GLYR1_RAT
ID GLYR1_RAT Reviewed; 552 AA.
AC Q5RKH0;
DT 04-DEC-2007, integrated into UniProtKB/Swiss-Prot.
DT 21-DEC-2004, sequence version 1.
DT 03-AUG-2022, entry version 142.
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|RGD:1309459}; Synonyms=Np60;
OS Rattus norvegicus (Rat).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Rattus.
OX NCBI_TaxID=10116;
RN [1]
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 [2]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-130, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22673903; DOI=10.1038/ncomms1871;
RA Lundby A., Secher A., Lage K., Nordsborg N.B., Dmytriyev A., Lundby C.,
RA Olsen J.V.;
RT "Quantitative maps of protein phosphorylation sites across 14 different rat
RT organs and tissues.";
RL Nat. Commun. 3:876-876(2012).
CC -!- FUNCTION: Cytokine-like nuclear factor with chromatin gene reader
CC activity involved in chromatin modification and regulation of gene
CC expression. Acts as a nucleosome-destabilizing factor that is recruited
CC to genes during transcriptional activation. Recognizes and binds
CC histone H3 without a preference for specific epigenetic markers and
CC also binds DNA. Interacts with KDM1B and promotes its histone
CC demethylase activity by facilitating the capture of H3 tails, they form
CC a multifunctional enzyme complex that modifies transcribed chromatin
CC and facilitates Pol II transcription through nucleosomes. Stimulates
CC the acetylation of 'Lys-56' of nucleosomal histone H3 (H3K56ac) by
CC EP300. With GATA4, co-binds a defined set of heart development genes
CC and coregulates their expression during cardiomyocyte differentiation.
CC Regulates p38 MAP kinase activity by mediating stress activation of
CC MAPK14/p38alpha and specifically regulating MAPK14 signaling.
CC Indirectly promotes phosphorylation of MAPK14 and activation of ATF2.
CC The phosphorylation of MAPK14 requires upstream activity of MAP2K4 and
CC MAP2K6. {ECO:0000250|UniProtKB:Q49A26}.
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 PWWP domain probably mediates the binding to H3K36me3.
CC {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; BC085931; AAH85931.1; -; mRNA.
DR RefSeq; NP_001007801.1; NM_001007800.1.
DR AlphaFoldDB; Q5RKH0; -.
DR SMR; Q5RKH0; -.
DR BioGRID; 261964; 1.
DR IntAct; Q5RKH0; 12.
DR STRING; 10116.ENSRNOP00000004159; -.
DR iPTMnet; Q5RKH0; -.
DR PhosphoSitePlus; Q5RKH0; -.
DR jPOST; Q5RKH0; -.
DR PaxDb; Q5RKH0; -.
DR PRIDE; Q5RKH0; -.
DR GeneID; 360477; -.
DR KEGG; rno:360477; -.
DR UCSC; RGD:1309459; rat.
DR CTD; 84656; -.
DR RGD; 1309459; Glyr1.
DR VEuPathDB; HostDB:ENSRNOG00000003065; -.
DR eggNOG; KOG0409; Eukaryota.
DR eggNOG; KOG1904; Eukaryota.
DR HOGENOM; CLU_018075_0_0_1; -.
DR InParanoid; Q5RKH0; -.
DR OMA; DNIMSKN; -.
DR OrthoDB; 885724at2759; -.
DR PhylomeDB; Q5RKH0; -.
DR TreeFam; TF324195; -.
DR PRO; PR:Q5RKH0; -.
DR Proteomes; UP000002494; Chromosome 10.
DR Bgee; ENSRNOG00000003065; Expressed in adult mammalian kidney and 19 other tissues.
DR Genevisible; Q5RKH0; RN.
DR GO; GO:0000786; C:nucleosome; ISS:UniProtKB.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0003682; F:chromatin binding; ISO:RGD.
DR GO; GO:0003677; F:DNA binding; ISO:RGD.
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:RGD.
DR GO; GO:0016491; F:oxidoreductase activity; IEA:UniProtKB-KW.
DR GO; GO:0035066; P:positive regulation of histone acetylation; ISO:RGD.
DR GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; ISO:RGD.
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..552
FT /note="Cytokine-like nuclear factor N-PAC"
FT /id="PRO_0000312123"
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..552
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 361
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000250|UniProtKB:Q49A26"
FT BINDING 504
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:0007744|PubMed:22673903"
FT MOD_RES 166
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q49A26"
FT MOD_RES 539
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"
SQ SEQUENCE 552 AA; 60421 MW; 5970FC59C54895FA CRC64;
MAAVSLRLGD LVWGKLGRYP PWPGKIVNPP KDLKKPRGKK CFFVKFFGTE DHAWIKVEQL
KPYHAHKEEM IKINKGKRFQ QAVDAVEEFL RRAKGKDQTS SHTSADDKNR RNSSEERSRP
NSGDEKRKLS LSEGKVKKNM GEGKKRVTSG SADRGSKCLK RAQEQSPRKR GRPPKDEKDL
TIPESSTVKG MMAGPMAAFK WQPTASEPVK DADPHFHHFL LSQTEKPAVC YQAITKKLKI
CEEETGSTSI QAADSTAVNG SITPTDKKIG FLGLGLMGSG IVSNLLKMGH TVTVWNRTAE
KCDLFIQEGA RLGRTPAEVV STCDITFACV SDPKAAKDLV LGPSGVLQGI RPGKCYVDMS
TVDADTVTEL AQVIVSRGGR FLEAPVSGNQ QLSNDGMLVI LAAGDRGLYE DCSSCFQAMG
KTSFFLGEVG NAAKMMLIVN MVQGSFMATI AEGLTLAQVT GQSQQTLLDI LNQGQLASIF
LDQKCQNILQ GNFKPDFYLK YIQKDLRLAI ALGDAVNHPT PMAAAANEVY KRAKALDQSD
NDMSAVYRAY IH
