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GLYR1_MOUSE
ID   GLYR1_MOUSE             Reviewed;         546 AA.
AC   Q922P9; Q3TX02; Q9CYQ1;
DT   04-DEC-2007, integrated into UniProtKB/Swiss-Prot.
DT   01-DEC-2001, sequence version 1.
DT   03-AUG-2022, entry version 153.
DE   RecName: Full=Cytokine-like nuclear factor N-PAC;
DE            Short=NPAC;
DE   AltName: Full=Glyoxylate reductase 1 homolog;
DE   AltName: Full=Nuclear protein NP60;
DE   AltName: Full=Putative oxidoreductase GLYR1;
GN   Name=Glyr1 {ECO:0000312|MGI:MGI:1921272}; Synonyms=Np60;
OS   Mus musculus (Mouse).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC   Murinae; Mus; Mus.
OX   NCBI_TaxID=10090;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   STRAIN=C57BL/6J; TISSUE=Bone marrow, and Embryo;
RX   PubMed=16141072; DOI=10.1126/science.1112014;
RA   Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N.,
RA   Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K.,
RA   Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.,
RA   Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R.,
RA   Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T.,
RA   Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A.,
RA   Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B.,
RA   Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M.,
RA   Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S.,
RA   Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E.,
RA   Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D.,
RA   Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M.,
RA   Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H.,
RA   Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V.,
RA   Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S.,
RA   Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H.,
RA   Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N.,
RA   Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F.,
RA   Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G.,
RA   Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z.,
RA   Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C.,
RA   Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y.,
RA   Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S.,
RA   Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K.,
RA   Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R.,
RA   van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H.,
RA   Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M.,
RA   Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C.,
RA   Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S.,
RA   Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K.,
RA   Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M.,
RA   Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C.,
RA   Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A.,
RA   Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.;
RT   "The transcriptional landscape of the mammalian genome.";
RL   Science 309:1559-1563(2005).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   STRAIN=FVB/N; TISSUE=Mammary tumor;
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   [3]
RP   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC   TISSUE=Brain;
RX   PubMed=16452087; DOI=10.1074/mcp.t500041-mcp200;
RA   Trinidad J.C., Specht C.G., Thalhammer A., Schoepfer R., Burlingame A.L.;
RT   "Comprehensive identification of phosphorylation sites in postsynaptic
RT   density preparations.";
RL   Mol. Cell. Proteomics 5:914-922(2006).
RN   [4]
RP   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC   TISSUE=Liver;
RX   PubMed=21183079; DOI=10.1016/j.cell.2010.12.001;
RA   Huttlin E.L., Jedrychowski M.P., Elias J.E., Goswami T., Rad R.,
RA   Beausoleil S.A., Villen J., Haas W., Sowa M.E., Gygi S.P.;
RT   "A tissue-specific atlas of mouse protein phosphorylation and expression.";
RL   Cell 143:1174-1189(2010).
RN   [5]
RP   FUNCTION.
RX   PubMed=29759984; DOI=10.1101/gad.313973.118;
RA   Fei J., Ishii H., Hoeksema M.A., Meitinger F., Kassavetis G.A., Glass C.K.,
RA   Ren B., Kadonaga J.T.;
RT   "NDF, a nucleosome-destabilizing factor that facilitates transcription
RT   through nucleosomes.";
RL   Genes Dev. 32:682-694(2018).
RN   [6]
RP   FUNCTION, AND MUTAGENESIS OF PRO-489.
RX   PubMed=35182466; DOI=10.1016/j.cell.2022.01.021;
RA   Gonzalez-Teran B., Pittman M., Felix F., Thomas R., Richmond-Buccola D.,
RA   Huettenhain R., Choudhary K., Moroni E., Costa M.W., Huang Y.,
RA   Padmanabhan A., Alexanian M., Lee C.Y., Maven B.E.J., Samse-Knapp K.,
RA   Morton S.U., McGregor M., Gifford C.A., Seidman J.G., Seidman C.E.,
RA   Gelb B.D., Colombo G., Conklin B.R., Black B.L., Bruneau B.G., Krogan N.J.,
RA   Pollard K.S., Srivastava D.;
RT   "Transcription factor protein interactomes reveal genetic determinants in
RT   heart disease.";
RL   Cell 0:0-0(2022).
CC   -!- FUNCTION: Cytokine-like nuclear factor with chromatin gene reader
CC       activity involved in chromatin modification and regulation of gene
CC       expression (PubMed:29759984). Acts as a nucleosome-destabilizing factor
CC       that is recruited to genes during transcriptional activation.
CC       Recognizes and binds histone H3 without a preference for specific
CC       epigenetic markers and also binds DNA. Interacts with KDM1B and
CC       promotes its histone demethylase activity by facilitating the capture
CC       of H3 tails, they form a multifunctional enzyme complex that modifies
CC       transcribed chromatin and facilitates Pol II transcription through
CC       nucleosomes. Stimulates the acetylation of 'Lys-56' of nucleosomal
CC       histone H3 (H3K56ac) by EP300 (By similarity). With GATA4, co-binds a
CC       defined set of heart development genes and coregulates their expression
CC       during cardiomyocyte differentiation (PubMed:35182466). Regulates p38
CC       MAP kinase activity by mediating stress activation of MAPK14/p38alpha
CC       and specifically regulating MAPK14 signaling. Indirectly promotes
CC       phosphorylation of MAPK14 and activation of ATF2. The phosphorylation
CC       of MAPK14 requires upstream activity of MAP2K4 and MAP2K6 (By
CC       similarity). {ECO:0000250|UniProtKB:Q49A26,
CC       ECO:0000269|PubMed:29759984, ECO:0000269|PubMed:35182466}.
CC   -!- SUBUNIT: Homotetramere. Interacts with MAPK14. Interacts with KDM1B at
CC       nucleosomes; this interaction stimulates H3K4me1 and H3K4me2
CC       demethylation. Binds to mononucleosomes. Interacts with GATA4; the
CC       interaction is required for a synergistic activation of GATA4 target
CC       genes transcription. {ECO:0000250|UniProtKB:Q49A26}.
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:Q49A26}.
CC       Chromosome {ECO:0000250|UniProtKB:Q49A26}. Note=Found in actively
CC       RNAPolII-transcribed gene bodies. {ECO:0000250|UniProtKB:Q49A26}.
CC   -!- DOMAIN: The A.T hook DNA-binding domain is required for the interaction
CC       with MAPK14. {ECO:0000250|UniProtKB:Q49A26}.
CC   -!- DOMAIN: The PWWP domain is a H3 reader and strongly binds DNA.
CC       {ECO:0000250|UniProtKB:Q49A26}.
CC   -!- DOMAIN: In the dehydrogenase domain, the conserved NAD(P)H-binding
CC       sites and sequence similarity to plant dehydrogenases suggest that this
CC       protein may have oxidoreductase activity. However, since the active
CC       site is not conserved, the dehydrogenase domain seems to serve as a
CC       catalytically inert oligomerization module.
CC       {ECO:0000250|UniProtKB:Q49A26}.
CC   -!- SIMILARITY: Belongs to the HIBADH-related family. NP60 subfamily.
CC       {ECO:0000305}.
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DR   EMBL; AK014456; BAB29363.1; -; mRNA.
DR   EMBL; AK150349; BAE29486.1; -; mRNA.
DR   EMBL; AK152887; BAE31570.1; -; mRNA.
DR   EMBL; AK159476; BAE35114.1; -; mRNA.
DR   EMBL; BC006893; AAH06893.1; -; mRNA.
DR   CCDS; CCDS27930.1; -.
DR   RefSeq; NP_082996.2; NM_028720.2.
DR   AlphaFoldDB; Q922P9; -.
DR   SMR; Q922P9; -.
DR   BioGRID; 216431; 7.
DR   IntAct; Q922P9; 3.
DR   MINT; Q922P9; -.
DR   STRING; 10090.ENSMUSP00000111510; -.
DR   iPTMnet; Q922P9; -.
DR   PhosphoSitePlus; Q922P9; -.
DR   EPD; Q922P9; -.
DR   MaxQB; Q922P9; -.
DR   PaxDb; Q922P9; -.
DR   PeptideAtlas; Q922P9; -.
DR   PRIDE; Q922P9; -.
DR   ProteomicsDB; 263378; -.
DR   Antibodypedia; 24437; 112 antibodies from 21 providers.
DR   Ensembl; ENSMUST00000023189; ENSMUSP00000023189; ENSMUSG00000022536.
DR   GeneID; 74022; -.
DR   KEGG; mmu:74022; -.
DR   UCSC; uc007ybm.1; mouse.
DR   CTD; 84656; -.
DR   MGI; MGI:1921272; Glyr1.
DR   VEuPathDB; HostDB:ENSMUSG00000022536; -.
DR   eggNOG; KOG0409; Eukaryota.
DR   eggNOG; KOG1904; Eukaryota.
DR   GeneTree; ENSGT00940000156435; -.
DR   InParanoid; Q922P9; -.
DR   BioGRID-ORCS; 74022; 9 hits in 75 CRISPR screens.
DR   ChiTaRS; Glyr1; mouse.
DR   PRO; PR:Q922P9; -.
DR   Proteomes; UP000000589; Chromosome 16.
DR   RNAct; Q922P9; protein.
DR   Bgee; ENSMUSG00000022536; Expressed in ear vesicle and 255 other tissues.
DR   ExpressionAtlas; Q922P9; baseline and differential.
DR   Genevisible; Q922P9; MM.
DR   GO; GO:0005829; C:cytosol; ISO:MGI.
DR   GO; GO:0005654; C:nucleoplasm; ISO:MGI.
DR   GO; GO:0000786; C:nucleosome; ISS:UniProtKB.
DR   GO; GO:0003682; F:chromatin binding; IDA:UniProtKB.
DR   GO; GO:0003677; F:DNA binding; IDA:UniProtKB.
DR   GO; GO:0042393; F:histone binding; ISS:UniProtKB.
DR   GO; GO:0035064; F:methylated histone binding; ISS:UniProtKB.
DR   GO; GO:0051287; F:NAD binding; IEA:InterPro.
DR   GO; GO:0050661; F:NADP binding; IEA:InterPro.
DR   GO; GO:0031491; F:nucleosome binding; ISO:MGI.
DR   GO; GO:0016491; F:oxidoreductase activity; IEA:UniProtKB-KW.
DR   GO; GO:0035066; P:positive regulation of histone acetylation; ISO:MGI.
DR   GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; ISO:MGI.
DR   CDD; cd05836; N_Pac_NP60; 1.
DR   Gene3D; 1.10.1040.10; -; 1.
DR   InterPro; IPR008927; 6-PGluconate_DH-like_C_sf.
DR   InterPro; IPR013328; 6PGD_dom2.
DR   InterPro; IPR006115; 6PGDH_NADP-bd.
DR   InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR   InterPro; IPR029154; NADP-bd.
DR   InterPro; IPR035501; NP60_PWWP.
DR   InterPro; IPR000313; PWWP_dom.
DR   Pfam; PF14833; NAD_binding_11; 1.
DR   Pfam; PF03446; NAD_binding_2; 1.
DR   Pfam; PF00855; PWWP; 1.
DR   SMART; SM00293; PWWP; 1.
DR   SUPFAM; SSF48179; SSF48179; 1.
DR   SUPFAM; SSF51735; SSF51735; 1.
DR   PROSITE; PS50812; PWWP; 1.
PE   1: Evidence at protein level;
KW   Chromosome; DNA-binding; Isopeptide bond; Nucleus; Phosphoprotein;
KW   Reference proteome; Ubl conjugation.
FT   CHAIN           1..546
FT                   /note="Cytokine-like nuclear factor N-PAC"
FT                   /id="PRO_0000312122"
FT   DOMAIN          8..66
FT                   /note="PWWP"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00162"
FT   DNA_BIND        167..179
FT                   /note="A.T hook"
FT                   /evidence="ECO:0000305"
FT   REGION          91..187
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          213..216
FT                   /note="Interaction with histone H3"
FT                   /evidence="ECO:0000250|UniProtKB:Q49A26"
FT   REGION          215..224
FT                   /note="Interaction with KDM1B"
FT                   /evidence="ECO:0000250|UniProtKB:Q49A26"
FT   REGION          260..546
FT                   /note="Dehydrogenase domain"
FT                   /evidence="ECO:0000250|UniProtKB:Q49A26"
FT   COMPBIAS        91..183
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   BINDING         270..284
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000250|UniProtKB:Q49A26"
FT   BINDING         355
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000250|UniProtKB:Q49A26"
FT   BINDING         498
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000250|UniProtKB:Q49A26"
FT   SITE            216
FT                   /note="Required to promote KDM1B demethylase activity
FT                   toward histone H3K4me1 and H3K4me2"
FT                   /evidence="ECO:0000250|UniProtKB:Q49A26"
FT   MOD_RES         130
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0000250|UniProtKB:Q49A26"
FT   MOD_RES         166
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0000250|UniProtKB:Q49A26"
FT   MOD_RES         533
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0000250|UniProtKB:Q49A26"
FT   CROSSLNK        135
FT                   /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT                   G-Cter in SUMO2)"
FT                   /evidence="ECO:0000250|UniProtKB:Q49A26"
FT   CROSSLNK        175
FT                   /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT                   G-Cter in SUMO2)"
FT                   /evidence="ECO:0000250|UniProtKB:Q49A26"
FT   CROSSLNK        178
FT                   /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT                   G-Cter in SUMO2)"
FT                   /evidence="ECO:0000250|UniProtKB:Q49A26"
FT   CROSSLNK        200
FT                   /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT                   G-Cter in SUMO2)"
FT                   /evidence="ECO:0000250|UniProtKB:Q49A26"
FT   CROSSLNK        210
FT                   /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT                   G-Cter in SUMO2)"
FT                   /evidence="ECO:0000250|UniProtKB:Q49A26"
FT   CROSSLNK        226
FT                   /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT                   G-Cter in SUMO2)"
FT                   /evidence="ECO:0000250|UniProtKB:Q49A26"
FT   CROSSLNK        236
FT                   /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT                   G-Cter in SUMO2)"
FT                   /evidence="ECO:0000250|UniProtKB:Q49A26"
FT   CROSSLNK        239
FT                   /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT                   G-Cter in SUMO2)"
FT                   /evidence="ECO:0000250|UniProtKB:Q49A26"
FT   CROSSLNK        268
FT                   /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT                   G-Cter in SUMO2)"
FT                   /evidence="ECO:0000250|UniProtKB:Q49A26"
FT   CROSSLNK        301
FT                   /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT                   G-Cter in SUMO2)"
FT                   /evidence="ECO:0000250|UniProtKB:Q49A26"
FT   MUTAGEN         489
FT                   /note="P->L: Mutant animals are born at expected Mendelian
FT                   ratios. 54% mutants display postnatal lethality between
FT                   days 0 and 1. They show centricular septal defects."
FT                   /evidence="ECO:0000269|PubMed:35182466"
FT   CONFLICT        50..51
FT                   /note="ED -> KN (in Ref. 1; BAB29363)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        109..110
FT                   /note="NR -> DW (in Ref. 1; BAB29363)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        296
FT                   /note="N -> S (in Ref. 1; BAE35114)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        535
FT                   /note="N -> S (in Ref. 1; BAE35114)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   546 AA;  59716 MW;  F5D2090DE1F64723 CRC64;
     MAAVSLRLGD LVWGKLGRYP PWPGKIVNPP KDLKKPRGKK CFFVKFFGTE DHAWIKVEQL
     KPYHAHKEEM IKINKGKRFQ QAVDAVEEFL RRAKGKDQTS SHTSADDKNR RNSSEERSRP
     NSGDEKRKLS LSEGKVKKNM GEGKKRVTSG SADRGSKCLK RAQEQSPRKR GRPPKDEKDL
     TIPESSTVKG MMAGPMAAFK WQPTATEPVK DADPHFHHFL LSQTEKPAVC YQAITKKLKI
     CEEETGSTSI QAADSTAVNG SITPTDKKIG FLGLGLMGSG IVSNLLKMGH TVTVWNRTAE
     KEGARLGRTP AEVVSTCDIT FACVSDPKAA KDLVLGPSGV LQGIRPGKCY VDMSTVDADT
     VTELAQVIVS RGGRFLEAPV SGNQQLSNDG MLVILAAGDR GLYEDCSSCF QAMGKTSFFL
     GEVGNAAKMM LIVNMVQGSF MATIAEGLTL AQVTGQSQQT LLDILNQGQL ASIFLDQKCQ
     NILQGNFKPD FYLKYIQKDL RLAIALGDAV NHPTPMAAAA NEVYKRAKAL DQSDNDMSAV
     YRAYIH
 
 
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