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15  structures 404  species 0  interactions 490  sequences 11  architectures

Family: ZinT (PF09223)

Summary: ZinT (YodA) periplasmic lipocalin-like zinc-recruitment

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This is the Wikipedia entry entitled "YodA domain". More...

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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 [4]. 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 [1].

Literature references

  1. David G, Blondeau K, Schiltz M, Penel S, Lewit-Bentley A; , J Biol Chem. 2003;278:43728-43735.: YodA from Escherichia coli is a metal-binding, lipocalin-like protein. PUBMED:12909634 EPMC:12909634

  2. Kershaw CJ, Brown NL, Hobman JL;, Biochem Biophys Res Commun. 2007;364:66-71.: Zinc dependence of zinT (yodA) mutants and binding of zinc, cadmium and mercury by ZinT. PUBMED:17931600 EPMC:17931600

  3. 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

  4. 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 ].

Gene Ontology

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Domain organisation

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

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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...

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You can also download a FASTA format file containing the full-length sequences for all sequences in the full 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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Seed source: pdb_1oej
Previous IDs: YodA;
Type: Domain
Sequence Ontology: SO:0000417
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 information View help on HMM parameters

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 27.0 27.0
Trusted cut-off 27.0 27.7
Noise cut-off 26.9 26.6
Model length: 181
Family (HMM) version: 14
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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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.

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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
P76344 View 3D Structure Click here
Q2G1U8 View 3D Structure Click here