Summary: C-terminus of bacterial fibrinogen-binding adhesin

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Wikipedia: SdrG C terminal protein domain
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SdrG C terminal protein domain Edit Wikipedia article

SdrG_C_C

crystal structure analysis of s.epidermidis adhesin sdrg binding to fibrinogen (adhesin-ligand complex)

Identifiers

Symbol

SdrG_C_C

Available protein structures:
Pfam Â	structures / ECOD Â
PDB	RCSB PDB; PDBe; PDBj
PDBsum	structure summary

This entry represents the fibrinogen-binding domain from bacterial proteins such as fibrinogen-binding adhesion SdrG and clumping factor A. In both SdrG and clumping factor A, there are two fibrinogen-binding domains with similar core beta-sandwich topologies, but with different modulations in their structure. This entry represents the second domain, while INTERPRO represents the first domain.

Gram-positive pathogens, such as Staphylococci, Streptococci, and Enterococci, contain multiple cell wall-anchored proteins. Some of these proteins act as adhesins and mediate bacterial attachment to host tissues through lock-and-interactions with host ligands, such as fibrinogen, a glycoprotein found in blood plasma that plays a key role in haemostasis and coagulation. For pathogenic bacteria that do not invade host cells, extracellular matrix proteins are preferred targets for bacterial adhesion; adhesins mediating these interactions have been termed MSCRAMMs (microbial surface components recognizing adhesive matrix molecules). A common binding domain organisation found within MSCRAMMs suggests a common ancestry. Both fibrinogen-binding adhesion SdrG and clumping factor A are MSCRAMMs.

Fibrinogen-binding adhesion SdrG is a cell wall-anchored adhesion found in the Gram-positive pathogen Mycobacterium farcinogenes that binds to the B-beta chain of human fibrinogen.^[1] SdrG allows attachment of the bacterium to host tissues via specific binding to the beta-chain of human fibrinogen (Fg). SdrG binds to its ligand with a dynamic "dock lock, and latch" mechanism which represents a general mode of ligand-binding for structurally related cell wall-anchored proteins in most Gram-positive bacteria. The C-terminal part of SdrG(276-596) is integral to the folding of the immunoglobulin-like whole to create the docking grooves necessary for Fg binding.^[1] Clumping factor A performs a similar function in Staphylococcus aureus by binding the gamma chain of fibrinogen.^[2]

References

^ ^a ^b Ponnuraj K, Bowden MG, Davis S, Gurusiddappa S, Moore D, Choe D, Xu Y, Hook M, Narayana SV (2003). "A "dock, lock, and latch" structural model for a staphylococcal adhesin binding to fibrinogen". Cell. 115 (2): 217â€“28. PMIDÂ 14567919. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
^ Deivanayagam CC, Wann ER, Chen W, Carson M, Rajashankar KR, HÃƒÂ¶ÃƒÂ¶k M, Narayana SV (2002). "A novel variant of the immunoglobulin fold in surface adhesins of Staphylococcus aureus: crystal structure of the fibrinogen-binding MSCRAMM, clumping factor A". EMBO J. 21 (24): 6660â€“72. PMCÂ 139082. PMIDÂ 12485987. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)

This article incorporates text from the public domain Pfam and InterPro: IPR011266

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

C-terminus of bacterial fibrinogen-binding adhesin Provide feedback

This is the C-terminal half of a bacterial fibrinogen-binding adhesin SdrG. SdrG is a Gram-positive cell-wall-anchored adhesin that allows attachment of the bacterium to host tissues via specific binding to the beta-chain of human fibrinogen (Fg). SdrG binds to its ligand with a dynamic "dock, lock, and latch" mechanism which represents a general mode of ligand-binding for structurally related cell wall-anchored proteins in most Gram-positive bacteria. The C-terminal part of SdrG(276-596) is integral to the folding of the immunoglobulin-like whole to create the docking grooves necessary for Fg binding. The domain is associated with families of Cna_B, PF05738 [1].

Literature references

Ponnuraj K, Bowden MG, Davis S, Gurusiddappa S, Moore D, Choe D, Xu Y, Hook M, Narayana SV; , Cell. 2003;115:217-228.: A "dock, lock, and latch" structural model for a staphylococcal adhesin binding to fibrinogen. PUBMED:14567919 EPMC:14567919

This tab holds annotation information from the InterPro database.

InterPro entry IPR011266

This entry represents the fibrinogen-binding domain from bacterial proteins such as fibrinogen-binding adhesion SdrG and clumping factor A. In both SdrG and clumping factor A, there are two fibrinogen-binding domains with similar core beta-sandwich topologies, but with different modulations in their structure. This entry represents the second domain, while INTERPRO represents the first domain.

Gram-positive pathogens, such as Staphylococci, Streptococci, and Enterococci, contain multiple cell wall-anchored proteins. Some of these proteins act as adhesins and mediate bacterial attachment to host tissues through lock-and-interactions with host ligands, such as fibrinogen, a glycoprotein found in blood plasma that plays a key role in haemostasis and coagulation. For pathogenic bacteria that do not invade host cells, extracellular matrix proteins are preferred targets for bacterial adhesion; adhesins mediating these interactions have been termed MSCRAMMs (microbial surface components recognizing adhesive matrix molecules). A common binding domain organisation found within MSCRAMMs suggests a common ancestry. Both fibrinogen-binding adhesion SdrG and clumping factor A are MSCRAMMs.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Cellular component	cell wall (GO:0005618)
Biological process	cell adhesion (GO:0007155)

Domain organisation

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

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Pfam Clan

This family is a member of clan Adhesin (CL0204), which has the following description:

This superfamily includes a variety of bacterial adhesins that have a jelly-roll beta-barrel fold [1]. These domains are involved in sugar recognition.

The clan contains the following 17 members:

Adhesin_Dr AfaD AgI_II_C2 Antig_Caf1 Antigen_C Collagen_bind DUF1120 Fim-adh_lectin FimA Fimbrial FimH_man-bind GramPos_pilinBB PapG_N Saf-Nte_pilin SCPU SdrG_C_C Sgo0707_N2

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 and the UniProtKB sequence database. More...

There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.

Alignment types

We make a range of alignments for each Pfam-A family:

seed: the curated alignment from which the HMM for the family is built
full: the alignment generated by searching the sequence database using the HMM
RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
UniProt: alignment generated by searching the UniProtKB sequence database using the family HMM

Viewing

You can see the alignments as HTML or in three different sequence viewers:

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PP/Heatmap: an HTML-based representation of the alignment, coloured according to the posterior-probability (PP) values from the HMM. As for the standard HTML view, heatmap alignments can also be very large and slow to render.

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You can download (or view in your browser) a text representation of a Pfam alignment in various formats:

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Downloading

You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.

View options

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 (10)	Full (52)	Representative proteomes				UniProt (1766)
	Seed (10)	Full (52)	RP15 (16)	RP35 (28)	RP55 (49)	RP75 (121)	UniProt (1766)
Jalview	View	View	View	View	View	View	View
HTML	View	View
PP/heatmap	₁	View

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

Key: available, not generated, — not available.

Format an alignment

	Seed (10)	Full (52)	Representative proteomes				UniProt (1766)
	Seed (10)	Full (52)	RP15 (16)	RP35 (28)	RP55 (49)	RP75 (121)	UniProt (1766)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

Download options

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 (10)	Full (52)	Representative proteomes				UniProt (1766)
	Seed (10)	Full (52)	RP15 (16)	RP35 (28)	RP55 (49)	RP75 (121)	UniProt (1766)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download
Gzipped	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.

Note: You can also download the data file for the tree.

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

Seed source:

Gene3D, pdb_1r17

Previous IDs:

none

Type:

Domain

Sequence Ontology:

SO:0000417

Author:

Finn RD

, Coggill P

Number in seed:

10

Number in full:

52

Average length of the domain:

151.4 aa

Average identity of full alignment:

18 %

Average coverage of the sequence by the domain:

10.21 %

HMM information

HMM build commands:

build method: hmmbuild -o /dev/null HMM SEED

search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	24.4	24.4
Trusted cut-off	24.4	24.4
Noise cut-off	22.6	21.8

Model length:

156

Family (HMM) version:

12

Download:

download the raw HMM for this family

Species distribution

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Colour assignments

Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.

How the sunburst is generated

The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.

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Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.

As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.

Anomalies in the taxonomy tree

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Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.

Unmapped species names

The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.

So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".

Sub-species

Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.

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Species trees

We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.

Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.

If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.

Interactive tree

For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.

We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.

Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.

We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.

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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 SdrG_C_C domain has been found. There are 43 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 sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein	Predicted structure	External Information
P14738	View 3D Structure	Click here
Q2FUY2	View 3D Structure	Click here
Q2G015	View 3D Structure	Click here
Q2G0L4	View 3D Structure	Click here
Q2G0L5	View 3D Structure	Click here
Q2G1T5	View 3D Structure	Click here

Showing 6 matches

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Family: SdrG_C_C (PF10425)

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