CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-000164
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Transcription intermediary factor 1-beta 
Protein Synonyms/Alias
 TIF1-beta; E3 SUMO-protein ligase TRIM28; KRAB-associated protein 1; Nuclear corepressor KAP-1; Tripartite motif-containing protein 28 
Gene Name
 Trim28 
Gene Synonyms/Alias
 Kap1; Tif1b 
Created Date
 July 27, 2013 
Organism
 Rattus norvegicus (Rat) 
NCBI Taxa ID
 10116 
Lysine Modification
Position
Peptide
Type
References
190HQRVKYTKDHTVRSTacetylation[1]
263KLLASLVKRLGDKHAacetylation[1]
321VLVNDAQKVTEGQQEubiquitination[2]
339RQHWTMTKIQKHQEHacetylation[1]
342WTMTKIQKHQEHILRacetylation[1]
379FQLHRALKMIVDPVEacetylation[1]
771QDVGRMFKQFNKLTEacetylation[1]
780FNKLTEDKADVQSIIacetylation[1]
Reference
 [1] Proteomic analysis of lysine acetylation sites in rat tissues reveals organ specificity and subcellular patterns.
 Lundby A, Lage K, Weinert BT, Bekker-Jensen DB, Secher A, Skovgaard T, Kelstrup CD, Dmytriyev A, Choudhary C, Lundby C, Olsen JV.
 Cell Rep. 2012 Aug 30;2(2):419-31. [PMID: 22902405]
 [2] Synaptic protein ubiquitination in rat brain revealed by antibody-based ubiquitome analysis.
 Na CH, Jones DR, Yang Y, Wang X, Xu Y, Peng J.
 J Proteome Res. 2012 Sep 7;11(9):4722-32. [PMID: 22871113] 
Functional Description
 Nuclear corepressor for KRAB domain-containing zinc finger proteins (KRAB-ZFPs). Mediates gene silencing by recruiting CHD3, a subunit of the nucleosome remodeling and deacetylation (NuRD) complex, and SETDB1 (which specifically methylates histone H3 at 'Lys-9' (H3K9me)) to the promoter regions of KRAB target genes. Enhances transcriptional repression by coordinating the increase in H3K9me, the decrease in histone H3 'Lys-9 and 'Lys-14' acetylation (H3K9ac and H3K14ac, respectively) and the disposition of HP1 proteins to silence gene expression. Recruitment of SETDB1 induces heterochromatinization. May play a role as a coactivator for CEBPB and NR3C1 in the transcriptional activation of ORM1. Also corepressor for ERBB4. Inhibits E2F1 activity by stimulating E2F1-HDAC1 complex formation and inhibiting E2F1 acetylation. May serve as a partial backup to prevent E2F1-mediated apoptosis in the absence of RB1. Important regulator of CDKN1A/p21(CIP1). Has E3 SUMO-protein ligase activity toward itself via its PHD-type zinc finger. Specifically sumoylates IRF7, thereby inhibiting its transactivation activity. Ubiquitinates p53/TP53 leading to its proteosomal degradation; the function is enhanced by MAGEC2 and MAGEA2, and possibly MAGEA3 and MAGEA6 (By similarity). 
Sequence Annotation
 DOMAIN 698 802 Bromo.
 ZN_FING 67 123 RING-type.
 ZN_FING 150 197 B box-type 1; atypical.
 ZN_FING 206 247 B box-type 2.
 ZN_FING 626 673 PHD-type.
 REGION 248 378 Leucine zipper alpha helical coiled-coil
 REGION 249 378 Interaction with MAGEC2 (By similarity).
 REGION 368 372 Involved in binding PPP1CA (By
 REGION 477 514 HP1 box.
 MOTIF 482 495 PxVxL motif.
 MOD_RES 24 24 Phosphoserine (By similarity).
 MOD_RES 52 52 Phosphoserine (By similarity).
 MOD_RES 306 306 N6-acetyllysine (By similarity).
 MOD_RES 342 342 N6-acetyllysine (By similarity).
 MOD_RES 379 379 N6-acetyllysine (By similarity).
 MOD_RES 441 441 Phosphoserine (By similarity).
 MOD_RES 472 472 Phosphoserine (By similarity).
 MOD_RES 474 474 Phosphoserine (By similarity).
 MOD_RES 480 480 Phosphoserine (By similarity).
 MOD_RES 490 490 Phosphoserine (By similarity).
 MOD_RES 502 502 Phosphoserine (By similarity).
 MOD_RES 595 595 Phosphoserine (By similarity).
 MOD_RES 684 684 Phosphoserine (By similarity).
 MOD_RES 698 698 Phosphoserine (By similarity).
 MOD_RES 753 753 Phosphoserine (By similarity).
 MOD_RES 758 758 Phosphoserine (By similarity).
 MOD_RES 771 771 N6-acetyllysine (By similarity).
 MOD_RES 775 775 N6-acetyllysine (By similarity).
 MOD_RES 825 825 Phosphoserine; by ATM and ATR and dsDNA
 CROSSLNK 555 555 Glycyl lysine isopeptide (Lys-Gly)
 CROSSLNK 677 677 Glycyl lysine isopeptide (Lys-Gly)
 CROSSLNK 751 751 Glycyl lysine isopeptide (Lys-Gly)
 CROSSLNK 780 780 Glycyl lysine isopeptide (Lys-Gly)
 CROSSLNK 805 805 Glycyl lysine isopeptide (Lys-Gly)  
Keyword
 Acetylation; Bromodomain; Complete proteome; Isopeptide bond; Ligase; Metal-binding; Nucleus; Phosphoprotein; Reference proteome; Repeat; Repressor; Transcription; Transcription regulation; Ubl conjugation; Ubl conjugation pathway; Zinc; Zinc-finger. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 835 AA 
Protein Sequence
MAASAAAATA AASAATAASA ASGSPGSGEG SAGGEKRPAA SSAAAASASA SSPAGGGGEA 60
QELLEHCGVC RERLRPERDP RLLPCLHSAC SACLGPATPA AANNSGDGGS AGDGAMVDCP 120
VCKQQCYSKD IVENYFMRDS GSKASSDSQD ANQCCTSCED NAPATSYCVE CSEPLCETCV 180
EAHQRVKYTK DHTVRSTGPA KTRDGERTVY CNVHKHEPLV LFCESCDTLT CRDCQLNAHK 240
DHQYQFLEDA VRNQRKLLAS LVKRLGDKHA TLQKNTKEVR SSIRQVSDVQ KRVQVDVKMA 300
ILQIMKELNK RGRVLVNDAQ KVTEGQQERL ERQHWTMTKI QKHQEHILRF ASWALESDNN 360
TALLLSKKLI YFQLHRALKM IVDPVEPHGE MKFQWDLNAW TKSAEAFGKI VAERPGTNST 420
GPGPMAPPRA PGPLSKQGSG SSQPMEVQEG YGFGTDDPYS SAEPHVSGMK RSRSGEGEVS 480
GLMRKVPRVS LERLDLDLTS DSQPPVFKVF PGSTTEDYNL IVIERGAAAA AAGQAGTVPP 540
GAPGAPPLPG MAIVKEEETE AAIGAPPAAP EGPETKPVLM ALTEGPGAEG PRLASPSGST 600
SSGLEVVAPE VTSAPVSGPG ILDDSATICR VCQKPGDLVM CNQCEFCFHL DCHLPSLQDV 660
PGEEWSCSLC HVLPDLKEED GSLSLDGADS TGVVAKLSPA NQRKCERVLL ALFCHEPCRP 720
LHQLATDSTF SMEQPGGTLD LTLIRARLQE KLSPPYSSPQ EFAQDVGRMF KQFNKLTEDK 780
ADVQSIIGLQ RFFETRMNDA FGDTKFSAVL VEPPPLNLPS AGLSSQELSG PGDGP 835 
Gene Ontology
 GO:0005719; C:nuclear euchromatin; IEA:Compara.
 GO:0005720; C:nuclear heterochromatin; IEA:Compara.
 GO:0005654; C:nucleoplasm; IEA:Compara.
 GO:0005634; C:nucleus; ISS:HGNC.
 GO:0004672; F:protein kinase activity; IEA:Compara.
 GO:0043565; F:sequence-specific DNA binding; IEA:Compara.
 GO:0003700; F:sequence-specific DNA binding transcription factor activity; IEA:Compara.
 GO:0003713; F:transcription coactivator activity; IEA:Compara.
 GO:0003714; F:transcription corepressor activity; IEA:Compara.
 GO:0004842; F:ubiquitin-protein ligase activity; IEA:Compara.
 GO:0008270; F:zinc ion binding; IEA:Compara.
 GO:0060028; P:convergent extension involved in axis elongation; IEA:Compara.
 GO:0006281; P:DNA repair; IEA:Compara.
 GO:0060669; P:embryonic placenta morphogenesis; IEA:Compara.
 GO:0001837; P:epithelial to mesenchymal transition; ISS:HGNC.
 GO:0000122; P:negative regulation of transcription from RNA polymerase II promoter; IEA:Compara.
 GO:0045739; P:positive regulation of DNA repair; IEA:Compara.
 GO:0045893; P:positive regulation of transcription, DNA-dependent; ISS:HGNC.
 GO:0046777; P:protein autophosphorylation; IEA:Compara.
 GO:0051259; P:protein oligomerization; IEA:Compara.
 GO:0016925; P:protein sumoylation; IEA:UniProtKB-UniPathway.
 GO:0006351; P:transcription, DNA-dependent; IEA:UniProtKB-KW. 
Interpro
 IPR003649; Bbox_C.
 IPR001487; Bromodomain.
 IPR019786; Zinc_finger_PHD-type_CS.
 IPR000315; Znf_B-box.
 IPR011011; Znf_FYVE_PHD.
 IPR001965; Znf_PHD.
 IPR019787; Znf_PHD-finger.
 IPR001841; Znf_RING.
 IPR013083; Znf_RING/FYVE/PHD. 
Pfam
 PF00628; PHD
 PF00643; zf-B_box 
SMART
 SM00502; BBC
 SM00336; BBOX
 SM00297; BROMO
 SM00249; PHD
 SM00184; RING 
PROSITE
 PS00633; BROMODOMAIN_1
 PS50014; BROMODOMAIN_2
 PS50119; ZF_BBOX
 PS01359; ZF_PHD_1
 PS50016; ZF_PHD_2
 PS00518; ZF_RING_1
 PS50089; ZF_RING_2 
PRINTS