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29  structures 15  species 0  interactions 21  sequences 3  architectures

Family: TbpB_A (PF17484)

Summary: N-Lobe handle Tf-binding protein B

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N-Lobe handle 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]. The 4-residue conserved LSAC motif found at the amino terminus of TbpB represents a prototypical lipobox, with the cysteine residue serving as the first amino acid in the mature protein which is subsequently modified by the addition of a diacyl glycerol. A second conserved motif of interest is located two amino acids downstream of the LSAC site. This region consists of four glycine residues in tandem. Deletion of the conserved polyglycine motif has significant negative effects on growth in certain conditions, while mutational analysis revealed that the LSAC motif constituting the lipobox of TbpB is necessary for lipidation and hence tethering of TbpB to the bacterial surface [4]. This domain family is found on the N-terminal region of TbpB proteins, which comprises the N lobe handle consisting of a four-stranded antiparallel beta sheets held together by a short surface-exposed alpha helix. Tf-binding activity primarily resides in the TbpB N lobe [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

  4. Ostberg KL, DeRocco AJ, Mistry SD, Dickinson MK, Cornelissen CN;, Infect Immun. 2013;81:3442-3450.: Conserved regions of gonococcal TbpB are critical for surface exposure and transferrin iron utilization. PUBMED:23836816 EPMC:23836816


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Domain organisation

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(15)
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RP75
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  Seed
(15)
Full
(21)
Representative proteomes UniProt
(528)
NCBI
(1307)
Meta
(0)
RP15
(5)
RP35
(9)
RP55
(21)
RP75
(53)
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  Seed
(15)
Full
(21)
Representative proteomes UniProt
(528)
NCBI
(1307)
Meta
(0)
RP15
(5)
RP35
(9)
RP55
(21)
RP75
(53)
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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

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This family is new in this Pfam release.

Seed source: Pfam-B_893 (release 3.0)
Previous IDs: Domain_A_TbpB;
Type: Domain
Author: Finn RD, Bateman A, El-Gebali S
Number in seed: 15
Number in full: 21
Average length of the domain: 136.00 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 21.47 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild --amino -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 33.4 31.0
Noise cut-off 20.2 21.6
Model length: 135
Family (HMM) version: 1
Download: download the raw HMM for this family

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence

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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 TbpB_A domain has been found. There are 29 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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