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Protein

DNA ligase 4

Gene

LIG4

Organism
Cryptococcus neoformans var. neoformans serotype D (strain B-3501A) (Filobasidiella neoformans)
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 (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 sitei295 – 2951ATPBy similarity
Active sitei297 – 2971N6-AMP-lysine intermediatePROSITE-ProRule annotation
Binding sitei302 – 3021ATPBy similarity
Binding sitei319 – 3191ATPBy similarity
Metal bindingi357 – 3571Magnesium 1Sequence Analysis
Metal bindingi452 – 4521Magnesium 2Sequence Analysis
Binding sitei457 – 4571ATPBy similarity
Binding sitei468 – 4681ATPBy similarity
Binding sitei474 – 4741ATPBy 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
Ordered Locus Names:CNBK2570
OrganismiCryptococcus neoformans var. neoformans serotype D (strain B-3501A) (Filobasidiella neoformans)
Taxonomic identifieri283643 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaBasidiomycotaAgaricomycotinaTremellomycetesTremellalesTremellaceaeFilobasidiellaFilobasidiella/Cryptococcus neoformans species complex
ProteomesiUP000001435 Componenti: Chromosome 11

Organism-specific databases

EuPathDBiFungiDB:CNBK2570.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 10651065DNA ligase 4PRO_0000410058Add
BLAST

Structurei

3D structure databases

ProteinModelPortaliP0CN09.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini696 – 77580BRCT 1PROSITE-ProRule annotationAdd
BLAST
Domaini954 – 1064111BRCT 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

KOiK10777.
OrthoDBiEOG7QC84G.

Family and domain databases

Gene3Di2.40.50.140. 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.
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.
[Graphical view]
SMARTiSM00292. BRCT. 2 hits.
[Graphical view]
SUPFAMiSSF50249. 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.

P0CN09-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAVHAPYNHA PPPTQEINGQ KPTLAPAITL ERPADCINRG QYPAFYIICG
60 70 80 90 100
YLNRLRADAP HKKYELLTRI FGNWREKVGP DLYPLIRLLL PDKDRERPVY
110 120 130 140 150
NLKESMLARC YIDILSLEKH SEAAQRLIKW KQPAGNSPNP TGDFAKVCYN
160 170 180 190 200
EIKARSTVEE GQLSVEAVNM LLDKLAVGKM KQKDYVPILK AINMQCTAEE
210 220 230 240 250
QEWIIRIILK DLHISIRERG VLSAFHPDAI DLYNVCSDLK RVCWTLYDPG
260 270 280 290 300
FRLNKNETHL ELFHSFLPQL CGRMNDASLE NIAKAIGAPK EFIMEEKLDG
310 320 330 340 350
ERIQLHMRGN GAQWFYCSRK AKDYTYLYGA HPGEGSLTRY IATAFQDNVR
360 370 380 390 400
NVILDGEMMV WDPVVERYLA FGTLKSAALA FSLVKVFDIL FLNDHCLSRK
410 420 430 440 450
RLSERKRLLR SGKIFKNIEN YKGRLEFVDE KRGKNAKDIR EYLERVVETK
460 470 480 490 500
GEGLVVKKTD VIYQTNSRGY DWIKVKPEYS DQMGENLEVL VLGGWWGKGG
510 520 530 540 550
RSGKISRLLC GLREQAFDDG TLQDFLFNRF WNELLGLRVD FVSHLMHLRS
560 570 580 590 600
MRCSPTHLSQ CRNKHKKHWR PFDRSNPPPF MKLGPVGLDD KPDVYIEPEN
610 620 630 640 650
SFVIEVKASE IVPAGYGIGF TLRFPRCKYI YYDKNSRDYA LDDECLWTVG
660 670 680 690 700
QGFFYKTRKL IKRTDFMDLF SRPKRSYDDS QGPGNFRGQK LSDADVETSI
710 720 730 740 750
FSDMTFSDLE ALVHKHGADF TQAQLSDLSA IVISPDQKNP LVRAQIRHGV
760 770 780 790 800
NVIKPEWVFE SIARRTALPF LKEFLVFASE EAQDGRYYNK TLEQYDKVSF
810 820 830 840 850
VRDRTGGALV DEDGDADVED EIMDGEDKDE IDVEESRESK NRRMAREDLK
860 870 880 890 900
EKESNRTLEQ KKLQEAWGLR SRASPGDSDS EPEEEMSLKE ESDTDSERSR
910 920 930 940 950
GLRAIYEDEE DGENDSHESD VGVNGDDYRA VPLSGLNDKE EGLMGESPEA
960 970 980 990 1000
MHYDEDRIFY HLAFYIDTAK NAAVNGLESS SPSFDTQERL VKVEKLLIEN
1010 1020 1030 1040 1050
GGRVARSISD PKLTHIIMDD EDSRRYVELT RKTAMPKRKH IVTPKWVEDC
1060
VDEETLLDED LYKPK
Length:1,065
Mass (Da):122,466
Last modified:June 28, 2011 - v1
Checksum:i7E0AC640AB2D6236
GO

Sequence cautioni

The sequence EAL18239.1 differs from that shown. Reason: Erroneous gene model prediction. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AAEY01000052 Genomic DNA. Translation: EAL18239.1. Sequence problems.
RefSeqiXP_772886.1. XM_767793.1.

Genome annotation databases

GeneIDi4938955.
KEGGicnb:CNBK2570.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AAEY01000052 Genomic DNA. Translation: EAL18239.1. Sequence problems.
RefSeqiXP_772886.1. XM_767793.1.

3D structure databases

ProteinModelPortaliP0CN09.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi4938955.
KEGGicnb:CNBK2570.

Organism-specific databases

EuPathDBiFungiDB:CNBK2570.

Phylogenomic databases

KOiK10777.
OrthoDBiEOG7QC84G.

Family and domain databases

Gene3Di2.40.50.140. 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.
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.
[Graphical view]
SMARTiSM00292. BRCT. 2 hits.
[Graphical view]
SUPFAMiSSF50249. 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 genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans."
    Loftus B.J., Fung E., Roncaglia P., Rowley D., Amedeo P., Bruno D., Vamathevan J., Miranda M., Anderson I.J., Fraser J.A., Allen J.E., Bosdet I.E., Brent M.R., Chiu R., Doering T.L., Donlin M.J., D'Souza C.A., Fox D.S.
    , Grinberg V., Fu J., Fukushima M., Haas B.J., Huang J.C., Janbon G., Jones S.J.M., Koo H.L., Krzywinski M.I., Kwon-Chung K.J., Lengeler K.B., Maiti R., Marra M.A., Marra R.E., Mathewson C.A., Mitchell T.G., Pertea M., Riggs F.R., Salzberg S.L., Schein J.E., Shvartsbeyn A., Shin H., Shumway M., Specht C.A., Suh B.B., Tenney A., Utterback T.R., Wickes B.L., Wortman J.R., Wye N.H., Kronstad J.W., Lodge J.K., Heitman J., Davis R.W., Fraser C.M., Hyman R.W.
    Science 307:1321-1324(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: B-3501A.

Entry informationi

Entry nameiDNLI4_CRYNB
AccessioniPrimary (citable) accession number: P0CN09
Secondary accession number(s): Q55JS6, Q5K9S5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 28, 2011
Last sequence update: June 28, 2011
Last modified: April 29, 2015
This is version 19 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete 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.