The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Functional site class:
di Arginine retention/retrieving signal
Functional site description:
The di-Arg ER retrieval and retention motif is present on membrane proteins where it serves for ER localisation. A variety of membrane proteins (some multimeric) possess this di-Arg motif. Here the motif functions as a quality control mechanism for correct folding and protein complex assembly governing the ER exit. The functional motif needs to be exposed within a cytosolic region of the membrane protein and requires a distinct proximity to the transmembrane region. Heteromerization, as well as the interaction with 14-3-3 proteins or PDZ domain containing proteins can render some di-Arg retention signals inactive, whereas the interaction with Coat protein complex I (COPI) supports ER retrieval. Finally, some di-Arg based ER-retention signals may be negatively regulated by phosphorylation of nearby residues.
ELM Description:
The di-Arg motif is present on the cytosolic side of many transmembrane proteins and serves as an ER-retrieval and retention motif. It is defined by two arginine residues, either next to each other or spaced by a single unconserved (RR, RXR). Longer insertions have been reported such as RXXR but we chose not to extend the motif in ELM due to the limited literature (Boulaflous,2009, Uemura,2009). Either before or after the Arg pair, there is a hydrophobic residue or a third Arg (Michelsen,2005). This implies that the motif may have two binding orientations, though this is not yet known. A combinatorial screening approach for the RXR sequence revealed that negatively charged or small, non-polar residues surrounding the arginines negatively affect the motif activity, whereas three or more arginines provide a strong ER-retention efficiency (Zerangue,2001). It is likely that the motif must be linked to one or more transmembrane regions and the distance from the transmembrane region to the di-Arg motif may be important (Zhang,2008, Michelsen,2005). Any di-Arg motif matches in non-membrane proteins should be disregarded.
Pattern: ([LIVMFYWPR]R[^YFWDE]{0,1}R)|(R[^YFWDE]{0,1}R[LIVMFYWPR])
Pattern Probability: 0.0053693
Present in taxon: Eukaryota
Interaction Domain:
WD40 (PF00400) WD domain, G-beta repeat (Stochiometry: 1 : 1)
o See 27 Instances for TRG_ER_diArg_1
o Abstract
The trafficking of proteins between vesicular compartments and delivery of proteins to particular subcellular locations are tightly regulated and essential for instance to achieve correct assembly of multimeric proteins and correct post-translational modifications. Arginine-based sorting motifs are shown to be critical in the biosynthetic processing of numerous transmembrane proteins. Schutze,1994 first described a di-Arg ER-retention motif determined by two adjacent Arginines (RR) localized on one form of the invariant chain (Ii33, P04233) of the major histocompatibility complex (MHC) class II (Schutze,1994). The initial presumptions of a required proximity to the N terminus and specificity for type II membrane proteins have been superceded. The di-Arg motif is most commonly found on an N- or C-terminal cytosolic region but can be found at other cytosolic protrusions of polytopic membrane proteins (Michelsen,2005). In the context of studying assembly and trafficking of ATP sensitive K+ channels (K-ATP), Zerangue,1999 found another variant of the di-Arg motif within the K-ATP subunits Kir6.1 (Q15842), Kir6.2 (Q14654) and SUR1 (Q09428). Mutational analysis and chimeric fusion proteins revealed an RXR-based sequence retaining single K-ATP subunits and incorrectly assembled complexes in the ER, preventing surface expression.
The di-Arg motif is not only present in K-ATP channel subunits but also in subunits of additional heteromeric membrane proteins like GABA (Q9UBS5), Kainate (Q16478) and NMDA (Q05586) receptors. Here the di-Arg ER-localization motif functions as a quality control mechanism governing the ER exit. Single subunits of unassembled multimeric proteins with an exposed di-Arg motif, which is suggested to be recognized by generic eukaryotic trafficking machinery, are retained in the ER. Only properly folded and fully assembled protein complexes can leave the ER and reach the cell surface (Zerangue,1999, Taneja,2009). Therefore the di-Arg motif represents a checkpoint for both the coordination of sequential assembly of multimeric membrane proteins and the regulation of their delivery to the cell membrane defining the number of protein complexes at the cell surface (Scott,2001). Precise regulation mechanisms are still unknown, but a simple explanation for the regulation of di-Arg based ER-retention in terms of surface expression of multimeric proteins is an inhibition of the motif by steric masking during heteromerization. Furthermore, the interaction with additional proteins like coat protein complex I (COPI), 14-3-3 proteins as well as PDZ domain containing proteins may act as regulatory switches. For example, unassembled K-ATP subunits possessing an exposed RXR motif are shown to be recognized by the COPI machinery and retrieved to ER by COPI coated vesicles, defining the di-Arg motif as an ER retrieval and retention motif (Taneja,2009). By contrast, 14-3-3 proteins may be qualified to probe the assembly status of multimeric membrane proteins and are often required in order to negatively regulate the di-Arg motif. 14-3-3 proteins reduce COPI mediated retention, which is necessary for the forward transport of the assembled protein complexes (Yuan,2003, Taneja,2009, Heusser,2006). For some instances (ADAM22 (Q9P0K1) and GPR15 (P49685) the 14-3-3 binding sequence overlaps with the di-Arg ER-retention motif, again indicating a regulatory switch by steric masking controlled by basophilic kinases, since 14-3-3 proteins bind phosphopeptides. Additionally, the di-Arg motif present in an NR1 (Q05586) subunit can be masked by recruitment of PDZ domain containing proteins (Scott,2001). Finally, di-Arg based ER-retention is likely regulated by phosphorylation of nearby residues. Either phosphomimetic mutations or activation of PKC enhanced the surface delivery of NR1, suggesting an inhibitory effect on di-Arg based ER-retention (Scott,2001). The CFTR protein is an unusual case. Cryptic di-Arg motifs are thought to become active due to cystic fibrosis unfolding mutations such as at F508 (Chang,1999). The instance in ELM is annotated as a false positive as this di-Arg is not a normal cellular motif.
o 12 selected references:

o 12 GO-Terms:

o 27 Instances for TRG_ER_diArg_1
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
Q05586-4 GRIN1
893 895 STLASSFKRRRSSKDTQYHP TP 2 Homo sapiens (Human)
Q01559 HMGR
3 6 MDVRRRSEKPAYPTKEFAAG TP 1 Nicotiana sylvestris (Wood tobacco)
Q63633 Slc12a5
1101 1104 VLLNMPGPPRNRNGDENYME TP 2 Rattus norvegicus (Norway rat)
O88829 St3gal5
11 13 TEAVGGAARRPQKLRSQAAA TP 5 Mus musculus (House mouse)
P13569 CFTR
553 556 GITLSGGQRARISLARAVYK FP 3 Homo sapiens (Human)
Q99572 P2RX7
575 578 AILPSCCRWRIRKEFPKSEG TP 2 Homo sapiens (Human)
C8ZIX9 EC1118_1P2_2553g
8 11 MSLSLVSYRLRKNPWVNIFL TP 4 Saccharomyces cerevisiae EC1118
Q01726 MC1R
160 163 YHSIVTLPRARRAVAAIWVA TP 4 Homo sapiens (Human)
P35610 SOAT1
10 13 VGEEKMSLRNRLSKSRENPE TP 3 Homo sapiens (Human)
7 9 MASADSRRVADGGGAGGTFQ TP 3 Homo sapiens (Human)
Q99720 SIGMAR1
7 9 MQWAVGRRWAWAALLLAVAA TP 3 Homo sapiens (Human)
P26678 PLN
12 14 VQYLTRSAIRRASTIEMPQQ TP 5 Homo sapiens (Human)
O14672 ADAM10
723 725 PLPGTLKRRRPPQPIQQPQR TP 4 Homo sapiens (Human)
O43292 GPAA1
9 11 MGLLSDPVRRRALARLVLRL TN 3 Homo sapiens (Human)
Q16478 GRIK5
862 865 SCRKTSRSRRRRRPGGPSRA TP 5 Homo sapiens (Human)
P30518 AVPR2
247 249 GPSERPGGRRRGRRTGSPGE TP 3 Homo sapiens (Human)
923 926 QLQSRQQLRSRRHPPTPPEP TP 3 Homo sapiens (Human)
Q96RI0 F2RL3
182 185 RYLALVHPLRARALRGRRLA TP 4 Homo sapiens (Human)
P04233 CD74
3 5 MHRRRSRSCREDQKPVMDDQ TP 4 Homo sapiens (Human)
P49685 GPR15
352 354 LSTFIHAEDFARRRKRSVSL TP 6 Homo sapiens (Human)
851 854 KKKIRGKRFRPRSNSTETLS TP 4 Homo sapiens (Human)
Q58F09 GCS1
7 9 MARGERRRRAVPAEGVRTAE TP 2 Homo sapiens (Human)
Q62968 Scn10a
495 497 SFLGLSSGRRRASHGSVFHF TP 4 Rattus norvegicus (Norway rat)
Q14654 KCNJ11
368 371 TLASARGPLRKRSVPMAKAK TP 9 Homo sapiens (Human)
Q15842 KCNJ8
380 383 SELSHQNSLRKRNSMRRNNS TP 5 Homo sapiens (Human)
Q09428 ABCC8
648 651 AVPLRVVNRKRPAREDCRGL TP 5 Homo sapiens (Human)
Q05586 GRIN1
893 895 STLASSFKRRRSSKDTSTGG TP 5 Homo sapiens (Human)
Please cite: ELM 2016-data update and new functionality of the eukaryotic linear motif resource. (PMID:26615199)

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