Summary: PilZ domain
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PilZ domain Edit Wikipedia article
the solution NMR structure of the protein of unknown function vca0042 from vibrio cholerae o1
The PilZ protein family is named after the type IV pilus control protein first identified in Pseudomonas aeruginosa, expressed as part of the pil operon. It has a cytoplasmic location and is essential for type IV fimbrial, or pilus, biogenesis. PilZ is a c-di-GMP binding domain and PilZ domain-containing proteins represent the best studied class of c-di-GMP effectors. C-di-GMP, cyclic diguanosine monophosphate, the second messenger in cells, is widespread in and unique to the bacterial kingdom. Elevated intracellular levels of c-di-GMP generally cause bacteria to change from a motile single-cell state to a sessile, adhesive surface-attached multicellular state called biofilm.
Proteins which contain PilZ are known to interact with the flagellar switch-complex proteins FliG and FliM and this is mediated via the c-di-GMP-PliZ complex. This interaction results in a reduction of torque-generation and induces counterclockwise motor bias that slows the motor and induces counterclockwise rotation, inhibiting chemotaxis.
Binding and mutagenesis studies of several PilZ domain proteins have shown that c-di-GMP binding depends on residues in RxxxR and D/NxSxxG sequence-motifs. The crystal structure, at 1.7 A, of a PilZ domain::c-di-GMP complex from Vibrio cholerae shows c-di-GMP contacting seven of nine strongly conserved residues. Binding of c-di-GMP causes a conformational switch whereby the C- and N-terminal domains are brought into close opposition forming a new allosteric interaction surface that spans these domains and the c-di-GMP at their interface.
- Alm RA, Bodero AJ, Free PD, Mattick JS (January 1996). "Identification of a novel gene, pilZ, essential for type 4 fimbrial biogenesis in Pseudomonas aeruginosa". J. Bacteriol. 178 (1): 46â€“53. PMC 177619. PMID 8550441.
- Ryjenkov, DA; Simm, R; RÃ¶mling, U; Gomelsky, M (Oct 13, 2006). "The PilZ domain is a receptor for the second messenger c-di-GMP: the PilZ domain protein YcgR controls motility in enterobacteria". The Journal of Biological Chemistry. 281 (41): 30310â€“4. doi:10.1074/jbc.C600179200. PMID 16920715.
- Amikam, D; Galperin, MY (Jan 1, 2006). "PilZ domain is part of the bacterial c-di-GMP binding protein". Bioinformatics. 22 (1): 3â€“6. doi:10.1093/bioinformatics/bti739. PMID 16249258.
- Mattick, JS (2002). "Type IV pili and twitching motility". Annual Review of Microbiology. 56: 289â€“314. doi:10.1146/annurev.micro.56.012302.160938. PMID 12142488.
- Wolfe, AJ; Visick, KL (Jan 2008). "Get the message out: cyclic-Di-GMP regulates multiple levels of flagellum-based motility". Journal of Bacteriology. 190 (2): 463â€“75. doi:10.1128/JB.01418-07. PMC 2223684. PMID 17993515.
- Paul, K; Nieto, V; Carlquist, WC; Blair, DF; Harshey, RM (Apr 9, 2010). "The c-di-GMP binding protein YcgR controls flagellar motor direction and speed to affect chemotaxis by a "backstop brake" mechanism". Molecular Cell. 38 (1): 128â€“39. doi:10.1016/j.molcel.2010.03.001. PMC 2929022. PMID 20346719.
- Benach, J; Swaminathan, SS; Tamayo, R; Handelman, SK; Folta-Stogniew, E; Ramos, JE; Forouhar, F; Neely, H; Seetharaman, J; Camilli, A; Hunt, JF (Dec 12, 2007). "The structural basis of cyclic diguanylate signal transduction by PilZ domains". The EMBO Journal. 26 (24): 5153â€“66. doi:10.1038/sj.emboj.7601918. PMC 2140105. PMID 18034161.
- Pitzer, JE; Sultan, SZ; Hayakawa, Y; Hobbs, G; Miller, MR; Motaleb, MA (May 2011). "Analysis of the Borrelia burgdorferi cyclic-di-GMP-binding protein PlzA reveals a role in motility and virulence". Infection and Immunity. 79 (5): 1815â€“25. doi:10.1128/IAI.00075-11. PMC 3088147. PMID 21357718.
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PilZ domain Provide feedback
PilZ is a c-di-GMP binding domain  which is found C terminal to PF07317. Proteins which contain PilZ are known to interact with the flagellar switch-complex proteins FliG and FliM. This interaction results in a reduction of torque generation and induces CCW motor bias . This domain forms a beta barrel structure.
Alm RA, Bodero AJ, Free PD, Mattick JS; , J Bacteriol 1996;178:46-53.: Identification of a novel gene, pilZ, essential for type 4 fimbrial biogenesis in Pseudomonas aeruginosa. PUBMED:8550441 EPMC:8550441
Ryjenkov DA, Simm R, Romling U, Gomelsky M;, J Biol Chem. 2006;281:30310-30314.: The PilZ domain is a receptor for the second messenger c-di-GMP: the PilZ domain protein YcgR controls motility in enterobacteria. PUBMED:16920715 EPMC:16920715
Benach J, Swaminathan SS, Tamayo R, Handelman SK, Folta-Stogniew E, Ramos JE, Forouhar F, Neely H, Seetharaman J, Camilli A, Hunt JF;, EMBO J. 2007;26:5153-5166.: The structural basis of cyclic diguanylate signal transduction by PilZ domains. PUBMED:18034161 EPMC:18034161
Paul K, Nieto V, Carlquist WC, Blair DF, Harshey RM;, Mol Cell. 2010;38:128-139.: The c-di-GMP binding protein YcgR controls flagellar motor direction and speed to affect chemotaxis by a "backstop brake" mechanism. PUBMED:20346719 EPMC:20346719
Internal database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR009875
The ubiquitous bacterial second messenger cyclic-di-GMP (c-di-GMP) is associated with the regulation of biofilm formation, the control of exopolysaccharide synthesis, flagellar- and pili-based motility, gene expression, interactions of bacteria with eukaryotic hosts and multicellular behaviour in diverse bacteria.
With the exception of bacterial cellulose synthases, the identities of c-di-GMP receptors and end targets of the proteins having one or more PilZ domains are mostly uncharacterised. However it was suggested that the PilZ domains present in the BcsA subunits of bacterial cellulose synthases function in c-di-GMP binding [ PUBMED:16249258 ]. More recently YcgR (see INTERPRO ) was found to bind c-di-GMP tightly and specifically; also isolated PilZ domains from YcgR and BcsA bound c-di-GMP indicating that the PilZ domain was sufficient for binding of c-di-GMP and significantly that site-directed mutagenesis performed on YcgR implicated the most conserved residues in the PilZ domain directly in c-di-GMP binding [ PUBMED:16920715 ]. It was suggested that c-di-GMP binding to PilZ brings about conformational changes in the protein that stabilise the bound ligand and probability initiates the downstream signal transduction cascade. In the case of YcgR, c-di-GMP binding regulates flagellum-based motility in a c-di-GMP-dependent manner (see INTERPRO ) [ PUBMED:16920715 ]. The association of the PilZ domain with a variety of other domains, including likely components of bacterial multidrug secretion system, could provide clues to multiple functions of the c-di-GMP in bacterial pathogenesis and cell development.
Binding and mutagenesis studies of several PilZ domain proteins have confirmed this observation and demonstrated that c-di-GMP binding depends on residues in RxxxR and D/NxSxxG sequence motifs. The crystal structure, at 1.7 A, of a PilZ domain::c-di-GMP complex from Vibrio cholerae shows c-di-GMP contacting seven of nine strongly conserved residues. Binding of c-di-GMP causes a conformational switch whereby the C- and N-terminal domains are brought into close opposition forming a new allosteric interaction surface that spans these domains and the c-di-GMP at their interface [ PUBMED:18034161 ].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||cyclic-di-GMP binding (GO:0035438)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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|Seed source:||Pfam-B_17421 (release 10.0)|
|Author:||Bateman A , Galperin MY|
|Number in seed:||190|
|Number in full:||13357|
|Average length of the domain:||100.50 aa|
|Average identity of full alignment:||16 %|
|Average coverage of the sequence by the domain:||40.16 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||16|
|Download:||download the raw HMM for this family|
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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 PilZ domain has been found. There are 44 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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