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Protein

Nuclear factor NF-kappa-B p100 subunit

Gene

nfkb2

Organism
Xenopus laevis (African clawed frog)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript leveli

Functioni

Appears to have dual functions such as cytoplasmic retention of attached NF-kappa-B proteins and generation of p52 by a cotranslational processing. The proteasome-mediated process ensures the production of both p52 and p100 and preserves their independent function. p52 binds to the kappa-B consensus sequence 5'-GGRNNYYCC-3', located in the enhancer region of genes involved in immune response and acute phase reactions. In concert with RELB, may play a role in the regulation of the circadian clock (By similarity).By similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Activator, Repressor

Keywords - Biological processi

Biological rhythms, Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Nuclear factor NF-kappa-B p100 subunit
Alternative name(s):
DNA-binding factor KBF2
Nuclear factor of kappa light polypeptide gene enhancer in B-cells 2
Cleaved into the following chain:
Gene namesi
Name:nfkb2
OrganismiXenopus laevis (African clawed frog)
Taxonomic identifieri8355 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiAmphibiaBatrachiaAnuraPipoideaPipidaeXenopodinaeXenopusXenopus

Organism-specific databases

XenbaseiXB-GENE-970090. nfkb2.

Subcellular locationi

  • Nucleus By similarity
  • Cytoplasm By similarity

  • Note: Nuclear, but also found in the cytoplasm in an inactive form complexed to an inhibitor (I-kappa-B).By similarity

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 958958Nuclear factor NF-kappa-B p100 subunitPRO_0000030327Add
BLAST
Chaini1 – 467467Nuclear factor NF-kappa-B p52 subunitBy similarityPRO_0000030328Add
BLAST

Post-translational modificationi

While translation occurs, the particular unfolded structure after the GRR repeat promotes the generation of p52 making it an acceptable substrate for the proteasome. This process is known as cotranslational processing. The processed form is active and the unprocessed form acts as an inhibitor (I kappa B-like), being able to form cytosolic complexes with NF-kappa B, trapping it in the cytoplasm. Complete folding of the region downstream of the GRR repeat precludes processing (By similarity).By similarity
Constitutive processing is tightly suppressed by its C-terminal processing inhibitory domain, named PID, which contains the death domain.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei467 – 4682Cleavage (when cotranslationally processed)

Expressioni

Tissue specificityi

Expressed in spleen.1 Publication

Interactioni

Subunit structurei

Active NF-kappa-B is a heterodimer of an about 52 kDa DNA-binding subunit and the weak DNA-binding subunit p65. Two heterodimers might form a labile tetramer (By similarity).By similarity

Protein-protein interaction databases

BioGridi99038. 1 interaction.
IntActiO73630. 1 interaction.

Structurei

3D structure databases

ProteinModelPortaliO73630.
SMRiO73630. Positions 44-333.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini40 – 230191RHDPROSITE-ProRule annotationAdd
BLAST
Repeati500 – 52930ANK 1Add
BLAST
Repeati539 – 56830ANK 2Add
BLAST
Repeati572 – 60332ANK 3Add
BLAST
Repeati610 – 63930ANK 4Add
BLAST
Repeati644 – 67431ANK 5Add
BLAST
Repeati678 – 70730ANK 6Add
BLAST
Domaini815 – 90187DeathAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni352 – 39039GRRAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi343 – 3475Nuclear localization signalSequence analysis

Domaini

The C-terminus of p100 might be involved in cytoplasmic retention, inhibition of DNA-binding by p52 homodimers, and/or transcription activation.By similarity
The glycine-rich region (GRR) appears to be a critical element in the generation of p52.By similarity

Sequence similaritiesi

Contains 6 ANK repeats.PROSITE-ProRule annotation
Contains 1 death domain.Curated
Contains 1 RHD (Rel-like) domain.PROSITE-ProRule annotation

Keywords - Domaini

ANK repeat, Repeat

Phylogenomic databases

HOVERGENiHBG052613.
KOiK04469.

Family and domain databases

Gene3Di1.10.533.10. 1 hit.
1.25.40.20. 1 hit.
2.60.40.10. 1 hit.
2.60.40.340. 1 hit.
InterProiIPR002110. Ankyrin_rpt.
IPR020683. Ankyrin_rpt-contain_dom.
IPR011029. DEATH-like_dom.
IPR000488. Death_domain.
IPR013783. Ig-like_fold.
IPR014756. Ig_E-set.
IPR002909. IPT.
IPR000451. NFkB/Dor.
IPR030497. NFkB_p100.
IPR008967. p53-like_TF_DNA-bd.
IPR030492. RHD_CS.
IPR032397. RHD_dimer.
IPR011539. RHD_DNA_bind_dom.
[Graphical view]
PANTHERiPTHR24169. PTHR24169. 2 hits.
PTHR24169:SF21. PTHR24169:SF21. 2 hits.
PfamiPF12796. Ank_2. 2 hits.
PF00531. Death. 1 hit.
PF16179. RHD_dimer. 1 hit.
PF00554. RHD_DNA_bind. 1 hit.
[Graphical view]
PRINTSiPR00057. NFKBTNSCPFCT.
SMARTiSM00248. ANK. 6 hits.
SM00005. DEATH. 1 hit.
SM00429. IPT. 1 hit.
[Graphical view]
SUPFAMiSSF47986. SSF47986. 1 hit.
SSF48403. SSF48403. 1 hit.
SSF49417. SSF49417. 1 hit.
SSF81296. SSF81296. 1 hit.
PROSITEiPS50297. ANK_REP_REGION. 1 hit.
PS50088. ANK_REPEAT. 5 hits.
PS01204. REL_1. 1 hit.
PS50254. REL_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

O73630-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MMSVLKIENF DPYSCNGIED RNGMGYSTAL LNPIVLGQDL LMSYLSIIEQ
60 70 80 90 100
PKQRGFRFRY VCEGPSHRGL PGASSEKGKK TFPTVKIFNY VGMARIEVDL
110 120 130 140 150
VTHTDPPRVH AHSLVGKHSN KTGNCIVTVG PEDMTAQFNN LGIVHVTKKS
160 170 180 190 200
QTEILKEKMK RNILRNTGRN TLTEVEERKI EQEVKDLKKV TDLSIVRLKF
210 220 230 240 250
TAYLPDSNGA YTLALPPVIS DPIHDSKSPG ASNLRISRMD KTAGSVKGGD
260 270 280 290 300
EVYLLCDKVQ KDDIEVQFYE DDENGWHAFG DFAPTDVHKQ YAIVFRTPPY
310 320 330 340 350
HTQKIDRPVT VFLQLKRKKG GDVSDSKQFT YYPLEQDKEE VERKRRKDLP
360 370 380 390 400
TFNNHFYGGG SPMGGAPPGS SFGQGGGSNI NYQYTGMNSA FYMSSPAGGG
410 420 430 440 450
YHSSGHMMKH CSATNSSEKN QQPSISIKKE GEEASACSQT DSATTAQKEA
460 470 480 490 500
QCQMIMRQAN LRMLSLTQRT SRALLDYATT ADPRMLLAVQ RHLTATQDEN
510 520 530 540 550
GDTPLHLAVI HGQSSVIEQL VQIILSIPNQ QILNMSNHLQ QTPLHLGVIT
560 570 580 590 600
KQYSVVAFLL KAGADPTILD RYGNSVLHLA VQSEDDKMLG VLLKYPSVGQ
610 620 630 640 650
KNLINMPDYH GLSPVHWSVK MKNEKCLVLL VKAGANVNSA ERKSGKSPLH
660 670 680 690 700
IAVEMDNLNL AVFLVKKLHA DINAKTYGGN TPLHLAASRG SPMLTRMLVN
710 720 730 740 750
EGANVLSEND EPVNKLPSCN SDTSESDSDV QMDTDSDHHG DSDTDSSTAV
760 770 780 790 800
DSECEHSAEE MHRREQRNIR PHCAMKRRYS GHTAVDLTKS QKVRDILSKH
810 820 830 840 850
TPGSASWKQK GPEPVNVLAL ETNTVQRLEK LLNEGQTGAD WTELASRLRL
860 870 880 890 900
QSLVETYKNT SSPTESLLRN YELAGGNLKE LINTLQSMGL NEGVELLCKS
910 920 930 940 950
ETYAKHHSPA ESKNDSAYES QSMEVDQSSG NLMDDSQKQT IPVSAAELCP

TTEPTIGQ
Length:958
Mass (Da):105,854
Last modified:August 1, 1998 - v1
Checksum:i192F5EDA791DCBC5
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB002629 mRNA. Translation: BAA25919.1.
RefSeqiNP_001081181.1. NM_001087712.1.
UniGeneiXl.815.

Genome annotation databases

GeneIDi397698.
KEGGixla:397698.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB002629 mRNA. Translation: BAA25919.1.
RefSeqiNP_001081181.1. NM_001087712.1.
UniGeneiXl.815.

3D structure databases

ProteinModelPortaliO73630.
SMRiO73630. Positions 44-333.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi99038. 1 interaction.
IntActiO73630. 1 interaction.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi397698.
KEGGixla:397698.

Organism-specific databases

CTDi4791.
XenbaseiXB-GENE-970090. nfkb2.

Phylogenomic databases

HOVERGENiHBG052613.
KOiK04469.

Family and domain databases

Gene3Di1.10.533.10. 1 hit.
1.25.40.20. 1 hit.
2.60.40.10. 1 hit.
2.60.40.340. 1 hit.
InterProiIPR002110. Ankyrin_rpt.
IPR020683. Ankyrin_rpt-contain_dom.
IPR011029. DEATH-like_dom.
IPR000488. Death_domain.
IPR013783. Ig-like_fold.
IPR014756. Ig_E-set.
IPR002909. IPT.
IPR000451. NFkB/Dor.
IPR030497. NFkB_p100.
IPR008967. p53-like_TF_DNA-bd.
IPR030492. RHD_CS.
IPR032397. RHD_dimer.
IPR011539. RHD_DNA_bind_dom.
[Graphical view]
PANTHERiPTHR24169. PTHR24169. 2 hits.
PTHR24169:SF21. PTHR24169:SF21. 2 hits.
PfamiPF12796. Ank_2. 2 hits.
PF00531. Death. 1 hit.
PF16179. RHD_dimer. 1 hit.
PF00554. RHD_DNA_bind. 1 hit.
[Graphical view]
PRINTSiPR00057. NFKBTNSCPFCT.
SMARTiSM00248. ANK. 6 hits.
SM00005. DEATH. 1 hit.
SM00429. IPT. 1 hit.
[Graphical view]
SUPFAMiSSF47986. SSF47986. 1 hit.
SSF48403. SSF48403. 1 hit.
SSF49417. SSF49417. 1 hit.
SSF81296. SSF81296. 1 hit.
PROSITEiPS50297. ANK_REP_REGION. 1 hit.
PS50088. ANK_REPEAT. 5 hits.
PS01204. REL_1. 1 hit.
PS50254. REL_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiNFKB2_XENLA
AccessioniPrimary (citable) accession number: O73630
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 10, 2004
Last sequence update: August 1, 1998
Last modified: May 11, 2016
This is version 98 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

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.