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Structural Insights into Separase Architecture and Substrate Recognition through Computational Modelling of Caspase-Like and Death Domains.

Winter A, Schmid R, Bayliss R - PLoS Comput. Biol. (2015)

Bottom Line: The surface features of this domain identify potential sites of protein-protein interactions.Notably, we identified a novel conserved region with the consensus sequence WWxxRxxLD predicted to be exposed on the surface of the death domain, which we termed the WR motif.We envisage that findings from our study will guide structural and functional studies of this important protein family.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, University of Leicester, Leicester, United Kingdom.

ABSTRACT
Separases are large proteins that mediate sister chromatid disjunction in all eukaryotes. They belong to clan CD of cysteine peptidases and contain a well-conserved C-terminal catalytic protease domain similar to caspases and gingipains. However, unlike other well-characterized groups of clan CD peptidases, there are no high-resolution structures of separases and the details of their regulation and substrate recognition are poorly understood. Here we undertook an in-depth bioinformatical analysis of separases from different species with respect to their similarity in amino acid sequence and protein fold in comparison to caspases, MALT-1 proteins (mucosa-associated lymphoidtissue lymphoma translocation protein 1) and gingipain-R. A comparative model of the single C-terminal caspase-like domain in separase from C. elegans suggests similar binding modes of substrate peptides between these protein subfamilies, and enables differences in substrate specificity of separase proteins to be rationalised. We also modelled a newly identified putative death domain, located N-terminal to the caspase-like domain. The surface features of this domain identify potential sites of protein-protein interactions. Notably, we identified a novel conserved region with the consensus sequence WWxxRxxLD predicted to be exposed on the surface of the death domain, which we termed the WR motif. We envisage that findings from our study will guide structural and functional studies of this important protein family.

No MeSH data available.


Related in: MedlinePlus

Separases from all species share a similar topology with highly conserved regions, which includes a caspase-like domain in their C-terminal region.(A) Consolidated secondary structure prediction of separase from C. elegans using both PsiPred and JPred predicts a largely helical N-terminus (dark grey) with an unstructured region around residue 400 and a region of three β-strands from residues 720 to 750 (light grey). The conserved C-terminal half harbours the caspase-like domain (black), residues 900 to 1140. The catalytic dyad is indicated as white lines. (B) Multiple sequence alignment of the caspase-like domain of separase from C. elegans in comparison with human caspase 3, gingipain-R and MALT-1. Alignment was manually adjusted using Jalview to match secondary structure elements from predictions (PsiPred) of separases to structural elements as observed in caspase 3 (3EDQ), MALT-1 (3UO8) and gingipain R (1CVR). α-helices are shown in dark grey and β-strands in light grey. The conserved catalytic dyad (C, H) is shown in bold letters.
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pcbi.1004548.g001: Separases from all species share a similar topology with highly conserved regions, which includes a caspase-like domain in their C-terminal region.(A) Consolidated secondary structure prediction of separase from C. elegans using both PsiPred and JPred predicts a largely helical N-terminus (dark grey) with an unstructured region around residue 400 and a region of three β-strands from residues 720 to 750 (light grey). The conserved C-terminal half harbours the caspase-like domain (black), residues 900 to 1140. The catalytic dyad is indicated as white lines. (B) Multiple sequence alignment of the caspase-like domain of separase from C. elegans in comparison with human caspase 3, gingipain-R and MALT-1. Alignment was manually adjusted using Jalview to match secondary structure elements from predictions (PsiPred) of separases to structural elements as observed in caspase 3 (3EDQ), MALT-1 (3UO8) and gingipain R (1CVR). α-helices are shown in dark grey and β-strands in light grey. The conserved catalytic dyad (C, H) is shown in bold letters.

Mentions: Next we set out to survey the sequence conservation among separase homologues from a wide range of taxa and predict the domain structure of the proteins using a comprehensive bioinformatical analysis. By combining multiple sequence alignments with secondary structure predictions we were able to identify several regions of separase that are well conserved (Fig 1A). Care was taken to avoid biasing the alignment towards a single taxonomic branch by aligning a representative set of separase protein sequences. The alignment revealed little sequence conservation in the N-terminal region of all proteins analysed. In all sequences, this region is predicted to consist of α-helices that do not appear to be conserved in either length or relative position within the respective protein sequence. This region is generally followed by a disordered region (residues 400 to 440 in C. elegans separase) as well as three β-strands (residues 720 to 750 in C. elegans separase). In some homologues these predicted β-strands were absent, only two strands predicted or interspersed with short helices. Finally, a well-conserved C-terminal region of approximately 240 amino acids was identified in all homologues that also contains the catalytically active residues histidine and cysteine (Fig 1A for a topological overview and S1 File).


Structural Insights into Separase Architecture and Substrate Recognition through Computational Modelling of Caspase-Like and Death Domains.

Winter A, Schmid R, Bayliss R - PLoS Comput. Biol. (2015)

Separases from all species share a similar topology with highly conserved regions, which includes a caspase-like domain in their C-terminal region.(A) Consolidated secondary structure prediction of separase from C. elegans using both PsiPred and JPred predicts a largely helical N-terminus (dark grey) with an unstructured region around residue 400 and a region of three β-strands from residues 720 to 750 (light grey). The conserved C-terminal half harbours the caspase-like domain (black), residues 900 to 1140. The catalytic dyad is indicated as white lines. (B) Multiple sequence alignment of the caspase-like domain of separase from C. elegans in comparison with human caspase 3, gingipain-R and MALT-1. Alignment was manually adjusted using Jalview to match secondary structure elements from predictions (PsiPred) of separases to structural elements as observed in caspase 3 (3EDQ), MALT-1 (3UO8) and gingipain R (1CVR). α-helices are shown in dark grey and β-strands in light grey. The conserved catalytic dyad (C, H) is shown in bold letters.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4626109&req=5

pcbi.1004548.g001: Separases from all species share a similar topology with highly conserved regions, which includes a caspase-like domain in their C-terminal region.(A) Consolidated secondary structure prediction of separase from C. elegans using both PsiPred and JPred predicts a largely helical N-terminus (dark grey) with an unstructured region around residue 400 and a region of three β-strands from residues 720 to 750 (light grey). The conserved C-terminal half harbours the caspase-like domain (black), residues 900 to 1140. The catalytic dyad is indicated as white lines. (B) Multiple sequence alignment of the caspase-like domain of separase from C. elegans in comparison with human caspase 3, gingipain-R and MALT-1. Alignment was manually adjusted using Jalview to match secondary structure elements from predictions (PsiPred) of separases to structural elements as observed in caspase 3 (3EDQ), MALT-1 (3UO8) and gingipain R (1CVR). α-helices are shown in dark grey and β-strands in light grey. The conserved catalytic dyad (C, H) is shown in bold letters.
Mentions: Next we set out to survey the sequence conservation among separase homologues from a wide range of taxa and predict the domain structure of the proteins using a comprehensive bioinformatical analysis. By combining multiple sequence alignments with secondary structure predictions we were able to identify several regions of separase that are well conserved (Fig 1A). Care was taken to avoid biasing the alignment towards a single taxonomic branch by aligning a representative set of separase protein sequences. The alignment revealed little sequence conservation in the N-terminal region of all proteins analysed. In all sequences, this region is predicted to consist of α-helices that do not appear to be conserved in either length or relative position within the respective protein sequence. This region is generally followed by a disordered region (residues 400 to 440 in C. elegans separase) as well as three β-strands (residues 720 to 750 in C. elegans separase). In some homologues these predicted β-strands were absent, only two strands predicted or interspersed with short helices. Finally, a well-conserved C-terminal region of approximately 240 amino acids was identified in all homologues that also contains the catalytically active residues histidine and cysteine (Fig 1A for a topological overview and S1 File).

Bottom Line: The surface features of this domain identify potential sites of protein-protein interactions.Notably, we identified a novel conserved region with the consensus sequence WWxxRxxLD predicted to be exposed on the surface of the death domain, which we termed the WR motif.We envisage that findings from our study will guide structural and functional studies of this important protein family.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, University of Leicester, Leicester, United Kingdom.

ABSTRACT
Separases are large proteins that mediate sister chromatid disjunction in all eukaryotes. They belong to clan CD of cysteine peptidases and contain a well-conserved C-terminal catalytic protease domain similar to caspases and gingipains. However, unlike other well-characterized groups of clan CD peptidases, there are no high-resolution structures of separases and the details of their regulation and substrate recognition are poorly understood. Here we undertook an in-depth bioinformatical analysis of separases from different species with respect to their similarity in amino acid sequence and protein fold in comparison to caspases, MALT-1 proteins (mucosa-associated lymphoidtissue lymphoma translocation protein 1) and gingipain-R. A comparative model of the single C-terminal caspase-like domain in separase from C. elegans suggests similar binding modes of substrate peptides between these protein subfamilies, and enables differences in substrate specificity of separase proteins to be rationalised. We also modelled a newly identified putative death domain, located N-terminal to the caspase-like domain. The surface features of this domain identify potential sites of protein-protein interactions. Notably, we identified a novel conserved region with the consensus sequence WWxxRxxLD predicted to be exposed on the surface of the death domain, which we termed the WR motif. We envisage that findings from our study will guide structural and functional studies of this important protein family.

No MeSH data available.


Related in: MedlinePlus