CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-012045
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; KAP-1; KRAB-interacting protein 1; KRIP-1; Nuclear corepressor KAP-1; RING finger protein 96; Tripartite motif-containing protein 28 
Gene Name
 TRIM28 
Gene Synonyms/Alias
 KAP1; RNF96; TIF1B 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
179KLLASLVKRLGDKHAubiquitination[1]
190DKHATLQKSTKEVRSubiquitination[1]
207RQVSDVQKRVQVDVKubiquitination[1]
214KRVQVDVKMAILQIMubiquitination[1]
222MAILQIMKELNKRGRubiquitination[1]
237VLVNDAQKVTEGQQEubiquitination[1]
283NTALLLSKKLIYFQLubiquitination[1]
295FQLHRALKMIVDPVEubiquitination[1]
308VEPHGEMKFQWDLNAubiquitination[1]
318WDLNAWTKSAEAFGKubiquitination[1]
325KSAEAFGKIVAERPGubiquitination[1]
352RAPGPLSKQGSGSSQubiquitination[1]
387EPHVSGVKRSRSGEGubiquitination[1]
425DSQPPVFKVFPGSTTubiquitination[1]
493ATEGPETKPVLMALAubiquitination[1]
613DSTGVVAKLSPANQRubiquitination[1]
668IRARLQEKLSPPYSSubiquitination[1]
692RMFKQFNKLTEDKADubiquitination[1]
697FNKLTEDKADVQSIIubiquitination[1]
Reference
 [1] Landscape of the PARKIN-dependent ubiquitylome in response to mitochondrial depolarization.
 Sarraf SA, Raman M, Guarani-Pereira V, Sowa ME, Huttlin EL, Gygi SP, Harper JW.
 Nature. 2013 Apr 18;496(7445):372-6. [PMID: 23503661] 
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. Also 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. 
Sequence Annotation
 DOMAIN 697 801 Bromo.
 ZN_FING 65 121 RING-type.
 ZN_FING 148 195 B box-type 1; atypical.
 ZN_FING 204 245 B box-type 2.
 ZN_FING 625 672 PHD-type.
 REGION 65 376 RBCC domain.
 REGION 246 376 Leucine zipper alpha helical coiled-coil
 REGION 247 376 Interaction with MAGEC2.
 REGION 366 370 Involved in binding PPP1CA.
 REGION 476 513 HP1 box.
 MOTIF 481 494 PxVxL motif.
 MOD_RES 2 2 N-acetylalanine.
 MOD_RES 19 19 Phosphoserine.
 MOD_RES 50 50 Phosphoserine.
 MOD_RES 304 304 N6-acetyllysine.
 MOD_RES 340 340 N6-acetyllysine.
 MOD_RES 377 377 N6-acetyllysine.
 MOD_RES 439 439 Phosphoserine.
 MOD_RES 471 471 Phosphoserine.
 MOD_RES 473 473 Phosphoserine.
 MOD_RES 479 479 Phosphoserine.
 MOD_RES 489 489 Phosphoserine.
 MOD_RES 501 501 Phosphoserine.
 MOD_RES 541 541 Phosphothreonine.
 MOD_RES 594 594 Phosphoserine.
 MOD_RES 683 683 Phosphoserine.
 MOD_RES 697 697 Phosphoserine.
 MOD_RES 752 752 Phosphoserine.
 MOD_RES 757 757 Phosphoserine.
 MOD_RES 770 770 N6-acetyllysine.
 MOD_RES 774 774 N6-acetyllysine.
 MOD_RES 824 824 Phosphoserine; by ATM and ATR and dsDNA
 CROSSLNK 554 554 Glycyl lysine isopeptide (Lys-Gly)
 CROSSLNK 676 676 Glycyl lysine isopeptide (Lys-Gly)
 CROSSLNK 750 750 Glycyl lysine isopeptide (Lys-Gly)
 CROSSLNK 779 779 Glycyl lysine isopeptide (Lys-Gly)
 CROSSLNK 804 804 Glycyl lysine isopeptide (Lys-Gly)  
Keyword
 3D-structure; Acetylation; Alternative splicing; Complete proteome; Direct protein sequencing; Isopeptide bond; Ligase; Metal-binding; Nucleus; Phosphoprotein; Polymorphism; 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
MAASAAAASA AAASAASGSP GPGEGSAGGE KRSTAPSAAA SASASAAASS PAGGGAEALE 60
LLEHCGVCRE RLRPEREPRL LPCLHSACSA CLGPAAPAAA NSSGDGGAAG DGTGPAKSRD 120
GERTVYCNVH KHEPLVLFCE SCDTLTCRDC QLNAHKDHQY QFLEDAVRNQ RKLLASLVKR 180
LGDKHATLQK STKEVRSSIR QVSDVQKRVQ VDVKMAILQI MKELNKRGRV LVNDAQKVTE 240
GQQERLERQH WTMTKIQKHQ EHILRFASWA LESDNNTALL LSKKLIYFQL HRALKMIVDP 300
VEPHGEMKFQ WDLNAWTKSA EAFGKIVAER PGTNSTGPAP MAPPRAPGPL SKQGSGSSQP 360
MEVQEGYGFG SGDDPYSSAE PHVSGVKRSR SGEGEVSGLM RKVPRVSLER LDLDLTADSQ 420
PPVFKVFPGS TTEDYNLIVI ERGAAAAATG QPGTAPAGTP GAPPLAGMAI VKEEETEAAI 480
GAPPTATEGP ETKPVLMALA EGPGAEGPRL ASPSGSTSSG LEVVAPEGTS APGGGPGTLD 540
DSATICRVCQ KPGDLVMCNQ CEFCFHLDCH LPALQDVPGE EWSCSLCHVL PDLKEEDGSL 600
SLDGADSTGV VAKLSPANQR KCERVLLALF CHEPCRPLHQ LATDSTFSLD QPGGTLDLTL 660
IRARLQEKLS PPYSSPQEFA QDVGRMFKQF NKLTEDKADV QSIIGLQRFF ETRMNEAFGD 720
TKFSAVLVEP PPMSLPGAGL SSQELSGGPG DGP 753 
Gene Ontology
 GO:0005719; C:nuclear euchromatin; IEA:Compara.
 GO:0005720; C:nuclear heterochromatin; IEA:Compara.
 GO:0005654; C:nucleoplasm; TAS:Reactome.
 GO:0003677; F:DNA binding; IDA:UniProtKB.
 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; IDA:UniProtKB.
 GO:0031625; F:ubiquitin protein ligase binding; IDA:UniProtKB.
 GO:0004842; F:ubiquitin-protein ligase activity; IDA:UniProtKB.
 GO:0008270; F:zinc ion binding; IDA:UniProtKB.
 GO:0060028; P:convergent extension involved in axis elongation; IEA:Compara.
 GO:0006281; P:DNA repair; IDA:UniProtKB.
 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:0045892; P:negative regulation of transcription, DNA-dependent; IDA:UniProtKB.
 GO:0045739; P:positive regulation of DNA repair; IDA:UniProtKB.
 GO:0045893; P:positive regulation of transcription, DNA-dependent; ISS:HGNC.
 GO:0046777; P:protein autophosphorylation; IEA:Compara.
 GO:0051259; P:protein oligomerization; IDA:UniProtKB.
 GO:0016925; P:protein sumoylation; IDA:UniProtKB.
 GO:0006367; P:transcription initiation from RNA polymerase II promoter; TAS:Reactome. 
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