RFXAP_HUMAN
ID RFXAP_HUMAN Reviewed; 272 AA.
AC O00287; B2R9T8; Q5VZM6; Q8TC40;
DT 15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
DT 01-JUL-1997, sequence version 1.
DT 03-AUG-2022, entry version 158.
DE RecName: Full=Regulatory factor X-associated protein;
DE Short=RFX-associated protein;
DE AltName: Full=RFX DNA-binding complex 36 kDa subunit;
GN Name=RFXAP;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE, AND
RP INVOLVEMENT IN BLS2.
RX PubMed=9118943; DOI=10.1093/emboj/16.5.1045;
RA Durand B., Sperisen P., Emery P., Barras E., Zufferey M., Mach B.,
RA Reith W.;
RT "RFXAP, a novel subunit of the RFX DNA binding complex is mutated in MHC
RT class II deficiency.";
RL EMBO J. 16:1045-1055(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Thalamus;
RX PubMed=14702039; DOI=10.1038/ng1285;
RA Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
RA Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
RA Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
RA Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
RA Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H.,
RA Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M.,
RA Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K.,
RA Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T.,
RA Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M.,
RA Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S.,
RA Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H.,
RA Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K.,
RA Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N.,
RA Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
RA Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
RA Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
RA Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
RA Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y.,
RA Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K.,
RA Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T.,
RA Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T.,
RA Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y.,
RA Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H.,
RA Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y.,
RA Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H.,
RA Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O.,
RA Isogai T., Sugano S.;
RT "Complete sequencing and characterization of 21,243 full-length human
RT cDNAs.";
RL Nat. Genet. 36:40-45(2004).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=15057823; DOI=10.1038/nature02379;
RA Dunham A., Matthews L.H., Burton J., Ashurst J.L., Howe K.L.,
RA Ashcroft K.J., Beare D.M., Burford D.C., Hunt S.E., Griffiths-Jones S.,
RA Jones M.C., Keenan S.J., Oliver K., Scott C.E., Ainscough R., Almeida J.P.,
RA Ambrose K.D., Andrews D.T., Ashwell R.I.S., Babbage A.K., Bagguley C.L.,
RA Bailey J., Bannerjee R., Barlow K.F., Bates K., Beasley H., Bird C.P.,
RA Bray-Allen S., Brown A.J., Brown J.Y., Burrill W., Carder C., Carter N.P.,
RA Chapman J.C., Clamp M.E., Clark S.Y., Clarke G., Clee C.M., Clegg S.C.,
RA Cobley V., Collins J.E., Corby N., Coville G.J., Deloukas P., Dhami P.,
RA Dunham I., Dunn M., Earthrowl M.E., Ellington A.G., Faulkner L.,
RA Frankish A.G., Frankland J., French L., Garner P., Garnett J.,
RA Gilbert J.G.R., Gilson C.J., Ghori J., Grafham D.V., Gribble S.M.,
RA Griffiths C., Hall R.E., Hammond S., Harley J.L., Hart E.A., Heath P.D.,
RA Howden P.J., Huckle E.J., Hunt P.J., Hunt A.R., Johnson C., Johnson D.,
RA Kay M., Kimberley A.M., King A., Laird G.K., Langford C.J., Lawlor S.,
RA Leongamornlert D.A., Lloyd D.M., Lloyd C., Loveland J.E., Lovell J.,
RA Martin S., Mashreghi-Mohammadi M., McLaren S.J., McMurray A., Milne S.,
RA Moore M.J.F., Nickerson T., Palmer S.A., Pearce A.V., Peck A.I., Pelan S.,
RA Phillimore B., Porter K.M., Rice C.M., Searle S., Sehra H.K., Shownkeen R.,
RA Skuce C.D., Smith M., Steward C.A., Sycamore N., Tester J., Thomas D.W.,
RA Tracey A., Tromans A., Tubby B., Wall M., Wallis J.M., West A.P.,
RA Whitehead S.L., Willey D.L., Wilming L., Wray P.W., Wright M.W., Young L.,
RA Coulson A., Durbin R.M., Hubbard T., Sulston J.E., Beck S., Bentley D.R.,
RA Rogers J., Ross M.T.;
RT "The DNA sequence and analysis of human chromosome 13.";
RL Nature 428:522-528(2004).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M.,
RA Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J.,
RA Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S.,
RA Turner R., Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H.,
RA Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K.,
RA Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D.,
RA Hunkapiller M.W., Myers E.W., Venter J.C.;
RL Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Testis;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [6]
RP PARTIAL PROTEIN SEQUENCE, IDENTIFICATION BY MASS SPECTROMETRY, AND
RP INVOLVEMENT IN BLS2.
RC TISSUE=Lymphoblast;
RX PubMed=10072068; DOI=10.1016/s1074-7613(00)80016-3;
RA Nagarajan U.M., Louis-Plence P., DeSandro A., Nilsen R., Bushey A.,
RA Boss J.M.;
RT "RFX-B is the gene responsible for the most common cause of the bare
RT lymphocyte syndrome, an MHC class II immunodeficiency.";
RL Immunity 10:153-162(1999).
RN [7]
RP ERRATUM OF PUBMED:10072068.
RA Nagarajan U.M., Louis-Plence P., DeSandro A., Nilsen R., Bushey A.,
RA Boss J.M.;
RL Immunity 10:399-399(1999).
RN [8]
RP SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-198, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=28112733; DOI=10.1038/nsmb.3366;
RA Hendriks I.A., Lyon D., Young C., Jensen L.J., Vertegaal A.C.,
RA Nielsen M.L.;
RT "Site-specific mapping of the human SUMO proteome reveals co-modification
RT with phosphorylation.";
RL Nat. Struct. Mol. Biol. 24:325-336(2017).
RN [9]
RP STRUCTURE BY NMR OF 214-272, SUBUNIT, AND DOMAIN C-TERMINAL.
RX PubMed=20732328; DOI=10.1016/j.jmb.2010.08.025;
RA Laird K.M., Briggs L.L., Boss J.M., Summers M.F., Garvie C.W.;
RT "Solution structure of the heterotrimeric complex between the interaction
RT domains of RFX5 and RFXAP from the RFX gene regulatory complex.";
RL J. Mol. Biol. 403:40-51(2010).
CC -!- FUNCTION: Part of the RFX complex that binds to the X-box of MHC II
CC promoters.
CC -!- SUBUNIT: The RFX heterotetrameric complex consists of 2 molecules of
CC RFX5 and one each of RFXAP and RFX-B/RFXANK; with each subunit
CC representing a separate complementation group. RFX forms cooperative
CC DNA binding complexes with X2BP and CBF/NF-Y. RFX associates with CIITA
CC to form an active transcriptional complex.
CC {ECO:0000269|PubMed:20732328}.
CC -!- INTERACTION:
CC O00287; P48382: RFX5; NbExp=11; IntAct=EBI-3929296, EBI-923266;
CC O00287; O14593: RFXANK; NbExp=3; IntAct=EBI-3929296, EBI-1057665;
CC -!- SUBCELLULAR LOCATION: Nucleus.
CC -!- TISSUE SPECIFICITY: Ubiquitous.
CC -!- DOMAIN: The C-terminal domain is necessary for the RFX complex
CC formation. {ECO:0000269|PubMed:20732328}.
CC -!- PTM: Phosphorylated.
CC -!- DISEASE: Bare lymphocyte syndrome 2 (BLS2) [MIM:209920]: A severe
CC combined immunodeficiency disease with early onset. It is characterized
CC by a profound defect in constitutive and interferon-gamma induced MHC
CC II expression, absence of cellular and humoral T-cell response to
CC antigen challenge, hypogammaglobulinemia and impaired antibody
CC production. The consequence include extreme susceptibility to viral,
CC bacterial and fungal infections. {ECO:0000269|PubMed:10072068,
CC ECO:0000269|PubMed:9118943}. Note=The disease is caused by variants
CC affecting the gene represented in this entry.
CC -!- WEB RESOURCE: Name=RFXAPbase; Note=RFXAP mutation db;
CC URL="http://structure.bmc.lu.se/idbase/RFXAPbase/";
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DR EMBL; Y12812; CAA73338.1; -; Genomic_DNA.
DR EMBL; AK313912; BAG36635.1; -; mRNA.
DR EMBL; AL159973; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CH471075; EAX08575.1; -; Genomic_DNA.
DR EMBL; BC026088; AAH26088.1; -; mRNA.
DR CCDS; CCDS9359.1; -.
DR RefSeq; NP_000529.1; NM_000538.3.
DR PDB; 2KW3; NMR; -; C=214-272.
DR PDBsum; 2KW3; -.
DR AlphaFoldDB; O00287; -.
DR SMR; O00287; -.
DR BioGRID; 111926; 22.
DR ComplexPortal; CPX-6461; RFX gene regulatory complex.
DR CORUM; O00287; -.
DR IntAct; O00287; 14.
DR STRING; 9606.ENSP00000255476; -.
DR iPTMnet; O00287; -.
DR PhosphoSitePlus; O00287; -.
DR BioMuta; RFXAP; -.
DR EPD; O00287; -.
DR jPOST; O00287; -.
DR MassIVE; O00287; -.
DR MaxQB; O00287; -.
DR PaxDb; O00287; -.
DR PeptideAtlas; O00287; -.
DR PRIDE; O00287; -.
DR ProteomicsDB; 47822; -.
DR Antibodypedia; 8059; 184 antibodies from 25 providers.
DR DNASU; 5994; -.
DR Ensembl; ENST00000255476.3; ENSP00000255476.3; ENSG00000133111.4.
DR GeneID; 5994; -.
DR KEGG; hsa:5994; -.
DR MANE-Select; ENST00000255476.3; ENSP00000255476.3; NM_000538.4; NP_000529.1.
DR UCSC; uc001uvu.2; human.
DR CTD; 5994; -.
DR DisGeNET; 5994; -.
DR GeneCards; RFXAP; -.
DR HGNC; HGNC:9988; RFXAP.
DR HPA; ENSG00000133111; Low tissue specificity.
DR MalaCards; RFXAP; -.
DR MIM; 209920; phenotype.
DR MIM; 601861; gene.
DR neXtProt; NX_O00287; -.
DR OpenTargets; ENSG00000133111; -.
DR Orphanet; 572; Immunodeficiency by defective expression of MHC class II.
DR PharmGKB; PA34358; -.
DR VEuPathDB; HostDB:ENSG00000133111; -.
DR eggNOG; ENOG502S2J4; Eukaryota.
DR GeneTree; ENSGT00390000006573; -.
DR HOGENOM; CLU_084944_0_0_1; -.
DR InParanoid; O00287; -.
DR OMA; HPCGGQD; -.
DR OrthoDB; 1504851at2759; -.
DR PhylomeDB; O00287; -.
DR TreeFam; TF332759; -.
DR PathwayCommons; O00287; -.
DR SignaLink; O00287; -.
DR SIGNOR; O00287; -.
DR BioGRID-ORCS; 5994; 23 hits in 1075 CRISPR screens.
DR ChiTaRS; RFXAP; human.
DR EvolutionaryTrace; O00287; -.
DR GeneWiki; RFXAP; -.
DR GenomeRNAi; 5994; -.
DR Pharos; O00287; Tbio.
DR PRO; PR:O00287; -.
DR Proteomes; UP000005640; Chromosome 13.
DR RNAct; O00287; protein.
DR Bgee; ENSG00000133111; Expressed in tendon of biceps brachii and 152 other tissues.
DR Genevisible; O00287; HS.
DR GO; GO:0016607; C:nuclear speck; IDA:HPA.
DR GO; GO:0005634; C:nucleus; IDA:ComplexPortal.
DR GO; GO:0090575; C:RNA polymerase II transcription regulator complex; IPI:GO_Central.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0045348; P:positive regulation of MHC class II biosynthetic process; IC:ComplexPortal.
DR GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; IDA:GO_Central.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR Gene3D; 6.10.290.30; -; 1.
DR IDEAL; IID00425; -.
DR InterPro; IPR038308; RFXAP_C_sf.
DR InterPro; IPR029316; RFXAP_RFXANK-bd.
DR PANTHER; PTHR15110; PTHR15110; 1.
DR Pfam; PF15289; RFXA_RFXANK_bdg; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; DNA-binding; Isopeptide bond;
KW Nucleus; Phosphoprotein; Reference proteome; SCID; Ubl conjugation.
FT CHAIN 1..272
FT /note="Regulatory factor X-associated protein"
FT /id="PRO_0000097310"
FT REGION 1..20
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 74..142
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 175..195
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 214..270
FT /note="C-terminal domain"
FT MOTIF 163..178
FT /note="Nuclear localization signal"
FT /evidence="ECO:0000255"
FT COMPBIAS 80..94
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CROSSLNK 198
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0007744|PubMed:28112733"
FT CONFLICT 5
FT /note="G -> S (in Ref. 5; AAH26088)"
FT /evidence="ECO:0000305"
FT HELIX 226..237
FT /evidence="ECO:0007829|PDB:2KW3"
FT HELIX 242..258
FT /evidence="ECO:0007829|PDB:2KW3"
SQ SEQUENCE 272 AA; 28232 MW; A6757F5F03D5F905 CRC64;
MEAQGVAEGA GPGAASGVPH PAALAPAAAP TLAPASVAAA ASQFTLLVMQ PCAGQDEAAA
PGGSVGAGKP VRYLCEGAGD GEEEAGEDEA DLLDTSDPPG GGESAASLED LEDEETHSGG
EGSSGGARRR GSGGGSMSKT CTYEGCSETT SQVAKQRKPW MCKKHRNKMY KDKYKKKKSD
QALNCGGTAS TGSAGNVKLE ESADNILSIV KQRTGSFGDR PARPTLLEQV LNQKRLSLLR
SPEVVQFLQK QQQLLNQQVL EQRQQQFPGT SM
