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46  structures 370  species 3  interactions 7941  sequences 17  architectures

Family: SusD_RagB (PF07980)

Summary: SusD family

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SusD family Provide feedback

This domain is found in bacterial cell surface proteins such SusD Q8A1G2 and SusD-like proteins A7LXT5 as as well RagB, outer membrane surface receptor antigen. Bacteroidetes, one of the two dominant bacterial phyla in the human gut, are Gram-negative saccharolytic microorganisms 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 α-helical, with 22 α-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 [1]. 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 α-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 [2].

Literature references

  1. Bolam DN, Koropatkin NM;, Curr Opin Struct Biol. 2012;22:563-569.: Glycan recognition by the Bacteroidetes Sus-like systems. PUBMED:22819666 EPMC:22819666

  2. Goulas T, Ferrer IG, Hutcherson JA, Potempa BA, Potempa J, Scott DA, Gomis-Ruth FX;, Mol Oral Microbiol. 2015; [Epub ahead of print]: Structure of RagB, a major immunodominant outer-membrane surface receptor antigen of Porphyromonas gingivalis. PUBMED:26441291 EPMC:26441291


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR012944

This domain occurs in several hypothetical proteins. It also occurs in RagB, SWISSPROT, a protein involved in signalling [PUBMED:7499430] and SusD, SWISSPROT, an outer membrane protein involved in nutrient binding [PUBMED:11717282].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(57)
Full
(7941)
Representative proteomes UniProt
(23474)
NCBI
(35183)
Meta
(720)
RP15
(839)
RP35
(3858)
RP55
(8382)
RP75
(15066)
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PP/heatmap 1                

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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Format an alignment

  Seed
(57)
Full
(7941)
Representative proteomes UniProt
(23474)
NCBI
(35183)
Meta
(720)
RP15
(839)
RP35
(3858)
RP55
(8382)
RP75
(15066)
Alignment:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(57)
Full
(7941)
Representative proteomes UniProt
(23474)
NCBI
(35183)
Meta
(720)
RP15
(839)
RP35
(3858)
RP55
(8382)
RP75
(15066)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_1855 (release 16.0)
Previous IDs: SusD_RagB; SusD;
Type: Domain
Author: Mistry J, Bateman A. El-Gebali S
Number in seed: 57
Number in full: 7941
Average length of the domain: 257.40 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 48.28 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.2 20.2
Trusted cut-off 20.2 20.2
Noise cut-off 20.1 20.1
Model length: 298
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
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Viroids Viroids Unclassified sequence Unclassified sequence

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Interactions

There are 3 interactions for this family. More...

SusD-like_3 SusD_RagB SusD-like_3

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the SusD_RagB domain has been found. There are 46 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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