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56  structures 206  species 3  interactions 462  sequences 13  architectures

Family: TbpB_B_D (PF01298)

Summary: C-lobe and N-lobe beta barrels of Tf-binding protein B

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C-lobe and N-lobe beta barrels of Tf-binding protein B Provide feedback

Bacterial lipoproteins represent a large group of specialized membrane proteins that perform a variety of functions including maintenance and stabilization of the cell envelope, protein targeting and transit to the outer membrane, membrane biogenesis, and cell adherence [1]. Pathogenic Gram-negative bacteria within the Neisseriaceae and Pasteurellaceae families rely on a specialized uptake system, characterized by an essential surface receptor complex that acquires iron from host transferrin (Tf) and transports the iron across the outer membrane. They have an iron uptake system composed of surface exposed lipoprotein, Tf-binding protein B (TbpB), and an integral outer-membrane protein, Tf-binding protein A (TbpA), that together function to extract iron from the host iron binding glycoprotein (Tf). TbpB is a bilobed (N and C lobe) lipid-anchored protein with each lobe consisting of an eight-stranded beta barrel flanked by a “handle” domain made up of four (N lobe) or eight (C lobe) beta strands [2]. TbpB extends from the outer membrane surface by virtue of an N-terminal peptide region that is anchored to the outer membrane by fatty acyl chains on the N-terminal cysteine and is involved in the initial capture of iron-loaded Tf [3]. This domain family is found in C and N lobe eight stranded beta barrel region of TbpB proteins. The eight-stranded barrel domains in N and C lobe draw comparisons to eight-stranded beta barrel outer-membrane protein W (OmpW). However, the barrel domains of TbpB have the hydrophobic residues line the inner surface of the beta barrels to create a stable hydrophobic core [2].

Literature references

  1. Vanini MM, Spisni A, Sforca ML, Pertinhez TA, Benedetti CE;, Proteins. 2008;71:2051-2064.: The solution structure of the outer membrane lipoprotein OmlA from Xanthomonas axonopodis pv. citri reveals a protein fold implicated in protein-protein interaction. PUBMED:18186471 EPMC:18186471

  2. Moraes TF, Yu RH, Strynadka NC, Schryvers AB;, Mol Cell. 2009;35:523-533.: Insights into the bacterial transferrin receptor: the structure of transferrin-binding protein B from Actinobacillus pleuropneumoniae. PUBMED:19716795 EPMC:19716795

  3. Adamiak P, Calmettes C, Moraes TF, Schryvers AB;, Microbiologyopen. 2015;4:491-504.: Patterns of structural and sequence variation within isotype lineages of the Neisseria meningitidis transferrin receptor system. PUBMED:25800619 EPMC:25800619


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001677

Bacterial lipoproteins represent a large group of specialized membrane proteins that perform a variety of functions including maintenance and stabilization of the cell envelope, protein targeting and transit to the outer membrane, membrane biogenesis, and cell adherence [PUBMED:18186471]. Pathogenic Gram-negative bacteria within the Neisseriaceae and Pasteurellaceae families rely on a specialized uptake system, characterized by an essential surface receptor complex that acquires iron from host transferrin (Tf) and transports the iron across the outer membrane. They have an iron uptake system composed of surface exposed lipoprotein, Tf-binding protein B (TbpB), and an integral outer-membrane protein, Tf-binding protein A (TbpA), that together function to extract iron from the host iron binding glycoprotein (Tf).

TbpB is a bilobed (N and C lobe) lipid-anchored protein with each lobe consisting of an eight-stranded beta barrel flanked by a 'handle' domain made up of four (N lobe) or eight (C lobe) beta strands [PUBMED:19716795]. TbpB extends from the outer membrane surface by virtue of an N-terminal peptide region that is anchored to the outer membrane by fatty acyl chains on the N-terminal cysteine and is involved in the initial capture of iron-loaded Tf [PUBMED:25800619]. This domain family is found in C and N lobe eight stranded beta barrel region of TbpB proteins. The eight-stranded barrel domains in N and C lobe draw comparisons to eight-stranded beta barrel outer-membrane protein W (OmpW). However, the barrel domains of TbpB have the hydrophobic residues line the inner surface of the beta barrels to create a stable hydrophobic core [PUBMED:19716795].

Domain organisation

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Alignments

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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
(83)
Full
(462)
Representative proteomes UniProt
(2312)
NCBI
(6210)
Meta
(15)
RP15
(75)
RP35
(238)
RP55
(427)
RP75
(720)
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  Seed
(83)
Full
(462)
Representative proteomes UniProt
(2312)
NCBI
(6210)
Meta
(15)
RP15
(75)
RP35
(238)
RP55
(427)
RP75
(720)
Alignment:
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Sequence:
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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
(83)
Full
(462)
Representative proteomes UniProt
(2312)
NCBI
(6210)
Meta
(15)
RP15
(75)
RP35
(238)
RP55
(427)
RP75
(720)
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

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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_893 (release 3.0)
Previous IDs: Lipoprotein_5; Domain_D_TbpB; Domain_B_D_TbpB;
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD , Bateman A , El-Gebali S
Number in seed: 83
Number in full: 462
Average length of the domain: 136.40 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 40.75 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild --amino -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.0 26.0
Trusted cut-off 26.0 26.0
Noise cut-off 25.9 25.9
Model length: 136
Family (HMM) version: 18
Download: download the raw HMM for this family

Species distribution

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

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Interactions

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

TbpB_B_D Transferrin Transferrin

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 TbpB_B_D domain has been found. There are 56 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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