DNA ligase 4 - Pongo abelii (Sumatran orangutan)

Preferred order of sections

Names and origin

Protein names

Recommended name:
DNA ligase 4
EC=6.5.1.1

Alternative name(s):
DNA ligase IV
Polydeoxyribonucleotide synthase [ATP] 4

Gene names

Name:

DNL4

Organism

Pongo abelii (Sumatran orangutan) (Pongo pygmaeus abelii) [Reference proteome]

Taxonomic identifier

9601 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Pongo

Protein attributes

Sequence length	911 AA.
Sequence status	Complete.
Protein existence	Evidence at transcript level

General annotation (Comments)

Function	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 activity	ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m).
Cofactor	Magnesium By similarity.
Subunit structure	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.
Subcellular location	Nucleus By similarity.
Sequence similarities	Belongs to the ATP-dependent DNA ligase family. Contains 2 BRCT domains.

Ontologies

Keywords
Biological process	Cell cycle Cell division DNA damage DNA recombination DNA repair DNA replication
Cellular component	Nucleus
Domain	Repeat
Ligand	ATP-binding Magnesium Metal-binding Nucleotide-binding
Molecular function	Ligase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA ligation involved in DNA repair Inferred from electronic annotation. Source: InterPro DNA recombination Inferred from electronic annotation. Source: UniProtKB-KW DNA replication Inferred from electronic annotation. Source: UniProtKB-KW cell cycle Inferred from electronic annotation. Source: UniProtKB-KW cell division Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	nonhomologous end joining complex Inferred from sequence or structural similarity. Source: UniProtKB nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW DNA binding Inferred from electronic annotation. Source: InterPro DNA ligase (ATP) activity Inferred from electronic annotation. Source: EC metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 911

911

DNA ligase 4

PRO_0000059578

Regions

Domain

654 – 743

90

BRCT 1

Domain

808 – 911

104

BRCT 2

Sites

Active site

273

1

N6-AMP-lysine intermediate By similarity

Metal binding

331

1

Magnesium 1 Potential

Metal binding

427

1

Magnesium 2 Potential

Binding site

271

1

ATP By similarity

Binding site

278

1

ATP By similarity

Binding site

293

1

ATP By similarity

Binding site

432

1

ATP By similarity

Binding site

443

1

ATP By similarity

Binding site

449

1

ATP By similarity

Sequences

Sequence

Length

Mass (Da)

Tools

Q5R6L3 [UniParc].

Last modified December 21, 2004. Version 1.
Checksum: C6AD9817E9EC2B59
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FASTA

911

104,053

        10         20         30         40         50         60 
MAASQTSQTV ASHVPFADLC STLERIQKSK GRAEKIRHFR EFLDSWRKFH DAFHKNQKDV 

        70         80         90        100        110        120 
TDSFYPAMRL ILPQLERERM AYGIKETMLA KLYIELLNLP RDGKDALKLL NYRTPTGTHG 

       130        140        150        160        170        180 
DAGDFAMIAY FVLKPRCLQK GSLTIQQVND LLDSIASNNS AKRKDLIKKS LLQLITQSSA 

       190        200        210        220        230        240 
LEQKWLIRMI IKDLKLGVSQ QTIFSVFHSD AVELHNVTTD LEKVCRQLHD PSVGLSDISI 

       250        260        270        280        290        300 
TLFSAFKPML AAIADIEHIE KDMKHQSFYI ETKLDGERMQ MHKDGDVYKY FSRNGYNYTD 

       310        320        330        340        350        360 
QFGASPTEGS LTPFIHNAFK TDIQICILDG EMMAYNPNTQ TFMQKGTKFD IKRMVEDSDL 

       370        380        390        400        410        420 
QTCYCVFDVL MVNNKKLGHE TLRKRYEILS SIFTPIPGRI EIVQKTQAHT KNEVIDALNE 

       430        440        450        460        470        480 
AIDKREEGIM IKQPLSIYKP DKRGEGWLKI KPEYVSGLMD ELDILIVGGY WGKGSRGGMM 

       490        500        510        520        530        540 
SHFLCAVAEK PPPGEKPSVF HTLSRVGSGC TMKELYDLGL KLAKYWKPFH KKAPPSSILC 

       550        560        570        580        590        600 
GTEKPEVYIE PCNSVIVQIK AAEIVPSDMY KTGCTLRFPR IEKIRDDKEW HECMTLDDLE 

       610        620        630        640        650        660 
QLRGKASGKL ASKHFYVGGD DEPQEKKRKA APKMKKVIGI IEHLKAPNLT NVNKISNIFE 

       670        680        690        700        710        720 
DVEFCVMSGT DSQPKPDLEN RIAEFGGYIV QNPGPDTYCV IAGSKNIRVK NIILSNKHDV 

       730        740        750        760        770        780 
VKPAWLLECF KTKSFVPWQP HFMIHMCPST KEHFAREYDC YGDSYFVDTD LNQLKEVFSG 

       790        800        810        820        830        840 
IKNSNEQTPE EMASLIADLE YRYSWDCSPL SMFRRHTVYL DLYAVINDLS TKNEGTRLAI 

       850        860        870        880        890        900 
KALELRFHGA KVVSCLAEGV SHVIIGEDHS RIADFKAFRR TFKRKFKILK ESWITDSIDK 

       910 
CELQEENQYL I

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References

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

Cross-references

Sequence databases
EMBL GenBank DDBJ	CR860475 mRNA. Translation: CAH92597.1.
RefSeq	NP_001126522.1. NM_001133050.1.
UniGene	Pab.18738.
3D structure databases
ProteinModelPortal	Q5R6L3.
SMR	Q5R6L3. Positions 654-759.
ModBase	Search...
Proteomic databases
PRIDE	Q5R6L3.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	100173511.
KEGG	pon:100173511.
Organism-specific databases
CTD	3981.
Phylogenomic databases
HOVERGEN	HBG005516.
InParanoid	Q5R6L3.
KO	K10777.
Family and domain databases
Gene3D	1.10.3260.10. 1 hit. 2.40.50.140. 1 hit.
InterPro	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. IPR012340. NA-bd_OB-fold. [Graphical view]
Pfam	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]
SMART	SM00292. BRCT. 2 hits. [Graphical view]
SUPFAM	SSF52113. BRCT. 2 hits. SSF50249. Nucleic_acid_OB. 1 hit. SSF117018. SSF117018. 1 hit.
TIGRFAMs	TIGR00574. dnl1. 1 hit.
PROSITE	PS50172. BRCT. 2 hits. PS00697. DNA_LIGASE_A1. 1 hit. PS00333. DNA_LIGASE_A2. 1 hit. PS50160. DNA_LIGASE_A3. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

DNLI4_PONAB

Accession

Primary (citable) accession number: Q5R6L3

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 7, 2006
Last sequence update:	December 21, 2004
Last modified:	March 6, 2013
This is version 51 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Sequences

References

Cross-references

Sequence databases

3D structure databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Family and domain databases

Entry information

Relevant documents