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Structural basis for cpSRP43 chromodomain selectivity and dynamics in Alb3 insertase interaction.

Horn A, Hennig J, Ahmed YL, Stier G, Wild K, Sattler M, Sinning I - Nat Commun (2015)

Bottom Line: Canonical membrane protein biogenesis requires co-translational delivery of ribosome-associated proteins to the Sec translocase and depends on the signal recognition particle (SRP) and its receptor (SR).Negative cooperativity in ligand binding can be explained by dynamics in the chromodomain interface.Our study provides a model for membrane recruitment of the transit complex and may serve as a prototype for a functional gain by the tandem arrangement of chromodomains.

View Article: PubMed Central - PubMed

Affiliation: Heidelberg University Biochemistry Center (BZH), INF 328, Heidelberg D-69120, Germany.

ABSTRACT
Canonical membrane protein biogenesis requires co-translational delivery of ribosome-associated proteins to the Sec translocase and depends on the signal recognition particle (SRP) and its receptor (SR). In contrast, high-throughput delivery of abundant light-harvesting chlorophyll a,b-binding proteins (LHCPs) in chloroplasts to the Alb3 insertase occurs post-translationally via a soluble transit complex including the cpSRP43/cpSRP54 heterodimer (cpSRP). Here we describe the molecular mechanisms of tethering cpSRP to the Alb3 insertase by specific interaction of cpSRP43 chromodomain 3 with a linear motif in the Alb3 C-terminal tail. Combining NMR spectroscopy, X-ray crystallography and biochemical analyses, we dissect the structural basis for selectivity of chromodomains 2 and 3 for their respective ligands cpSRP54 and Alb3, respectively. Negative cooperativity in ligand binding can be explained by dynamics in the chromodomain interface. Our study provides a model for membrane recruitment of the transit complex and may serve as a prototype for a functional gain by the tandem arrangement of chromodomains.

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Ligand recognition by chromodomains.(a) Close-up view of the backbone interactions of CD3 with A3CT IV. Hydrogen bonds are indicated by dashed lines. (b) Sequence alignment of chromodomain ligands. The 0 position binding to the cage is depicted in red. (c) Specific read-out of the 0 position in different chromodomains. Left: A3CT IV in CD3, middle: RRKRp in CD2, right: H3K9me3 in HP1. (d) Schematic representations of the respective chromodomain–ligand interactions.
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f3: Ligand recognition by chromodomains.(a) Close-up view of the backbone interactions of CD3 with A3CT IV. Hydrogen bonds are indicated by dashed lines. (b) Sequence alignment of chromodomain ligands. The 0 position binding to the cage is depicted in red. (c) Specific read-out of the 0 position in different chromodomains. Left: A3CT IV in CD3, middle: RRKRp in CD2, right: H3K9me3 in HP1. (d) Schematic representations of the respective chromodomain–ligand interactions.

Mentions: The accommodation of the ligand as strand β1′ in CD3 results in the formation of a β-barrel as described for the CD2 interaction with RRKRp25 (Supplementary Fig. 4b,d). Strand β1′ is hereby sandwiched between strand β2a and a short strand β5 formed by the loop between strand β4 and helix α1. The combined chromodomain–ligand β–barrel is peculiar in the sense that the parallel strands β4 and β5 (the latter not formed in CD3) span only half of the barrel and are laterally offset by an inserted helical turn, thus creating a void in the barrel between strands β4 and β1′, which is filled by the ligand bound to its ‘cage' (Fig. 2f). In the classical chromodomain interaction with histone tails, the cage is formed by three aromatic residues that accommodate the methylated lysine of the tail (Fig. 3c, Supplementary Fig. 4c). In the CD2CD3–IV complex ligand binding is modified for the specific recognition of an arginine residue (see below) and the absence of strand β5 is due to a twist (usually 25° in β-sheets) of strand β1′ with respect to the neighbouring strands β2a (50°) and the ‘β5' region (0°) (Fig. 2f). Therefore, strands β1′ and β2a are shorter as observed in the cpSRP43ΔCD3–RRKRp complex25 (Supplementary Fig. 5), which is reflected by the lower binding affinity of motif IV compared with the RRKR motif (Supplementary Table 1a,b).


Structural basis for cpSRP43 chromodomain selectivity and dynamics in Alb3 insertase interaction.

Horn A, Hennig J, Ahmed YL, Stier G, Wild K, Sattler M, Sinning I - Nat Commun (2015)

Ligand recognition by chromodomains.(a) Close-up view of the backbone interactions of CD3 with A3CT IV. Hydrogen bonds are indicated by dashed lines. (b) Sequence alignment of chromodomain ligands. The 0 position binding to the cage is depicted in red. (c) Specific read-out of the 0 position in different chromodomains. Left: A3CT IV in CD3, middle: RRKRp in CD2, right: H3K9me3 in HP1. (d) Schematic representations of the respective chromodomain–ligand interactions.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4660199&req=5

f3: Ligand recognition by chromodomains.(a) Close-up view of the backbone interactions of CD3 with A3CT IV. Hydrogen bonds are indicated by dashed lines. (b) Sequence alignment of chromodomain ligands. The 0 position binding to the cage is depicted in red. (c) Specific read-out of the 0 position in different chromodomains. Left: A3CT IV in CD3, middle: RRKRp in CD2, right: H3K9me3 in HP1. (d) Schematic representations of the respective chromodomain–ligand interactions.
Mentions: The accommodation of the ligand as strand β1′ in CD3 results in the formation of a β-barrel as described for the CD2 interaction with RRKRp25 (Supplementary Fig. 4b,d). Strand β1′ is hereby sandwiched between strand β2a and a short strand β5 formed by the loop between strand β4 and helix α1. The combined chromodomain–ligand β–barrel is peculiar in the sense that the parallel strands β4 and β5 (the latter not formed in CD3) span only half of the barrel and are laterally offset by an inserted helical turn, thus creating a void in the barrel between strands β4 and β1′, which is filled by the ligand bound to its ‘cage' (Fig. 2f). In the classical chromodomain interaction with histone tails, the cage is formed by three aromatic residues that accommodate the methylated lysine of the tail (Fig. 3c, Supplementary Fig. 4c). In the CD2CD3–IV complex ligand binding is modified for the specific recognition of an arginine residue (see below) and the absence of strand β5 is due to a twist (usually 25° in β-sheets) of strand β1′ with respect to the neighbouring strands β2a (50°) and the ‘β5' region (0°) (Fig. 2f). Therefore, strands β1′ and β2a are shorter as observed in the cpSRP43ΔCD3–RRKRp complex25 (Supplementary Fig. 5), which is reflected by the lower binding affinity of motif IV compared with the RRKR motif (Supplementary Table 1a,b).

Bottom Line: Canonical membrane protein biogenesis requires co-translational delivery of ribosome-associated proteins to the Sec translocase and depends on the signal recognition particle (SRP) and its receptor (SR).Negative cooperativity in ligand binding can be explained by dynamics in the chromodomain interface.Our study provides a model for membrane recruitment of the transit complex and may serve as a prototype for a functional gain by the tandem arrangement of chromodomains.

View Article: PubMed Central - PubMed

Affiliation: Heidelberg University Biochemistry Center (BZH), INF 328, Heidelberg D-69120, Germany.

ABSTRACT
Canonical membrane protein biogenesis requires co-translational delivery of ribosome-associated proteins to the Sec translocase and depends on the signal recognition particle (SRP) and its receptor (SR). In contrast, high-throughput delivery of abundant light-harvesting chlorophyll a,b-binding proteins (LHCPs) in chloroplasts to the Alb3 insertase occurs post-translationally via a soluble transit complex including the cpSRP43/cpSRP54 heterodimer (cpSRP). Here we describe the molecular mechanisms of tethering cpSRP to the Alb3 insertase by specific interaction of cpSRP43 chromodomain 3 with a linear motif in the Alb3 C-terminal tail. Combining NMR spectroscopy, X-ray crystallography and biochemical analyses, we dissect the structural basis for selectivity of chromodomains 2 and 3 for their respective ligands cpSRP54 and Alb3, respectively. Negative cooperativity in ligand binding can be explained by dynamics in the chromodomain interface. Our study provides a model for membrane recruitment of the transit complex and may serve as a prototype for a functional gain by the tandem arrangement of chromodomains.

Show MeSH