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Protein

DNA ligase 4

Gene

DNL4

Organism
Pongo abelii (Sumatran orangutan) (Pongo pygmaeus abelii)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript leveli

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 and V(D)J recombination. The LIG4-XRCC4 complex is responsible for the NHEJ ligation step, and XRCC4 enhances the joining activity of LIG4. Binding of the LIG4-XRCC4 complex to DNA ends is dependent on the assembly of the DNA-dependent protein kinase complex DNA-PK to these DNA ends (By similarity).By similarity

Catalytic activityi

ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m).PROSITE-ProRule annotation

Cofactori

Mg2+By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei271 – 2711ATPBy similarity
Active sitei273 – 2731N6-AMP-lysine intermediatePROSITE-ProRule annotation
Binding sitei278 – 2781ATPBy similarity
Binding sitei293 – 2931ATPBy similarity
Metal bindingi331 – 3311Magnesium 1Sequence Analysis
Metal bindingi427 – 4271Magnesium 2Sequence Analysis
Binding sitei432 – 4321ATPBy similarity
Binding sitei443 – 4431ATPBy similarity
Binding sitei449 – 4491ATPBy similarity

GO - Molecular functioni

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

GO - Biological processi

  1. cell cycle Source: UniProtKB-KW
  2. cell division Source: UniProtKB-KW
  3. DNA biosynthetic process Source: InterPro
  4. DNA ligation involved in DNA repair Source: InterPro
  5. DNA recombination Source: UniProtKB-KW
  6. DNA replication Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

Cell cycle, Cell division, 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:DNL4
OrganismiPongo abelii (Sumatran orangutan) (Pongo pygmaeus abelii)
Taxonomic identifieri9601 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaePongo
ProteomesiUP000001595: Unplaced

Subcellular locationi

Nucleus By similarity

GO - Cellular componenti

  1. nonhomologous end joining complex Source: UniProtKB
  2. nucleus Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 911911DNA ligase 4PRO_0000059578Add
BLAST

Proteomic databases

PRIDEiQ5R6L3.

Interactioni

Subunit structurei

Binds to XRCC4. The LIG4-XRCC4 complex has probably a 1:2 stoichiometry. The LIG4-XRCC4 heteromer associates in a DNA-dependent manner with the DNA-dependent protein kinase complex DNA-PK, formed by the Ku p70/p86 dimer (G22P1/G22P2) and PRKDC. Interacts with APLF (By similarity).By similarity

Structurei

3D structure databases

ProteinModelPortaliQ5R6L3.
SMRiQ5R6L3. Positions 654-759.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini654 – 74390BRCT 1PROSITE-ProRule annotationAdd
BLAST
Domaini808 – 911104BRCT 2PROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

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

Keywords - Domaini

Repeat

Phylogenomic databases

HOVERGENiHBG005516.
InParanoidiQ5R6L3.
KOiK10777.

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.
IPR016059. DNA_ligase_ATP-dep_CS.
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. 2 hits.
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.
PS00697. DNA_LIGASE_A1. 1 hit.
PS00333. DNA_LIGASE_A2. 1 hit.
PS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q5R6L3-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MAASQTSQTV ASHVPFADLC STLERIQKSK GRAEKIRHFR EFLDSWRKFH
60 70 80 90 100
DAFHKNQKDV TDSFYPAMRL ILPQLERERM AYGIKETMLA KLYIELLNLP
110 120 130 140 150
RDGKDALKLL NYRTPTGTHG DAGDFAMIAY FVLKPRCLQK GSLTIQQVND
160 170 180 190 200
LLDSIASNNS AKRKDLIKKS LLQLITQSSA LEQKWLIRMI IKDLKLGVSQ
210 220 230 240 250
QTIFSVFHSD AVELHNVTTD LEKVCRQLHD PSVGLSDISI TLFSAFKPML
260 270 280 290 300
AAIADIEHIE KDMKHQSFYI ETKLDGERMQ MHKDGDVYKY FSRNGYNYTD
310 320 330 340 350
QFGASPTEGS LTPFIHNAFK TDIQICILDG EMMAYNPNTQ TFMQKGTKFD
360 370 380 390 400
IKRMVEDSDL QTCYCVFDVL MVNNKKLGHE TLRKRYEILS SIFTPIPGRI
410 420 430 440 450
EIVQKTQAHT KNEVIDALNE AIDKREEGIM IKQPLSIYKP DKRGEGWLKI
460 470 480 490 500
KPEYVSGLMD ELDILIVGGY WGKGSRGGMM SHFLCAVAEK PPPGEKPSVF
510 520 530 540 550
HTLSRVGSGC TMKELYDLGL KLAKYWKPFH KKAPPSSILC GTEKPEVYIE
560 570 580 590 600
PCNSVIVQIK AAEIVPSDMY KTGCTLRFPR IEKIRDDKEW HECMTLDDLE
610 620 630 640 650
QLRGKASGKL ASKHFYVGGD DEPQEKKRKA APKMKKVIGI IEHLKAPNLT
660 670 680 690 700
NVNKISNIFE DVEFCVMSGT DSQPKPDLEN RIAEFGGYIV QNPGPDTYCV
710 720 730 740 750
IAGSKNIRVK NIILSNKHDV VKPAWLLECF KTKSFVPWQP HFMIHMCPST
760 770 780 790 800
KEHFAREYDC YGDSYFVDTD LNQLKEVFSG IKNSNEQTPE EMASLIADLE
810 820 830 840 850
YRYSWDCSPL SMFRRHTVYL DLYAVINDLS TKNEGTRLAI KALELRFHGA
860 870 880 890 900
KVVSCLAEGV SHVIIGEDHS RIADFKAFRR TFKRKFKILK ESWITDSIDK
910
CELQEENQYL I
Length:911
Mass (Da):104,053
Last modified:December 21, 2004 - v1
Checksum:iC6AD9817E9EC2B59
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CR860475 mRNA. Translation: CAH92597.1.
RefSeqiNP_001126522.1. NM_001133050.1.

Genome annotation databases

GeneIDi100173511.
KEGGipon:100173511.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CR860475 mRNA. Translation: CAH92597.1.
RefSeqiNP_001126522.1. NM_001133050.1.

3D structure databases

ProteinModelPortaliQ5R6L3.
SMRiQ5R6L3. Positions 654-759.
ModBaseiSearch...
MobiDBiSearch...

Proteomic databases

PRIDEiQ5R6L3.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi100173511.
KEGGipon:100173511.

Organism-specific databases

CTDi3981.

Phylogenomic databases

HOVERGENiHBG005516.
InParanoidiQ5R6L3.
KOiK10777.

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.
IPR016059. DNA_ligase_ATP-dep_CS.
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. 2 hits.
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.
PS00697. DNA_LIGASE_A1. 1 hit.
PS00333. DNA_LIGASE_A2. 1 hit.
PS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. The German cDNA consortium
    Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Brain cortex.

Entry informationi

Entry nameiDNLI4_PONAB
AccessioniPrimary (citable) accession number: Q5R6L3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 7, 2006
Last sequence update: December 21, 2004
Last modified: January 7, 2015
This is version 58 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.