; catalytic; via pros nitrogen; for 3'-phosphoesterase activity
Metal binding481Manganese 1; catalytic; via tele nitrogen; for 3'-phosphoesterase activity
Metal binding501Manganese 1; catalytic; for 3'-phosphoesterase activity
Metal binding2401Manganese 2 By similarity
Metal binding3761Manganese 2 By similarity
Metal binding6691Manganese 3
Metal binding6691Manganese 4
Metal binding6711Manganese 3
Metal binding7591Manganese 4
Binding site6041ATP
Binding site6511ATP
Binding site6711ATP
Binding site7681ATP
Site841Transition state stabilizer; for 3'-phosphoesterase activity Probable

Experimental info

Mutagenesis141R → A: 77% ribonuclease activity, loss of 3'-phosphatase activity (in PE domain). Ref.4
Mutagenesis151D → A: 3% 3'-phosphatase activity (in PE domain). Ref.4
Mutagenesis211E → A: Loss of 3'-phosphatase activity (in PE domain). Ref.4
Mutagenesis401Q → A: 41% ribonuclease activity, 7% 3'-phosphatase activity (in PE domain). Ref.4
Mutagenesis421H → A: Loss of ribonuclease and 3'-phosphatase activity (in PE domain). Ref.4
Mutagenesis461R → A: 16% ribonuclease activity, 20% 3'-phosphatase activity (in PE domain). Ref.4
Mutagenesis481H → A: Loss of ribonuclease and 3'-phosphatase activity (in PE domain). Ref.4
Mutagenesis501D → A: Loss of nuclease and 3'-phosphatase activity (in PE domain). Ref.3
Mutagenesis521R → A: Loss of nuclease and 3'-phosphatase activity (in PE domain). Ref.3
Mutagenesis541E → A: Nearly wild-type nuclease and 3'-phosphatase activity (in PE domain). Ref.3
Mutagenesis661K → A: 3% ribonuclease activity, 28% 3'-phosphatase activity (in PE domain). Ref.4
Mutagenesis761R → A: 1% ribonuclease activity, 16% 3'-phosphatase activity (in PE domain). Ref.4
Mutagenesis821E → A: Selective loss of 3'-phosphatase activity (in PE domain). Ref.3
Mutagenesis831D → A: 57% ribonuclease activity, 50% 3'-phosphatase activity (in PE domain). Ref.4
Mutagenesis841H → A: Loss of nuclease and 3'-phosphatase activity (in PE domain). Ref.3
Mutagenesis881Y → A: 7% ribonuclease activity, loss of 3'-phosphatase activity (in PE domain). Ref.4
Mutagenesis553 – 56614HPQRL…IQASK → APQALIDPSIQASA: 5'-phosphate at distal end of gap no longer advantageous for rNTP or dNTP addition (in Pol domain). Ref.5
Mutagenesis553 – 56614HPQRL…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). Ref.5
Mutagenesis5531H → A: Wild-type gap closing by rNTP or dNTP addition (in Pol domain). Ref.5
Mutagenesis5561R → A: Decreases gap closing efficiency by rNTP, wild-type by dNTP (in Pol domain). Ref.5
Mutagenesis5661K → 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). Ref.5
Mutagenesis6031F → A: Last nucleotide rarely added during gap closing for dNTP or rNTP addition, (in Pol domain). Stacks a DNA template base. Ref.5
Mutagenesis6041F → A: Nearly complete loss of templated dNTP or rNTP addition (in Pol domain). Ref.6
Mutagenesis669 – 6713DLD → ALA: Loss of templated and non-templated DNA synthesis (in Pol domain). Ref.2 Ref.6
Mutagenesis6691D → A or N: Loss of templated DNA synthesis (in Pol domain). Ref.6
Mutagenesis6691D → E: Partial loss of templated DNA synthesis (in Pol domain). Ref.6
Mutagenesis6711D → A, E or N: Loss of templated DNA synthesis (in Pol domain). Ref.6
Mutagenesis7101H → A: Loss of templated DNA synthesis (in Pol domain). Ref.6
Mutagenesis7101H → N: Partial loss of templated DNA synthesis (in Pol domain). Ref.6
Mutagenesis7101H → Q: Nearly wild-type templated DNA synthesis (in Pol domain). Ref.6
Mutagenesis7521R → A or Q: Loss of templated DNA synthesis (in Pol domain). Ref.6
Mutagenesis7521R → K: Partial loss of templated DNA synthesis (in Pol domain). Ref.6
Mutagenesis7591D → A or N: Loss of templated DNA synthesis (in Pol domain). Ref.6
Mutagenesis7591D → E: Partial loss of templated DNA synthesis (in Pol domain). Ref.6
Mutagenesis7761R → A: Loss of templated DNA synthesis (in Pol domain). Ref.6
Mutagenesis7761R → K: Nearly wild-type templated DNA synthesis (in Pol domain). Ref.6
Mutagenesis7761R → Q: Partial loss of templated DNA synthesis (in Pol domain). Ref.6
Mutagenesis7781R → A: Nearly wild-type templated dNTP or rNTP addition (in Pol domain). Ref.6

Sequences

Sequence LengthMass (Da)Tools
Q9I1X7 [UniParc].

Last modified March 1, 2001. Version 1.
Checksum: 5CAE7929CC5F29C7

FASTA84094,030
        10         20         30         40         50         60 
MPSSKPLAEY ARKRDFRQTP EPSGRKPRKD STGLLRYCVQ KHDASRLHYD FRLELDGTLK 

        70         80         90        100        110        120 
SWAVPKGPCL DPAVKRLAVQ VEDHPLDYAD FEGSIPQGHY GAGDVIVWDR GAWTPLDDPR 

       130        140        150        160        170        180 
EGLEKGHLSF ALDGEKLSGR WHLIRTNLRG KQSQWFLVKA KDGEARSLDR FDVLKERPDS 

       190        200        210        220        230        240 
VLSERTLLPR HGEAATPAAR PARRGKSGGK TPMPEWIAPE LASLVEQPPR GEWAYELKLD 

       250        260        270        280        290        300 
GYRLMSRIED GHVRLLTRNG HDWTERLPHL EKALAGLGLQ RSWLDGELVV LDEEGRPDFQ 

       310        320        330        340        350        360 
ALQNAFEEGR GENILYVLFD LPYHEGEDLR DVALEERRAR LEALLEGRDE DPLRFSATLA 

       370        380        390        400        410        420 
EDPRDLLASA CKLGLEGVIG KRLGSAYRSR RSNDWIKLKC QLRQEFVIVG YTEPKGSRRH 

       430        440        450        460        470        480 
IGALLLGLYS PDEERRLRYA GKVGSGFTAA SLKKVRERLE PLAVRSSPLA KVPPARETGS 

       490        500        510        520        530        540 
VQWVRPQQLC EVSYAQMTRG GIIRQAVFHG LREDKPAREV TGERPAGPPP LRGARKASAG 

       550        560        570        580        590        600 
ASRAATAGVR ISHPQRLIDP SIQASKLELA EFHARYADLL LRDLRERPVS LVRGPDGIGG 

       610        620        630        640        650        660 
ELFFQKHAAR LKIPGIVQLD PALDPGHPPL LQIRSAEALV GAVQMGSIEF HTWNASLANL 

       670        680        690        700        710        720 
ERPDRFVLDL DPDPALPWKR MLEATQLSLT LLDELGLRAF LKTSGGKGMH LLVPLERRHG 

       730        740        750        760        770        780 
WDEVKDFAQA ISQHLARLMP ERFSAVSGPR NRVGKIFVDY LRNSRGASTV AAYSVRAREG 

       790        800        810        820        830        840 
LPVSVPVFRE ELDSLQGANQ WNLRSLPQRL DELAGDDPWA DYAGTRQRIS AAMRRQLGRG 

« Hide

References

« Hide 'large scale' references
[1]"Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen."
Stover C.K., Pham X.-Q.T., Erwin A.L., Mizoguchi S.D., Warrener P., Hickey M.J., Brinkman F.S.L., Hufnagle W.O., Kowalik D.J., Lagrou M., Garber R.L., Goltry L., Tolentino E., Westbrock-Wadman S., Yuan Y., Brody L.L., Coulter S.N., Folger K.R. expand/collapse author list , Kas A., Larbig K., Lim R.M., Smith K.A., Spencer D.H., Wong G.K.-S., Wu Z., Paulsen I.T., Reizer J., Saier M.H. Jr., Hancock R.E.W., Lory S., Olson M.V.
Nature 406:959-964(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228.
[2]"A primer-dependent polymerase function of pseudomonas aeruginosa ATP-dependent DNA ligase (LigD)."
Zhu H., Shuman S.
J. Biol. Chem. 280:418-427(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION AS A LIGASE, FUNCTION AS A DNA POLYMERASE, COFACTOR, SUBUNIT, DOMAIN, MUTAGENESIS OF 669-ASP--ASP-671.
[3]"Novel 3'-ribonuclease and 3'-phosphatase activities of the bacterial non-homologous end-joining protein, DNA ligase D."
Zhu H., Shuman S.
J. Biol. Chem. 280:25973-25981(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN RESECTION, COFACTOR, DOMAIN, MUTAGENESIS OF ASP-50; ARG-52; GLU-54; GLU-82 AND HIS-84.
[4]"Essential constituents of the 3'-phosphoesterase domain of bacterial DNA ligase D, a nonhomologous end-joining enzyme."
Zhu H., Wang L.K., Shuman S.
J. Biol. Chem. 280:33707-33715(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, COFACTOR, DOMAIN, MUTAGENESIS OF ARG-14; ASP-15; GLU-21; GLN-40; HIS-42; ARG-46; HIS-48; LYS-66; ARG-76; ASP-83 AND TYR-88.
[5]"Gap filling activities of Pseudomonas DNA ligase D (LigD) polymerase and functional interactions of LigD with the DNA end-binding Ku protein."
Zhu H., Shuman S.
J. Biol. Chem. 285:4815-4825(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN GAP-FILLING, ENZYME REGULATION, MUTAGENESIS OF HIS-553; 553-HIS--LYS-566; ARG-556; LYS-566 AND PHE-603.
[6]"Atomic structure and nonhomologous end-joining function of the polymerase component of bacterial DNA ligase D."
Zhu H., Nandakumar J., Aniukwu J., Wang L.K., Glickman M.S., Lima C.D., Shuman S.
Proc. Natl. Acad. Sci. U.S.A. 103:1711-1716(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.50 ANGSTROMS) OF 533-840 OF APOENZYME AND IN COMPLEX WITH ATP AND MANGANESE, COFACTOR, ATP-BINDING, MUTAGENESIS OF PHE-604; ASP-669; ASP-671; HIS-710; ARG-752; ASP-759; ARG-776 AND ARG-778.
[7]"Structure of bacterial LigD 3'-phosphoesterase unveils a DNA repair superfamily."
Nair P.A., Smith P., Shuman S.
Proc. Natl. Acad. Sci. U.S.A. 107:12822-12827(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.92 ANGSTROMS) OF 17-187 IN COMPLEX WITH MANGANESE, FUNCTION, REACTION MECHANISM.
[8]"Solution structure and DNA-binding properties of the phosphoesterase domain of DNA ligase D."
Natarajan A., Dutta K., Temel D.B., Nair P.A., Shuman S., Ghose R.
Nucleic Acids Res. 40:2076-2088(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR OF 1-177, DNA-BINDING.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AE004091 Genomic DNA. Translation: AAG05526.1.
PIRC83378.
RefSeqNP_250828.1. NC_002516.2.

3D structure databases

PDBe
RCSB PDB
PDBj
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[»]
ProteinModelPortalQ9I1X7.
SMRQ9I1X7. Positions 33-163, 172-523, 543-837.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING208964.PA2138.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID880451.
KEGGpae:PA2138.
PATRIC19838710. VBIPseAer58763_2235.

Organism-specific databases

PseudoCAPPA2138.

Phylogenomic databases

HOGENOMHOG000222509.
KOK01971.
OMAHPLDYAD.
OrthoDBEOG661H49.
ProtClustDBPRK05972.

Family and domain databases

Gene3D2.40.50.140. 1 hit.
InterProIPR012309. DNA_ligase_ATP-dep_C.
IPR012310. DNA_ligase_ATP-dep_cent.
IPR014146. DNA_pol_LigD_ligase_dom.
IPR002755. DNA_primase_S.
IPR014144. LigD_PE_domain.
IPR014145. LigD_pol.
IPR012340. NA-bd_OB-fold.
IPR014143. NHEJ_ligase_prk.
[Graphical view]
PfamPF04679. DNA_ligase_A_C. 1 hit.
PF01068. DNA_ligase_A_M. 1 hit.
PF01896. DNA_primase_S. 1 hit.
PF13298. LigD_N. 1 hit.
[Graphical view]
SUPFAMSSF50249. SSF50249. 1 hit.
TIGRFAMsTIGR02777. LigD_PE_dom. 1 hit.
TIGR02778. ligD_pol. 1 hit.
TIGR02779. NHEJ_ligase_lig. 1 hit.
TIGR02776. NHEJ_ligase_prk. 1 hit.
PROSITEPS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceQ9I1X7.

Entry information

Entry nameLIGD_PSEAE
AccessionPrimary (citable) accession number: Q9I1X7
Entry history
Integrated into UniProtKB/Swiss-Prot: March 19, 2014
Last sequence update: March 1, 2001
Last modified: April 16, 2014
This is version 88 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references