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Protein

DNA ligase 4

Gene

LIG4

Organism
Coprinopsis cinerea (strain Okayama-7 / 130 / ATCC MYA-4618 / FGSC 9003) (Inky cap fungus) (Hormographiella aspergillata)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Protein inferred from homologyi

Functioni

Involved in ds DNA break repair. Has a role in non-homologous integration (NHI) pathways where it is required in the final step of non-homologus end-joining.

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 sitei289 – 2891ATPBy similarity
Active sitei291 – 2911N6-AMP-lysine intermediatePROSITE-ProRule annotation
Binding sitei296 – 2961ATPBy similarity
Binding sitei311 – 3111ATPBy similarity
Metal bindingi349 – 3491Magnesium 1Sequence analysis
Metal bindingi447 – 4471Magnesium 2Sequence analysis
Binding sitei452 – 4521ATPBy similarity
Binding sitei463 – 4631ATPBy similarity
Binding sitei469 – 4691ATPBy similarity

GO - Molecular functioni

GO - Biological processi

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:CC1G_14831
OrganismiCoprinopsis cinerea (strain Okayama-7 / 130 / ATCC MYA-4618 / FGSC 9003) (Inky cap fungus) (Hormographiella aspergillata)
Taxonomic identifieri240176 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaBasidiomycotaAgaricomycotinaAgaricomycetesAgaricomycetidaeAgaricalesPsathyrellaceaeCoprinopsis
Proteomesi
  • UP000001861 Componenti: Unassembled WGS sequence

Organism-specific databases

EuPathDBiFungiDB:CC1G_14831.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 10251025DNA ligase 4PRO_0000333259Add
BLAST

Structurei

3D structure databases

ProteinModelPortaliA8N936.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini667 – 76397BRCT 1PROSITE-ProRule annotationAdd
BLAST
Domaini915 – 1025111BRCT 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

InParanoidiA8N936.
KOiK10777.
OrthoDBiEOG7QC84G.

Family and domain databases

Gene3Di1.10.3260.10. 1 hit.
2.40.50.140. 1 hit.
3.40.50.10190. 1 hit.
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.
IPR029710. LIG4.
IPR012340. NA-bd_OB-fold.
[Graphical view]
PANTHERiPTHR10459:SF7. PTHR10459:SF7. 1 hit.
PfamiPF16589. BRCT_2. 2 hits.
PF04679. DNA_ligase_A_C. 1 hit.
PF01068. DNA_ligase_A_M. 1 hit.
PF04675. DNA_ligase_A_N. 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.

A8N936-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MMQPTPAPSS APGSPQRTQA EPEMETPSYP QPPQNVGTAP FSVLVKLFEK
60 70 80 90 100
LATERKQERR RKLLDAWFRH WRREKGFDLY PVLRLLLPQK DRDRAVYGLK
110 120 130 140 150
EKNLAKTYIK LIPLGMRDPD AIRLLNWKKP TERDKSSGDF PQVLCEVVSK
160 170 180 190 200
RSSVIEGTLT IDELNEILDD IAKNMGKSDV QSKILRRIYN NSTADEQRWI
210 220 230 240 250
IRIILKDMNI SVKETTVFAV FHPDAQDLYN TCSDLKKVAW ELWDPSRRLN
260 270 280 290 300
AKDKEIQIFH AFAPMLCKRP TRKIEETVKA MGGSKFIIEE KLDGERMQLH
310 320 330 340 350
KRGNEYFYCS RKGKDYTYLY GKHIGAGSLT PFIDSAFDSR IDDIILDGEM
360 370 380 390 400
LVWDPVSERN LPFGTLKTAA LDRSKKENNP RPCFKVFDLL YLNGMSLLDK
410 420 430 440 450
TVKFRKNNLR HCIKPIPGRI EFVEEYQGET ANDIRKRMEQ VMENRGEGLV
460 470 480 490 500
IKHPKAKYIL NGRNTDWIKV KPEYMDNMGE TVDVLVVAGN YGSGKRGGGV
510 520 530 540 550
STLICAVMDD RRPDSDDEPK YSSFVRIGTG LSFADYVWVR SKPWKVWDPK
560 570 580 590 600
NPPEFLQTAK KGQEDKGDVY LEPEDSFILK VKAAEITPSD QYHMGFTMRF
610 620 630 640 650
PRALAIRDDL SIADCMTATE VFESLKSERK RKMEDDAGIT TKKRKTTVKK
660 670 680 690 700
VALLPEYSGP NLKKVAVKTD IFNGMKFVVF SDPKSRTGEA DKKELMKTIH
710 720 730 740 750
ANGGTCSQIV NKNSEAIVIY GGSITPYDLK LVIDKGIHDV IKPSWITDSV
760 770 780 790 800
TLGEPAPFKK KYFFHATEER KYADEYNEDD GEEEGAVPSA DEQERDVKSG
810 820 830 840 850
TVEPGSETED EDEEQAPEIK EEQDGELHEW LKVDDRKSPA LPAHDEEDSV
860 870 880 890 900
TEDDSDNADV ADEEEPDLDD WFQVKGETED EGAGALATAS RHRETTPDVD
910 920 930 940 950
GDVKMGESEE AMDYDPDVIF KHLCFYLDSP ANAQRHGMAT RPKYEAAITK
960 970 980 990 1000
SFEEVEKLIK DNGGKIVDLD EPKLTHVVLD KRDDSRRVEL MKRTSKPRRR
1010 1020
HLVLSDYIEA CIDEGTLLDE EGESF
Length:1,025
Mass (Da):116,801
Last modified:May 20, 2008 - v2
Checksum:iB216FFD40932868C
GO

Sequence cautioni

The sequence EFI27358.1 differs from that shown. Reason: Erroneous gene model prediction. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AACS02000007 Genomic DNA. Translation: EFI27358.1. Sequence problems.
RefSeqiXP_002910852.1. XM_002910806.1.

Genome annotation databases

EnsemblFungiiEFI27358; EFI27358; CC1G_14831.
GeneIDi9379321.
KEGGicci:CC1G_14831.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AACS02000007 Genomic DNA. Translation: EFI27358.1. Sequence problems.
RefSeqiXP_002910852.1. XM_002910806.1.

3D structure databases

ProteinModelPortaliA8N936.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiEFI27358; EFI27358; CC1G_14831.
GeneIDi9379321.
KEGGicci:CC1G_14831.

Organism-specific databases

EuPathDBiFungiDB:CC1G_14831.

Phylogenomic databases

InParanoidiA8N936.
KOiK10777.
OrthoDBiEOG7QC84G.

Family and domain databases

Gene3Di1.10.3260.10. 1 hit.
2.40.50.140. 1 hit.
3.40.50.10190. 1 hit.
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.
IPR029710. LIG4.
IPR012340. NA-bd_OB-fold.
[Graphical view]
PANTHERiPTHR10459:SF7. PTHR10459:SF7. 1 hit.
PfamiPF16589. BRCT_2. 2 hits.
PF04679. DNA_ligase_A_C. 1 hit.
PF01068. DNA_ligase_A_M. 1 hit.
PF04675. DNA_ligase_A_N. 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. "Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus)."
    Stajich J.E., Wilke S.K., Ahren D., Au C.H., Birren B.W., Borodovsky M., Burns C., Canbaeck B., Casselton L.A., Cheng C.K., Deng J., Dietrich F.S., Fargo D.C., Farman M.L., Gathman A.C., Goldberg J., Guigo R., Hoegger P.J.
    , Hooker J.B., Huggins A., James T.Y., Kamada T., Kilaru S., Kodira C., Kuees U., Kupfer D., Kwan H.S., Lomsadze A., Li W., Lilly W.W., Ma L.-J., Mackey A.J., Manning G., Martin F., Muraguchi H., Natvig D.O., Palmerini H., Ramesh M.A., Rehmeyer C.J., Roe B.A., Shenoy N., Stanke M., Ter-Hovhannisyan V., Tunlid A., Velagapudi R., Vision T.J., Zeng Q., Zolan M.E., Pukkila P.J.
    Proc. Natl. Acad. Sci. U.S.A. 107:11889-11894(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Okayama-7 / 130 / ATCC MYA-4618 / FGSC 9003.

Entry informationi

Entry nameiDNLI4_COPC7
AccessioniPrimary (citable) accession number: A8N936
Secondary accession number(s): D6RNV6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 20, 2008
Last sequence update: May 20, 2008
Last modified: June 8, 2016
This is version 61 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

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 one 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.