Summary: ZinT (YodA) periplasmic lipocalin-like zinc-recruitment
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ZinT (YodA) periplasmic lipocalin-like zinc-recruitment Provide feedback
ZinT plays a critical role in recruiting periplasmic zinc to the bacterial zinc-uptake complex ZnuABC, consisting of families PF01297 PF00005 regulated by the transcription-regulator FUR, PF01475 [2,3]. ZinT acts as a Zn2+-buffering protein that delivers Zn2+ to ZnuA (TroA), PF01297 . Members of this family of prokaryotic domains were first identified as part of the response of bacteria to a challenge with the toxic heavy metal cadmium. They are able to bind to cadmium, and ensure its subsequent elimination .
Gabbianelli R, Scotti R, Ammendola S, Petrarca P, Nicolini L, Battistoni A;, BMC Microbiol. 2011;11:36.: Role of ZnuABC and ZinT in Escherichia coli O157:H7 zinc acquisition and interaction with epithelial cells. PUBMED:21338480 EPMC:21338480
Ilari A, Alaleona F, Tria G, Petrarca P, Battistoni A, Zamparelli C, Verzili D, Falconi M, Chiancone E;, Biochim Biophys Acta. 2014;1840:535-544.: The Salmonella enterica ZinT structure, zinc affinity and interaction with the high-affinity uptake protein ZnuA provide insight into the management of periplasmic zinc. PUBMED:24128931 EPMC:24128931
Internal database links
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR015304
This domain is found in prokaryotic proteins that were first identified as part of the response of bacteria to a challenge with the toxic heavy metal cadmium. They are able to bind to cadmium and ensure its subsequent elimination [ PUBMED:12909634 ]. Previously known YodA, these proteins have been renamed as ZinT, and have been shown to bind zinc with high affinity. They may play a role in zinc homeostasis and growth under zinc limited conditions [ PUBMED:17931600 ].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||zinc ion binding (GO:0008270)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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The calycin structural superfamily [1-3] includes the lipocalins, the fatty acid-binding proteins (FABPs).
The clan contains the following 44 members:ApoM Calycin_like CpeS CpeT CrtC DUF1579 DUF1934 DUF2147 DUF3255 DUF3598 DUF3642 DUF3833 DUF4166 DUF4488 DUF4822 DUF4847 DUF4923 DUF5004 DUF5640 GH43_C His_binding Lipocalin Lipocalin_2 Lipocalin_3 Lipocalin_4 Lipocalin_5 Lipocalin_7 Lipocalin_8 Lipocalin_9 Luciferase_cat META MoaF MoaF_C MxiM Nitrophorin NlpE PA_decarbox Pallilysin Svf1 Svf1_C THAP4_heme-bd Triabin VDE ZinT
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
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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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|Author:||Sammut SJ , Bateman A|
|Number in seed:||34|
|Number in full:||490|
|Average length of the domain:||175.30 aa|
|Average identity of full alignment:||43 %|
|Average coverage of the sequence by the domain:||55.20 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||14|
|Download:||download the raw HMM for this family|
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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 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.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
Colouring and labels
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.
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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.
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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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The tree shows the occurrence of this domain across different species. More...
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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.
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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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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 ZinT domain has been found. There are 15 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.
Loading structure mapping...
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|
|P76344||View 3D Structure||Click here|
|Q2G1U8||View 3D Structure||Click here|