CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-020109
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 E3 ubiquitin-protein ligase TRIM56 
Protein Synonyms/Alias
 RING finger protein 109; Tripartite motif-containing protein 56 
Gene Name
 TRIM56 
Gene Synonyms/Alias
 RNF109 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
87NGLLDLVKARACGDLubiquitination[1, 2]
98CGDLRAGKPACALCPubiquitination[2]
270LRALLAQKQEVLGQLubiquitination[1, 2, 3, 4]
Reference
 [1] Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass.
 Povlsen LK, Beli P, Wagner SA, Poulsen SL, Sylvestersen KB, Poulsen JW, Nielsen ML, Bekker-Jensen S, Mailand N, Choudhary C.
 Nat Cell Biol. 2012 Oct;14(10):1089-98. [PMID: 23000965]
 [2] Refined preparation and use of anti-diglycine remnant (K-ε-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments.
 Udeshi ND, Svinkina T, Mertins P, Kuhn E, Mani DR, Qiao JW, Carr SA.
 Mol Cell Proteomics. 2013 Mar;12(3):825-31. [PMID: 23266961]
 [3] Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition.
 Udeshi ND, Mani DR, Eisenhaure T, Mertins P, Jaffe JD, Clauser KR, Hacohen N, Carr SA.
 Mol Cell Proteomics. 2012 May;11(5):148-59. [PMID: 22505724]
 [4] Integrated proteomic analysis of post-translational modifications by serial enrichment.
 Mertins P, Qiao JW, Patel J, Udeshi ND, Clauser KR, Mani DR, Burgess MW, Gillette MA, Jaffe JD, Carr SA.
 Nat Methods. 2013 Jul;10(7):634-7. [PMID: 23749302] 
Functional Description
 E3 ubiquitin-protein ligase that mediates 'Lys-63'- linked polyubiquitination of TMEM173/STING, thereby playing a key role in innate immunity. TMEM173/STING 'Lys-63'-linked ubiquitination activates the production of type I interferon IFN- beta following detection of pathogen- and host-derived double- stranded DNA (By similarity). 
Sequence Annotation
 ZN_FING 21 60 RING-type.
 ZN_FING 98 149 B box-type 1.
 ZN_FING 164 205 B box-type 2.
 MOD_RES 314 314 Phosphoserine (By similarity).
 MOD_RES 418 418 Phosphothreonine.
 MOD_RES 442 442 Phosphothreonine.
 MOD_RES 469 469 Phosphoserine (By similarity).
 MOD_RES 471 471 Phosphoserine (By similarity).
 MOD_RES 475 475 Phosphoserine.  
Keyword
 Alternative splicing; Antiviral defense; Coiled coil; Complete proteome; Cytoplasm; Immunity; Innate immunity; Ligase; Metal-binding; Phosphoprotein; Reference proteome; Repeat; Ubl conjugation pathway; Zinc; Zinc-finger. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 755 AA 
Protein Sequence
MVSHGSSPSL LEALSSDFLA CKICLEQLRA PKTLPCLHTY CQDCLAQLAD GGRVRCPECR 60
ETVPVPPEGV ASFKTNFFVN GLLDLVKARA CGDLRAGKPA CALCPLVGGT STGGPATARC 120
LDCADDLCQA CADGHRCTRQ THTHRVVDLV GYRAGWYDEE ARERQAAQCP QHPGEALRFL 180
CQPCSQLLCR ECRLDPHLDH PCLPLAEAVR ARRPGLEGLL AGVDNNLVEL EAARRVEKEA 240
LARLREQAAR VGTQVEEAAE GVLRALLAQK QEVLGQLRAH VEAAEEAARE RLAELEGREQ 300
VARAAAAFAR RVLSLGREAE ILSLEGAIAQ RLRQLQGCPW APGPAPCLLP QLELHPGLLD 360
KNCHLLRLSF EEQQPQKDGG KDGAGTQGGE ESQSRREDEP KTERQGGVQP QAGDGAQTPK 420
EEKAQTTREE GAQTLEEDRA QTPHEDGGPQ PHRGGRPNKK KKFKGRLKSI SREPSPALGP 480
NLDGSGLLPR PIFYCSFPTR MPGDKRSPRI TGLCPFGPRE ILVADEQNRA LKRFSLNGDY 540
KGTVPVPEGC SPCSVAALQS AVAFSASARL YLINPNGEVQ WRRALSLSQA SHAVAALPSG 600
DRVAVSVAGH VEVYNMEGSL ATRFIPGGKA SRGLRALVFL TTSPQGHFVG SDWQQNSVVI 660
CDGLGQVVGE YKGPGLHGCQ PGSVSVDKKG YIFLTLREVN KVVILDPKGS LLGDFLTAYH 720
GLEKPRVTTM VDGRYLVVSL SNGTIHIFRV RSPDS 755 
Gene Ontology
 GO:0005737; C:cytoplasm; ISS:UniProtKB.
 GO:0004842; F:ubiquitin-protein ligase activity; ISS:UniProtKB.
 GO:0008270; F:zinc ion binding; IEA:InterPro.
 GO:0051607; P:defense response to virus; ISS:UniProtKB.
 GO:0032608; P:interferon-beta production; ISS:UniProtKB.
 GO:0070534; P:protein K63-linked ubiquitination; ISS:UniProtKB.
 GO:0034340; P:response to type I interferon; ISS:UniProtKB. 
Interpro
 IPR011042; 6-blade_b-propeller_TolB-like.
 IPR000315; Znf_B-box.
 IPR001841; Znf_RING.
 IPR013083; Znf_RING/FYVE/PHD.
 IPR017907; Znf_RING_CS. 
Pfam
 PF00643; zf-B_box 
SMART
 SM00336; BBOX
 SM00184; RING 
PROSITE
 PS50119; ZF_BBOX
 PS00518; ZF_RING_1
 PS50089; ZF_RING_2 
PRINTS