RagB/SusD family nutrient uptake outer membrane protein similar to Bacteroides thetaiotaomicron starch-binding protein SusD, which is a major starch-binding protein present at the surface of the cell and mediates starch-binding before starch transport in the periplasm for degradation
starch binding outer membrane protein SusD; SusD-like proteins from Bacteroidetes, members of ...
38-510
2.46e-30
starch binding outer membrane protein SusD; SusD-like proteins from Bacteroidetes, members of the human distal gut microbiota, are part of the starch utilization system (Sus). Sus is one of the large clusters of glycosyl hydrolases, called polysaccharide utilization loci (PULs), which play an important role in polysaccharide recognition and uptake, and it is needed for growth on amylose, amylopectin, pullulan, and maltooligosaccharides. SusD, together with SusC, a predicted beta-barrel porin, forms the minimum outer-membrane starch-binding complex. The adult human distal gut microbiota is essential for digestion of a large variety of dietary polysaccharides, for which humans lack the necessary glycosyl hydrolases.
The actual alignment was detected with superfamily member cd08977:
Pssm-ID: 451378 [Multi-domain] Cd Length: 359 Bit Score: 122.14 E-value: 2.46e-30
starch binding outer membrane protein SusD; SusD-like proteins from Bacteroidetes, members of ...
38-510
2.46e-30
starch binding outer membrane protein SusD; SusD-like proteins from Bacteroidetes, members of the human distal gut microbiota, are part of the starch utilization system (Sus). Sus is one of the large clusters of glycosyl hydrolases, called polysaccharide utilization loci (PULs), which play an important role in polysaccharide recognition and uptake, and it is needed for growth on amylose, amylopectin, pullulan, and maltooligosaccharides. SusD, together with SusC, a predicted beta-barrel porin, forms the minimum outer-membrane starch-binding complex. The adult human distal gut microbiota is essential for digestion of a large variety of dietary polysaccharides, for which humans lack the necessary glycosyl hydrolases.
Pssm-ID: 185760 [Multi-domain] Cd Length: 359 Bit Score: 122.14 E-value: 2.46e-30
SusD family; This domain is found in bacterial cell surface proteins such SusD and SusD-like ...
286-586
5.53e-28
SusD family; This domain is found in bacterial cell surface proteins such SusD and SusD-like proteins as well RagB, outer membrane surface receptor antigen. Bacteroidetes, one of the two dominant bacterial phyla in the human gut, are Gram-negative saccharolytic microorganizms that utilize a diverse array of glycans. Hence, they express starch-utilization system (Sus) for glycan uptake. SusD has 551 amino acids, and is almost entirely alpha-helical, with 22 alpha-helices, eight of which form 4 tetra-trico peptide repeats (TPRs: helix-turn-helix motifs involved in protein-protein interactions). The four TPRs pack together to create a right-handed super-helix. This is predicted to mediate the formation of SusD and SusC porin complex at the cell surface. The interaction between SusC and TPR1/TPR2 region of SusD is predicted to be of functional importance since it allows SusD to be in position for oligosaccharide capture from other Sus lipoproteins and delivery of these glycans to the SusC porin. The non-TPR containing portion of SusD is where starch binding occurs. The binding site is a shallow surface cavity located on top of TPR1. SusD homologs such as SusD-like proteins have a critical role in carbohydrate acquisition. Both SusD and its homologs, contain 15-20 residues at the N-terminus that might be a flexible linker region, anchoring the protein to the membrane and the glycan-binding domain. Other homologs to SusD have been examined in Porphyromonas gingivalis such as RagB, an immunodominant outer-membrane surface receptor antigen. Structural characterization of RagB shows substantial similarity with Bacteroides thetaiotaomicron SusD (i.e alpha-helices and TPR regions). Based on this structural similarity, functional studies suggest that, RagB binding of glycans occurs at pockets on the molecular surface that are distinct from those of SusD.
Pssm-ID: 429768 Cd Length: 294 Bit Score: 113.74 E-value: 5.53e-28
starch binding outer membrane protein SusD; SusD-like proteins from Bacteroidetes, members of ...
38-510
2.46e-30
starch binding outer membrane protein SusD; SusD-like proteins from Bacteroidetes, members of the human distal gut microbiota, are part of the starch utilization system (Sus). Sus is one of the large clusters of glycosyl hydrolases, called polysaccharide utilization loci (PULs), which play an important role in polysaccharide recognition and uptake, and it is needed for growth on amylose, amylopectin, pullulan, and maltooligosaccharides. SusD, together with SusC, a predicted beta-barrel porin, forms the minimum outer-membrane starch-binding complex. The adult human distal gut microbiota is essential for digestion of a large variety of dietary polysaccharides, for which humans lack the necessary glycosyl hydrolases.
Pssm-ID: 185760 [Multi-domain] Cd Length: 359 Bit Score: 122.14 E-value: 2.46e-30
SusD family; This domain is found in bacterial cell surface proteins such SusD and SusD-like ...
286-586
5.53e-28
SusD family; This domain is found in bacterial cell surface proteins such SusD and SusD-like proteins as well RagB, outer membrane surface receptor antigen. Bacteroidetes, one of the two dominant bacterial phyla in the human gut, are Gram-negative saccharolytic microorganizms that utilize a diverse array of glycans. Hence, they express starch-utilization system (Sus) for glycan uptake. SusD has 551 amino acids, and is almost entirely alpha-helical, with 22 alpha-helices, eight of which form 4 tetra-trico peptide repeats (TPRs: helix-turn-helix motifs involved in protein-protein interactions). The four TPRs pack together to create a right-handed super-helix. This is predicted to mediate the formation of SusD and SusC porin complex at the cell surface. The interaction between SusC and TPR1/TPR2 region of SusD is predicted to be of functional importance since it allows SusD to be in position for oligosaccharide capture from other Sus lipoproteins and delivery of these glycans to the SusC porin. The non-TPR containing portion of SusD is where starch binding occurs. The binding site is a shallow surface cavity located on top of TPR1. SusD homologs such as SusD-like proteins have a critical role in carbohydrate acquisition. Both SusD and its homologs, contain 15-20 residues at the N-terminus that might be a flexible linker region, anchoring the protein to the membrane and the glycan-binding domain. Other homologs to SusD have been examined in Porphyromonas gingivalis such as RagB, an immunodominant outer-membrane surface receptor antigen. Structural characterization of RagB shows substantial similarity with Bacteroides thetaiotaomicron SusD (i.e alpha-helices and TPR regions). Based on this structural similarity, functional studies suggest that, RagB binding of glycans occurs at pockets on the molecular surface that are distinct from those of SusD.
Pssm-ID: 429768 Cd Length: 294 Bit Score: 113.74 E-value: 5.53e-28
Starch-binding associating with outer membrane; SusD is a secreted polysaccharide-binding ...
44-195
3.67e-13
Starch-binding associating with outer membrane; SusD is a secreted polysaccharide-binding protein with an N-terminal lipid moiety that allows it to associate with the outer membrane. SusD probably mediates xyloglucan-binding prior to xyloglucan transport in the periplasm for degradation. This domain is found N-terminal to pfam07980.
Pssm-ID: 405073 Cd Length: 185 Bit Score: 68.21 E-value: 3.67e-13
Starch-binding associating with outer membrane; SusD is a secreted starch-binding protein with ...
83-198
9.62e-05
Starch-binding associating with outer membrane; SusD is a secreted starch-binding protein with an N-terminal lipid tail that allows it to associate with the outer membrane.
Pssm-ID: 463695 Cd Length: 415 Bit Score: 45.08 E-value: 9.62e-05
Database: CDSEARCH/cdd Low complexity filter: no Composition Based Adjustment: yes E-value threshold: 0.01
References:
Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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