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Q5R6L3

- DNLI4_PONAB

UniProt

Q5R6L3 - DNLI4_PONAB

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Protein

DNA ligase 4

Gene
DNL4
Organism
Pongo abelii (Sumatran orangutan) (Pongo pygmaeus abelii)
Status
Reviewed - 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.

Catalytic activityi

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

Cofactori

Magnesium By similarity.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei271 – 2711ATP By similarity
Active sitei273 – 2731N6-AMP-lysine intermediate By similarity
Binding sitei278 – 2781ATP By similarity
Binding sitei293 – 2931ATP By similarity
Metal bindingi331 – 3311Magnesium 1 Reviewed prediction
Metal bindingi427 – 4271Magnesium 2 Reviewed prediction
Binding sitei432 – 4321ATP By similarity
Binding sitei443 – 4431ATP By similarity
Binding sitei449 – 4491ATP By 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 ligation involved in DNA repair Source: InterPro
  4. DNA recombination Source: UniProtKB-KW
  5. 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.

Structurei

3D structure databases

ProteinModelPortaliQ5R6L3.
SMRiQ5R6L3. Positions 654-759.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini654 – 74390BRCT 1Add
BLAST
Domaini808 – 911104BRCT 2Add
BLAST

Sequence similaritiesi

Contains 2 BRCT domains.

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.
IPR012340. NA-bd_OB-fold.
[Graphical view]
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

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MAASQTSQTV ASHVPFADLC STLERIQKSK GRAEKIRHFR EFLDSWRKFH    50
DAFHKNQKDV TDSFYPAMRL ILPQLERERM AYGIKETMLA KLYIELLNLP 100
RDGKDALKLL NYRTPTGTHG DAGDFAMIAY FVLKPRCLQK GSLTIQQVND 150
LLDSIASNNS AKRKDLIKKS LLQLITQSSA LEQKWLIRMI IKDLKLGVSQ 200
QTIFSVFHSD AVELHNVTTD LEKVCRQLHD PSVGLSDISI TLFSAFKPML 250
AAIADIEHIE KDMKHQSFYI ETKLDGERMQ MHKDGDVYKY FSRNGYNYTD 300
QFGASPTEGS LTPFIHNAFK TDIQICILDG EMMAYNPNTQ TFMQKGTKFD 350
IKRMVEDSDL QTCYCVFDVL MVNNKKLGHE TLRKRYEILS SIFTPIPGRI 400
EIVQKTQAHT KNEVIDALNE AIDKREEGIM IKQPLSIYKP DKRGEGWLKI 450
KPEYVSGLMD ELDILIVGGY WGKGSRGGMM SHFLCAVAEK PPPGEKPSVF 500
HTLSRVGSGC TMKELYDLGL KLAKYWKPFH KKAPPSSILC GTEKPEVYIE 550
PCNSVIVQIK AAEIVPSDMY KTGCTLRFPR IEKIRDDKEW HECMTLDDLE 600
QLRGKASGKL ASKHFYVGGD DEPQEKKRKA APKMKKVIGI IEHLKAPNLT 650
NVNKISNIFE DVEFCVMSGT DSQPKPDLEN RIAEFGGYIV QNPGPDTYCV 700
IAGSKNIRVK NIILSNKHDV VKPAWLLECF KTKSFVPWQP HFMIHMCPST 750
KEHFAREYDC YGDSYFVDTD LNQLKEVFSG IKNSNEQTPE EMASLIADLE 800
YRYSWDCSPL SMFRRHTVYL DLYAVINDLS TKNEGTRLAI KALELRFHGA 850
KVVSCLAEGV SHVIIGEDHS RIADFKAFRR TFKRKFKILK ESWITDSIDK 900
CELQEENQYL I 911
Length:911
Mass (Da):104,053
Last modified:December 21, 2004 - v1
Checksum:iC6AD9817E9EC2B59
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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:
EMBL
GenBank
DDBJ
Links Updated
CR860475 mRNA. Translation: CAH92597.1 .
RefSeqi NP_001126522.1. NM_001133050.1.

3D structure databases

ProteinModelPortali Q5R6L3.
SMRi Q5R6L3. Positions 654-759.
ModBasei Search...
MobiDBi Search...

Proteomic databases

PRIDEi Q5R6L3.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

GeneIDi 100173511.
KEGGi pon:100173511.

Organism-specific databases

CTDi 3981.

Phylogenomic databases

HOVERGENi HBG005516.
InParanoidi Q5R6L3.
KOi K10777.

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.
IPR016059. DNA_ligase_ATP-dep_CS.
IPR012308. DNA_ligase_ATP-dep_N.
IPR021536. DNA_ligase_IV_dom.
IPR012340. NA-bd_OB-fold.
[Graphical view ]
Pfami PF00533. 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 ]
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.
PS00697. DNA_LIGASE_A1. 1 hit.
PS00333. DNA_LIGASE_A2. 1 hit.
PS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view ]
ProtoNeti Search...

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: September 3, 2014
This is version 54 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

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