The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Accession:
Functional site class:
WRxxL motif
Functional site description:
The WRxxL motif binds to the RuBisCO small subunit. RuBisCO is the most abundant enzyme on earth and is responsible for the first step in the carbon fixation process. In algal chloroplasts, RuBisCO is concentrated in a membrane-less compartment called the Pyrenoid. Formation of the Pyrenoid and its different structures is dependent on proteins containing the WRxxL motif.
ELM Description:
The WRxxL motif binds to the small chain subunit of the RuBisCO holoenzyme. Upon binding, the motif adopts a short α-helical structure that binds to the RuBisCO surface (7JFO; 7JSX). The Tryptophan at position +1 and a hydrophobic residue at position +5 (usually Leucine) in the motif stabilises the interaction via hydrophobic interactions, while the positively charged amino acid in position +2 forms a salt bridge with E24 of the RBCS (RuBisCO Small Subunit) (He,2020). A carboxyl group seems to be functionally important after position +5, either at the C-terminus or through a negatively charged amino acid (Meyer,2020). Negatively charged amino acids are also present within the motif as they tend to form a salt bridge with R91 of the RBCS (He,2020).
Amino acids at position -1 are usually N or D and might play a role in helix capping. P is preferred at -3 but could not be included in the motif pattern. A hydrophobic residue at position -4 is observed to be packing together with the W at position +1 in a hydrophobic pocket. Occasionally the -4 position may be a positively-charged residue. Positively-charged amino acids are also preferred around flanking positions -7 and +9, as they form salt bridges with D31 and D23 of RCBS respectively (He,2020): however these positions are not well enough conserved to be included in the ELM motif pattern. An optimal WRxxL motif could be RxxLPxNWRxxLExxxR.
Pattern: [ILVATSRK][^EDN].[NDS]W[RK][^P][^P][LIVAPS]
Pattern Probability: 0.0000232
Present in taxon: Chlorophyceae
Interaction Domain:
RuBisCO_small (PF00101) Ribulose bisphosphate carboxylase, small chain (Stochiometry: 1 : 1)
o See 20 Instances for LIG_RuBisCO_WRxxL_1
o Abstract
RuBisCO (Ribulose-1,5-bisphosphate carboxylase/oxygenase; P00875) is the most prevalent enzyme on earth. It is responsible for the carboxylation of ribulose-1,5-bisphosphate, the first step in the carbon fixation process. The RuBisCO complex is a 16mer (Heterohexadecamer) with 8 copies of the catalytic large subunit and 8 copies of the small subunit. RuBisCO enzymes possess a slow catalytic rate, but plants have overcome this by evolving different CO2 concentrating mechanisms to increase RuBisCO performance. One such mechanism is formation of the Pyrenoid, a membrane-less compartment mainly composed of RuBisCO within the stroma of chloroplasts of some algae such as Chlamydomonas. Additional structures are formed at the Pyrenoid to concentrate CO2, such as the traversing tubules and a starch sheath, in limiting CO2 conditions (Wang,2015).
EPYC1 (Essential Pyrenoid Component 1; A0A2K3DA85) is another abundant protein in the Pyrenoid. EPYC1 is a ~35 kDa intrinsically disordered protein that has been shown to phase separate with RuBisCO and form liquid droplets in vitro (Wunder,2018). Meyer,2020 determined that the WRxxL motif was the element by which EPYC1 and the RuBisCO small subunit (RBCS) interact. EPYC1 contains multiple copies of this motif and is able to bind to any of the 8 RuBisCO’s RBCSs. Motif instances are spaced far enough away from each other to allow EPYC1 to interact with multiple RuBisCO complexes (He,2020).
Other less abundant pyrenoid proteins also contain instances of the WRxxL motif. Furthermore, they also possess additional protein domains for binding to structured assemblies of the Pyrenoid: SAGA1 & SAGA2 (A0A2K3D7T6;A0A2K3DEH1) for the starch sheath and RBMP1, RBMP2 (A0A2K3DMS8;A0A2K3DG19) for the traversing tubules. Other chloroplast non-pyrenoid proteins can be targeted to the Pyrenoid by adding the motif, which would allow them to bind to the RBSC. In Meyer,2020 the authors propose a role for the WRxxL motif as the organiser of the Pyrenoid’s architecture. First by allowing the multivalent EPYC1:RuBisCO interaction which would maintain the Pyrenoid matrix, and then other motif-containing proteins would dock to the Pyrenoid and assemble the extra structures using specific interaction domains (Meyer,2020).
o 2 selected references:

o 10 GO-Terms:

o 20 Instances for LIG_RuBisCO_WRxxL_1
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
A0A2K3DA85 CHLRE_10g436550v5
A0A2K3DA85_CHLRE
122 130 PSRSALPSNWKQELESLRSS TP 8 Chlamydomonas reinhardtii
1 
A0A2K3DA85 CHLRE_10g436550v5
A0A2K3DA85_CHLRE
59 67 PTRSVLPANWRQELESLRNG TP 10 Chlamydomonas reinhardtii
1 
A8IIK4 CSP41a
A8IIK4_CHLRE
431 439 GRSATTGRSGSVPKDWRSSL TP 4 Chlamydomonas reinhardtii
1 
A0A2K3DG19 CHLRE_09g416850v5
A0A2K3DG19_CHLRE
1682 1690 LSPSERLAREARMRDWRARV TP 4 Chlamydomonas reinhardtii
1 
A0A2K3DMS8 CHLRE_06g261750v5
A0A2K3DMS8_CHLRE
660 668 DTELSEANRPRTRPDWRNQL TP 4 Chlamydomonas reinhardtii
1 
A0A2K3DEH1 CHLRE_09g394621v5
A0A2K3DEH1_CHLRE
1808 1816 RRNASPVRRTAIPANWRDAL TP 4 Chlamydomonas reinhardtii
1 
A0A2K3D7T6 CHLRE_11g467712v5
A0A2K3D7T6_CHLRE
1618 1626 GRGTGDSPTRRAFGDWRKNL TP 4 Chlamydomonas reinhardtii
1 
A0A2K3DA85 CHLRE_10g436550v5
A0A2K3DA85_CHLRE
309 317 GKSKPEIKRTALPADWRKGL TP 4 Chlamydomonas reinhardtii
1 
A8IIK4 CSP41a
A8IIK4_CHLRE
401 409 IKRTVLPANWRDSLDEDEPA TP 5 Chlamydomonas reinhardtii
1 
A0A2K3DG19 CHLRE_09g416850v5
A0A2K3DG19_CHLRE
1635 1643 SAGSRAPSNWRQQVDGGSNG TP 5 Chlamydomonas reinhardtii
1 
A0A2K3DG19 CHLRE_09g416850v5
A0A2K3DG19_CHLRE
1589 1597 SASAVVPRDWRRELQSSAGE TP 4 Chlamydomonas reinhardtii
1 
A0A2K3DG19 CHLRE_09g416850v5
A0A2K3DG19_CHLRE
1342 1350 TSRSRSVTNWRDQVEAEAAR TP 5 Chlamydomonas reinhardtii
1 
A0A2K3DG19 CHLRE_09g416850v5
A0A2K3DG19_CHLRE
1316 1324 SFRSASRSSWRDEVAAEAVP TP 4 Chlamydomonas reinhardtii
1 
A0A2K3DG19 CHLRE_09g416850v5
A0A2K3DG19_CHLRE
1123 1131 ARASTVMSNWRDVIDSGAEV TP 5 Chlamydomonas reinhardtii
1 
A0A2K3DMS8 CHLRE_06g261750v5
A0A2K3DMS8_CHLRE
588 596 SDSSRRPVNWRDELQSLKAT TP 5 Chlamydomonas reinhardtii
1 
A0A2K3DEH1 CHLRE_09g394621v5
A0A2K3DEH1_CHLRE
1483 1491 PAPAKTKPDWREQAQAPVQA TP 4 Chlamydomonas reinhardtii
1 
A0A2K3DEH1 CHLRE_09g394621v5
A0A2K3DEH1_CHLRE
655 663 GGETVTKANWREALAAAHDA TP 4 Chlamydomonas reinhardtii
1 
A0A2K3D7T6 CHLRE_11g467712v5
A0A2K3D7T6_CHLRE
1585 1593 QPGRSTSADWRRLVSGGDAA TP 5 Chlamydomonas reinhardtii
1 
A0A2K3DA85 CHLRE_10g436550v5
A0A2K3DA85_CHLRE
243 251 PSRSALPSNWKQELESLRSN TP 5 Chlamydomonas reinhardtii
1 
A0A2K3DA85 CHLRE_10g436550v5
A0A2K3DA85_CHLRE
182 190 PSRSALPSNWKQELESLRSS TP 5 Chlamydomonas reinhardtii
1 
Please cite: ELM — the eukaryotic linear motif resource in 2020. (PMID:31680160)

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