The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Accession:
Functional site class:
Rb pocket B binding ligand
Functional site description:
The LxCxE motif is found in multiple host and viral interactors of the retinoblastoma protein family (Rb, p107 and p130).
ELM Description:
The LxCxE motif mediates binding to a highly conserved shallow groove in the B domain of Rb. The central Cysteine is highly conserved in all instances, however the Leucine and Glutamic Acid positions tolerate substitution of physicochemically similar residues allowing a less stringent definition of [LI]xCx[DE]. The staggered arrangement, evenly spaced and one residue apart, of the conserved residues cover one side of an extended, beta-strand-like conformation and bind the groove orthogonally, not by beta augmentation like many similar staggered motifs. The Leucine and Cysteine positions bind a hydrophobic region of the groove with tight complementarity. The Glutamic Acid forms hydrogen bonds with two backbone amide groups of an alpha helix forming one side of the binding groove. The interaction is further stabilized by additional hydrogen bonds to the peptide backbone adding rigidity. Phosphorylation of Rb at Thr821 and Thr826 inhibits LxCxE binding.
Pattern: ([DEST]|^).{0,4}[LI].C.E.{1,4}[FLMIVAWPHY].{0,8}([DEST]|$)
Pattern Probability: 0.0005417
Present in taxons: Metazoa Viridiplantae
Interaction Domain:
RB_B (PF01857) Retinoblastoma-associated protein B domain (Stochiometry: 1 : 1)
PDB Structure: 1GUX
o See 45 Instances for LIG_Rb_LxCxE_1
o Abstract
The retinoblastoma susceptibility gene, Rb, was the first tumour suppressor gene to be identified and characterized. Rb belongs to the family of so-called pocket proteins, which also includes p107 and p130. Inactivation of Rb may contribute to many human malignancies including familial retinoblastoma, small-cell lung carcinomas, cervical carcinomas, prostate carcinomas, breast carcinomas, and some forms of leukemias. The most studied function of Rb protein is in the regulation of cell cycle progression at the G1/S boundary (Giacinti,2006). However, Rb is also considered to be involved in chromatin remodeling, development, differentiation and apoptosis. Due to the important position of Rb as a regulator of cell cycle progression at the G1/S phase boundary, Rb is highly regulated. Hypophosphorylated Rb binds E2F and recruits histone deacetylases and methytransferases to repress the expression of E2F controlled gene expression. Phosphorylation by cyclin/CDKs over the course of G1-phase leads to hyperphosphorylation, disassociation of Rb from E2F and the expression of E2F controlled S-phase inducing genes (Trimarchi,2002).

The multiple roles of Rb are facilitated by its interaction with different protein partners, dependent on the cell type, and on the developmental and cell cycle stages. The interactions of Rb with its binding partners are conserved throughout a wide variety of taxa, from plants to invertebrates and mammals (van den Heuvel,2008). The Rb protein is commonly represented as consisting of three modules, the N-domain, pocket domain and the C-domain (Morris,2001). The pocket domain is further separated into the A and B domains which each possess the helical cyclin fold. The pocket domain acts as a binding region for numerous cellular proteins, including the E2F transcription factors, histone deacetylases and cell cycle regulators as well as viral oncoproteins (Fattaey,1992).

To date, two pocket domain binding motifs have been identified. An LxCxE motif mediates binding to the conserved "pocket region" in the B-domain and an LxxLFD motif that binds a deep conserved groove between the pocket A and B domains. The LxCxE motif is found in numerous kinases, histone deacetylases and methytransferases (e.g. Kim,2001, Lee,2002, Dahiya,2000). Recruitment of histone deacetylases and methytransferases via the LxCxE binding pocket mediates repression of E2F controlled genes. The LxxLFD motif in the transactivation (TA) domain of E2F transcription factors is partially responsible for the recruitment of Rb (Rb also contacts E2F through an additional larger disordered region that binds across the E2F/DP1 interface (2AZE)) thereby repressing E2F mediated transcription. Deregulation of Rb-E2F interaction or the LxCxE mediated binding results in hyperproliferation, lack of differentiation, apoptosis and can lead to cancer.

Rb is a common target of viral oncoproteins, predominantly of DNA viruses, most often via the LxCxE motif (first identified in the adenovirus E1A and papilloma virus E7 proteins (Jones,1990)). Convergently evolved mimics are known in multiple viruses including both plant (RepA in wheat dwarf virus and Clink in faba bean necrotic yellows virus) and mammalian (EBNAC in Epstein-Barr Virus (EBV), pp71 in Human cytomegalovirus, Ta in SV40, E7 in HPV, E4 and E1A in Adenovirus, NSP90 in Rubella, Tax in HTLV) viral proteins. Adenovirus E1A has both an LxCxE and an LxxLFD motif (SV40 Lt and HPV E7 are also proposed to contain both motifs however possess insufficient evidence for high confidence in the LxxLFD motif, see below). These viral proteins use their Rb targeting motifs to deregulate E2F binding to Rb, alleviating the Rb-mediated repression and forcing the cell into S-Phase thereby activating the replication machinery necessary for completion of the DNA viral life cycle. For example, the LxxLFD motif contained in the CR1 region of Adenovirus E1A and the TA domain of E2F use analogous residues to directly compete for the AB pocket of Rb (Liu,2007). E1A has also been shown to recruit Rb to anti-viral promoters leading to their repression.

Cellular C/EPBs, SV40 Lt and HPV E7 have been proposed to possess the pocket groove-binding motif yet they do not match the motif conservation of the canonical E2F and E1A motifs (these both have structural evidence for pocket groove binding (Lee,2002, Liu,2007)). There might be a possibility of additional binding sites as the surface of the pocket domain contains extensive grooves outside the LxxLFD and LxCxE binding sites. Furthermore, the structure of the extended E2F peptide revealed an interface adjacent to the LxxLFD binding site.
o 10 selected references:

o 6 GO-Terms:

o 45 Instances for LIG_Rb_LxCxE_1
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
Q13547 HDAC1
HDAC1_HUMAN
411 428 SDKRIACEEEFSDSEEEGEG TP 15 Homo sapiens (Human)
1 
B8ZX42 LT-Ag
B8ZX42_9POLY
211 229 DLFCDESLSSPEPPSSSEEP TP 9 Merkel cell polyomavirus
P03070 Large T antig
LT_SV40
101 119 ENLFCSEEMPSSDDEATADS TP 7 Simian virus 40
1 
Q5T8A7 PPP1R26
PPR26_HUMAN
478 493 DTSAELMCAEAILDISKTIL TP 5 Homo sapiens (Human)
Q13029 PRDM2
PRDM2_HUMAN
309 328 EIRCDEKPEDLLEEPKTTSE TP 9 Homo sapiens (Human)
1 
P42753 CYCD3-1
CCD31_ARATH
20 38 DALYCEEEKWDDEGEEVEEN TP 4 Arabidopsis thaliana (Thale cress)
1 
P42752 CYCD2-1
CCD21_ARATH
3 22 ENLACGETSESWIIDNDDDD TP 4 Arabidopsis thaliana (Thale cress)
1 
P42751 CYCD1-1
CCD11_ARATH
21 40 DLFCGEDSGVFSGESTVDFS TP 3 Arabidopsis thaliana (Thale cress)
1 
P30281 CCND3
CCND3_HUMAN
2 18 MELLCCEGTRHAPRAGPDPR TP 3 Homo sapiens (Human)
1 
P30279 CCND2
CCND2_HUMAN
2 17 MELLCHEVDPVRRAVRDRNL TP 4 Homo sapiens (Human)
1 
P17480 UBTF
UBF1_HUMAN
306 323 YSLYCAELMANMKDVPSTER FP 3 Homo sapiens (Human)
1 
O14777 NDC80
NDC80_HUMAN
229 245 YTIKCYESFMSGADSFDEMN TP 5 Homo sapiens (Human)
1 
Q92769 HDAC2
HDAC2_HUMAN
412 429 SDKRIACDEEFSDSEDEGEG TP 5 Homo sapiens (Human)
1 
Q62661 Hbp1
HBP1_RAT
31 51 SLELLQCNENVPSSPGYNSCD TP 9 Rattus norvegicus (Norway rat)
1 
P51532 SMARCA4
SMCA4_HUMAN
1355 1371 VERLTCEEEEEKMFGRGSRH TP 4 Homo sapiens (Human)
1 
Q63928 brg1
Q63928_9MURI
730 746 VERLTCEEEEEKMFGRGSRH TP 5 Mus sp.
1 
Q77J94 Wsv056
Q77J94_WSSVS
214 226 GHGMGHSDLSCDEISEFLVQ TP 3 Shrimp white spot syndrome virus (isolate Tongan)
1 
Q77J89 Wsv069
Q77J89_WSSVS
213 224 EGHGVGHSDLTCDEISGFFV TP 3 Shrimp white spot syndrome virus (isolate Tongan)
1 
P0C6X9 rep
R1AB_CVMA5
6857 6871 FKDFQFMLWCNEEKVMTFYP FP 4 Murine hepatitis virus strain A59
1 
Q9Y6B2 EID1
EID1_HUMAN
175 187 LMVVNRLTEELGCDEIIDRE TP 7 Homo sapiens (Human)
1 
Q9WKM8 Putative unch
Q9WKM8_BBTV
110 126 QDLYCDEVLSSSSTEEEDVG TP 2 Banana bunchy top virus
1 
Q9WIJ4 DNA-C
CLINK_FBNY1
109 127 DLSCRELLPPEEDDDITYED TP 4 Faba bean necrotic yellows virus
1 
Q9R002 Ifi202
IFI2_MOUSE
413 433 TIRLVCFELTSNADEWFLRST FP 4 Mus musculus (House mouse)
1 
Q99708 RBBP8
COM1_HUMAN
152 169 AELECEEDVIPDSPITAFSF FP 5 Homo sapiens (Human)
1 
Q98178 MC007L
Q98178_MCV1
140 158 DLYCHENLRYESDVSEDEDK TP 2 Molluscum contagiosum virus subtype 1
1 
Q98178 MC007L
Q98178_MCV1
173 196 TLLDLLACSEDASGFSPPEDSFSS TP 2 Molluscum contagiosum virus subtype 1
1 
Q13107 USP4
UBP4_HUMAN
458 472 KSTLVCPECAKVSVTFDPFC FP 3 Homo sapiens (Human)
1 
Q12931 TRAP1
TRAP1_HUMAN
523 543 EVLFCFEQFDELTLLHLREFD FP 2 Homo sapiens (Human)
1 
P51531 SMARCA2
SMCA2_HUMAN
1292 1308 VERLTCEEEEEKIFGRGSRQ TP 5 Homo sapiens (Human)
1 
P35869 AHR
AHR_HUMAN
329 346 ADMLYCAESHIRMIKTGESG FP 8 Homo sapiens (Human)
1 
P35251 RFC1
RFC1_HUMAN
662 680 SLVCQELGYSYVELNASDTR FP 3 Homo sapiens (Human)
1 
P32519 ELF1
ELF1_HUMAN
47 67 SYAGLACVEEPNDMITESSLD FP 4 Homo sapiens (Human)
1 
P29375 KDM5A
KDM5A_HUMAN
1370 1388 EPNLFCDEEIPIKSEEVVTH TP 4 Homo sapiens (Human)
1 
P29374 ARID4A
ARI4A_HUMAN
956 973 ETLVCHEVDLDDLDEKDKTS TP 5 Homo sapiens (Human)
1 
P24385 CCND1
CCND1_HUMAN
2 19 MEHQLLCCEVETIRRAYPDA TP 4 Homo sapiens (Human)
1 
P16788 UL97
GCVK_HCMVA
144 167 DGYHGLRCRETSAMWSFEYDRDGD TP 1 Human herpesvirus 5 strain AD169
1 
P15092 Ifi204
IFI4_MOUSE
418 434 IDRQPKLVCGEHSFIKISKR FP 2 Mus musculus (House mouse)
1 
P14990 C1
REPA_MSVS
197 216 DLLCNESINDWLQPNIFQVS TP 2 Maize streak virus - [South Africa]
1 
P06847 C1
REPA_WDVS
191 212 TESLICHETIESWKNEHLYSVS TP 2 Wheat dwarf virus - [Sweden]
1 
P45973 CBX5
CBX5_HUMAN
54 75 EKNLDCPELISEFMKKYKKMKE FP 4 Homo sapiens (Human)
1 
P03255 Early E1A 32
E1A_ADE05
118 140 EVIDLTCHEAGFPPSDDEDEEGE TP 4 Human adenovirus 5
1 
P03129 E7
VE7_HPV16
21 37 TDLYCYEQLNDSSEEEDEID TP 5 Human papillomavirus type 16
1 
O75884 RBBP9
RBBP9_HUMAN
62 76 ETELHCDEKTIIIGHSSGAI FP 4 Homo sapiens (Human)
1 
O75150 RNF40
BRE1B_HUMAN
106 127 EALLRCHESQGELSSAPEAPGT FP 4 Homo sapiens (Human)
1 
O39521 C1
REPA_BEYDV
180 199 DLRCHEDLHNWRETHLYHVS TP 2 Bean yellow dwarf virus
1 
Please cite: ELM 2016-data update and new functionality of the eukaryotic linear motif resource. (PMID:26615199)

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