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Q54CR9

- DNLI4_DICDI

UniProt

Q54CR9 - DNLI4_DICDI

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Protein

DNA ligase 4

Gene

lig4

Organism
Dictyostelium discoideum (Slime mold)
Status
Reviewed - Annotation score: 4 out of 5- Protein inferred from homologyi

Functioni

Efficiently joins single-strand breaks in a double-stranded polydeoxynucleotide in an ATP-dependent reaction. Involved in DNA nonhomologous end joining (NHEJ) required for double-strand break repair (By similarity).By similarity

Catalytic activityi

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

Cofactori

Mg2+By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei414 – 4141ATPBy similarity
Active sitei416 – 4161N6-AMP-lysine intermediateBy similarity
Binding sitei421 – 4211ATPBy similarity
Binding sitei436 – 4361ATPBy similarity
Metal bindingi467 – 4671Magnesium 1Sequence Analysis
Metal bindingi574 – 5741Magnesium 2Sequence Analysis
Binding sitei579 – 5791ATPBy similarity
Binding sitei590 – 5901ATPBy similarity
Binding sitei596 – 5961ATPBy similarity

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. DNA binding Source: dictyBase
  3. DNA ligase (ATP) activity Source: dictyBase
  4. metal ion binding Source: UniProtKB-KW

GO - Biological processi

  1. DNA biosynthetic process Source: InterPro
  2. DNA ligation Source: RefGenome
  3. DNA ligation involved in DNA repair Source: InterPro
  4. DNA recombination Source: UniProtKB-KW
  5. double-strand break repair via nonhomologous end joining Source: RefGenome
  6. lagging strand elongation Source: RefGenome
  7. nucleotide-excision repair Source: RefGenome
  8. single strand break repair Source: dictyBase
Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

DNA damage, DNA recombination, DNA repair, DNA replication

Keywords - Ligandi

ATP-binding, Magnesium, Metal-binding, Nucleotide-binding

Names & Taxonomyi

Protein namesi
Recommended name:
DNA ligase 4 (EC:6.5.1.1)
Alternative name(s):
DNA ligase IV
Polydeoxyribonucleotide synthase [ATP] 4
Gene namesi
Name:lig4
ORF Names:DDB_G0292760
OrganismiDictyostelium discoideum (Slime mold)
Taxonomic identifieri44689 [NCBI]
Taxonomic lineageiEukaryotaAmoebozoaMycetozoaDictyosteliidaDictyostelium
ProteomesiUP000002195: Chromosome 6, UP000002195: Unassembled WGS sequence

Organism-specific databases

dictyBaseiDDB_G0292760. lig4.

Subcellular locationi

Nucleus By similarity

GO - Cellular componenti

  1. chromosome Source: RefGenome
  2. DNA-dependent protein kinase-DNA ligase 4 complex Source: dictyBase
  3. DNA ligase IV complex Source: RefGenome
  4. nucleus Source: dictyBase
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 10881088DNA ligase 4PRO_0000351216Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi44689.DDB_0232255.

Structurei

3D structure databases

ProteinModelPortaliQ54CR9.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini827 – 91791BRCT 1PROSITE-ProRule annotationAdd
BLAST
Domaini984 – 1088105BRCT 2PROSITE-ProRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi39 – 5214Poly-AsnAdd
BLAST
Compositional biasi72 – 787Poly-Thr
Compositional biasi110 – 12314Poly-ThrAdd
BLAST
Compositional biasi969 – 9757Poly-Thr

Sequence similaritiesi

Belongs to the ATP-dependent DNA ligase family.Curated
Contains 2 BRCT domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiCOG1793.
InParanoidiQ54CR9.
KOiK10777.
OMAiHMCPSTK.
PhylomeDBiQ54CR9.

Family and domain databases

Gene3Di1.10.3260.10. 1 hit.
2.40.50.140. 1 hit.
3.40.50.10190. 2 hits.
InterProiIPR001357. BRCT_dom.
IPR000977. DNA_ligase_ATP-dep.
IPR012309. DNA_ligase_ATP-dep_C.
IPR012310. DNA_ligase_ATP-dep_cent.
IPR012308. DNA_ligase_ATP-dep_N.
IPR021536. DNA_ligase_IV_dom.
IPR029710. LIG4.
IPR012340. NA-bd_OB-fold.
[Graphical view]
PANTHERiPTHR10459:SF7. PTHR10459:SF7. 1 hit.
PfamiPF00533. BRCT. 1 hit.
PF04679. DNA_ligase_A_C. 1 hit.
PF01068. DNA_ligase_A_M. 1 hit.
PF04675. DNA_ligase_A_N. 1 hit.
PF11411. DNA_ligase_IV. 1 hit.
[Graphical view]
SMARTiSM00292. BRCT. 2 hits.
[Graphical view]
SUPFAMiSSF117018. SSF117018. 1 hit.
SSF50249. SSF50249. 1 hit.
SSF52113. SSF52113. 2 hits.
TIGRFAMsiTIGR00574. dnl1. 1 hit.
PROSITEiPS50172. BRCT. 2 hits.
PS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q54CR9-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MALSLYYDED DDENENENKD KPNNDFKNQQ QINTSKTTNN NNNINNKNNY
60 70 80 90 100
NNKFNDDDIF NNDKIITKPR VTTTTTTTKN TSTNSNINKT KFNDDDIFDD
110 120 130 140 150
EDEDSNSNKT TTTTTTTTTT TDTIITNDYR YQKTVPFSSF CDLMNRIIND
160 170 180 190 200
TKISNKKNYL EKFMNHYKDE PNNFYQLLRL ILPQLDKDRN SYGLKEKTLA
210 220 230 240 250
RLYVELLNIS PESVDAMRLL NWKKSTNDEI GGDFGTAVYL SLKNRCNNDN
260 270 280 290 300
GRIKVSMGDI NESLDQLSQP LTDKKTKVSI LKKVLRSTTA QEQKWFVRII
310 320 330 340 350
LKEMKNGLSD NITLKFFHPD AIDHFNITSN LRLVCTNLFY MTQSKQKELK
360 370 380 390 400
DKQKLEEKEN LLKQQQQQQN DLDIYKLEIK LFNPIKPMLA NRQSIDNLSM
410 420 430 440 450
ILNSAISATQ FVVEKKFDGE RIQIHKDGEQ VKYFSRNSND STGIYGSMFT
460 470 480 490 500
PIVKECVLAE RCILDGELIV WDSISQRFED FGNLKTLALN KDGISGSGDP
510 520 530 540 550
LGINYGKQLC FIAFDILFVK DQSVMNLPLM QRLMLLKRCV TIKSKQFEIS
560 570 580 590 600
EQTTVNSISQ IISLLESAII NREEGLMLKN LHSLYVPAER KDKWVKIKPE
610 620 630 640 650
YIDGMGNGAD DLDLVIIGGY YGSGLNRRGG TISHFMLGVP FIADSTDTDI
660 670 680 690 700
DDESTFDKNV IFYSFCKVGS GYTDIQLKSL QKDLDPHWNN FSTSKPPSII
710 720 730 740 750
QLAEPFKEKP DVWIDPRVYS KVLQIKASQI VVTDKYKCGY TLRFPRVLKI
760 770 780 790 800
RDDKGWKDCC SHEEIIDLFT NYSTNLNFKR DHEYGDGSGG KNKKLKKSKK
810 820 830 840 850
TTNQLLADSG LKVLSIFQDT DTSGIIPTQN IFQGIEICVI KGSSGEYTKS
860 870 880 890 900
KLEIMIVEMG GSKVQYPSRN TNYVISSKEV VKIQNLIQSG FIDIVSFNWI
910 920 930 940 950
VDCYNEKRLV PLGPKYMIFS TESTKKRFLL DSDQFGDSYI NETTEQSLKD
960 970 980 990 1000
SFNQIDKLKL KKQLSINSTT TTTTTSISKY FSNCWWSLFK EFTFYLDLYQ
1010 1020 1030 1040 1050
VVGEKSTLIE NNNLELSNLN IQFYGGKISI EFNNKITHVV LDSLDLSRIT
1060 1070 1080
FIKNKINSLS LPIQIVTTNW IQLSINNYSI QPILEILD
Length:1,088
Mass (Da):124,791
Last modified:May 24, 2005 - v1
Checksum:iFE1B3C00A20B5E76
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AAFI02000196 Genomic DNA. Translation: EAL61054.1.
RefSeqiXP_629472.1. XM_629470.1.

Genome annotation databases

EnsemblProtistsiDDB0232255; DDB0232255; DDB_G0292760.
GeneIDi8628862.
KEGGiddi:DDB_G0292760.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AAFI02000196 Genomic DNA. Translation: EAL61054.1 .
RefSeqi XP_629472.1. XM_629470.1.

3D structure databases

ProteinModelPortali Q54CR9.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 44689.DDB_0232255.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblProtistsi DDB0232255 ; DDB0232255 ; DDB_G0292760 .
GeneIDi 8628862.
KEGGi ddi:DDB_G0292760.

Organism-specific databases

dictyBasei DDB_G0292760. lig4.

Phylogenomic databases

eggNOGi COG1793.
InParanoidi Q54CR9.
KOi K10777.
OMAi HMCPSTK.
PhylomeDBi Q54CR9.

Miscellaneous databases

PROi Q54CR9.

Family and domain databases

Gene3Di 1.10.3260.10. 1 hit.
2.40.50.140. 1 hit.
3.40.50.10190. 2 hits.
InterProi IPR001357. BRCT_dom.
IPR000977. DNA_ligase_ATP-dep.
IPR012309. DNA_ligase_ATP-dep_C.
IPR012310. DNA_ligase_ATP-dep_cent.
IPR012308. DNA_ligase_ATP-dep_N.
IPR021536. DNA_ligase_IV_dom.
IPR029710. LIG4.
IPR012340. NA-bd_OB-fold.
[Graphical view ]
PANTHERi PTHR10459:SF7. PTHR10459:SF7. 1 hit.
Pfami PF00533. BRCT. 1 hit.
PF04679. DNA_ligase_A_C. 1 hit.
PF01068. DNA_ligase_A_M. 1 hit.
PF04675. DNA_ligase_A_N. 1 hit.
PF11411. DNA_ligase_IV. 1 hit.
[Graphical view ]
SMARTi SM00292. BRCT. 2 hits.
[Graphical view ]
SUPFAMi SSF117018. SSF117018. 1 hit.
SSF50249. SSF50249. 1 hit.
SSF52113. SSF52113. 2 hits.
TIGRFAMsi TIGR00574. dnl1. 1 hit.
PROSITEi PS50172. BRCT. 2 hits.
PS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "The genome of the social amoeba Dictyostelium discoideum."
    Eichinger L., Pachebat J.A., Gloeckner G., Rajandream M.A., Sucgang R., Berriman M., Song J., Olsen R., Szafranski K., Xu Q., Tunggal B., Kummerfeld S., Madera M., Konfortov B.A., Rivero F., Bankier A.T., Lehmann R., Hamlin N.
    , Davies R., Gaudet P., Fey P., Pilcher K., Chen G., Saunders D., Sodergren E.J., Davis P., Kerhornou A., Nie X., Hall N., Anjard C., Hemphill L., Bason N., Farbrother P., Desany B., Just E., Morio T., Rost R., Churcher C.M., Cooper J., Haydock S., van Driessche N., Cronin A., Goodhead I., Muzny D.M., Mourier T., Pain A., Lu M., Harper D., Lindsay R., Hauser H., James K.D., Quiles M., Madan Babu M., Saito T., Buchrieser C., Wardroper A., Felder M., Thangavelu M., Johnson D., Knights A., Loulseged H., Mungall K.L., Oliver K., Price C., Quail M.A., Urushihara H., Hernandez J., Rabbinowitsch E., Steffen D., Sanders M., Ma J., Kohara Y., Sharp S., Simmonds M.N., Spiegler S., Tivey A., Sugano S., White B., Walker D., Woodward J.R., Winckler T., Tanaka Y., Shaulsky G., Schleicher M., Weinstock G.M., Rosenthal A., Cox E.C., Chisholm R.L., Gibbs R.A., Loomis W.F., Platzer M., Kay R.R., Williams J.G., Dear P.H., Noegel A.A., Barrell B.G., Kuspa A.
    Nature 435:43-57(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: AX4.

Entry informationi

Entry nameiDNLI4_DICDI
AccessioniPrimary (citable) accession number: Q54CR9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 23, 2008
Last sequence update: May 24, 2005
Last modified: November 26, 2014
This is version 69 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Dictyostelium discoideum
    Dictyostelium discoideum: entries, gene names and cross-references to dictyBase
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3