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25  structures 595  species 0  interactions 1056  sequences 12  architectures

Family: Zn_dep_PLPC (PF00882)

Summary: Zinc dependent phospholipase C

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This is the Wikipedia entry entitled "Zinc-dependent phospholipase C". More...

Zinc-dependent phospholipase C Edit Wikipedia article

Zinc dependent phospholipase C
1olp opm.png
Alpha toxin of Clostridium showing the zinc dependent phospholipase domain in red and the PLAT domain in yellow
Identifiers
Symbol Zn_dep_PLPC
Pfam PF00882
InterPro IPR001531
PROSITE PDOC00357
SCOP 1ah7
SUPERFAMILY 1ah7
OPM superfamily 88
OPM protein 1olp
CDD cd11009

In molecular biology Zinc-dependent phospholipases C is a family of bacterial phospholipases C enzymes, some of which are also known as alpha toxins.

Bacillus cereus contains a monomeric phospholipase C EC 3.1.4.3 (PLC) of 245 amino-acid residues. Although PLC prefers to act on phosphatidylcholine, it also shows weak catalytic activity with sphingomyelin and phosphatidylinositol.[1] Sequence studies have shown the protein to be similar both to alpha toxin from Clostridium perfringens and Clostridium bifermentans, a phospholipase C involved in haemolysis and cell rupture,[2] and to lecithinase from Listeria monocytogenes, which aids cell-to-cell spread by breaking down the 2-membrane vacuoles that surround the bacterium during transfer.[3]

Each of these proteins is a zinc-dependent enzyme, binding 3 zinc ions per molecule.[4] The enzymes catalyse the conversion of phosphatidylcholine and water to 1,2-diacylglycerol and choline phosphate.[1][2][4]

In Bacillus cereus, there are nine residues known to be involved in binding the zinc ions: 5 His, 2 Asp, 1 Glu and 1 Trp. These residues are all conserved in the Clostridium alpha-toxin.

Some examples of this enzyme contain a C-terminal sequence extension that contains a PLAT domain which is thought to be involved in membrane localisation.[5][6]

References

  1. ^ a b Nakamura S, Yamada A, Tsukagoshi N, Udaka S, Sasaki T, Makino S, Little C, Tomita M, Ikezawa H (1988). "Nucleotide sequence and expression in Escherichia coli of the gene coding for sphingomyelinase of Bacillus cereus". Eur. J. Biochem. 175 (2): 213–220. doi:10.1111/j.1432-1033.1988.tb14186.x. PMID 2841128. 
  2. ^ a b Titball RW, Rubidge T, Hunter SE, Martin KL, Morris BC, Shuttleworth AD, Anderson DW, Kelly DC (1989). "Molecular cloning and nucleotide sequence of the alpha-toxin (phospholipase C) of Clostridium perfringens". Infect. Immun. 57 (2): 367–376. PMC 313106. PMID 2536355. 
  3. ^ Kocks C, Dramsi S, Ohayon H, Geoffroy C, Mengaud J, Cossart P, Vazquez-Boland JA (1992). "Nucleotide sequence of the lecithinase operon of Listeria monocytogenes and possible role of lecithinase in cell-to-cell spread". Infect. Immun. 60 (1): 219–230. PMC 257526. PMID 1309513. 
  4. ^ a b Titball RW, Rubidge T (1990). "The role of histidine residues in the alpha toxin of Clostridium perfringens". FEMS Microbiol. Lett. 56 (3): 261–265. doi:10.1111/j.1574-6968.1988.tb03188.x. PMID 2111259. 
  5. ^ Bateman A, Sandford R (1999). "The PLAT domain: a new piece in the PKD1 puzzle". Curr. Biol. 9 (16): –. doi:10.1016/S0960-9822(99)80380-7. PMID 10469604. 
  6. ^ Ponting CP, Hofmann K, Bork P (August 1999). "A latrophilin/CL-1-like GPS domain in polycystin-1". Curr. Biol. 9 (16): R585–8. doi:10.1016/S0960-9822(99)80379-0. PMID 10469603. 

This article incorporates text from the public domain Pfam and InterPro IPR001531


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Zinc dependent phospholipase C Provide feedback

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Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR008947

The enzymes belonging to this family are involved in phosphate ester hydrolysis and contain a triad of closely spaced zinc ions at their active centres. Both families of enzymes hydrolyse phosphodiesters. Substrates for phospholipase C are phosphatidylinositol and phosphatidylcholine, while P1 nuclease is an endonuclease hydrolysing single stranded ribo- and deoxyribonucleotides. P1 nuclease also has activity as a phosphomonoesterase against 3'-terminal phosphates of nucleotides. The Zn ions in both enzymes form almost identical trinuclear sites [PUBMED:1525473].

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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Pfam Clan

This family is a member of clan PhosC-NucP1 (CL0368), which has the following description:

This superfamily includes the Phospholipase C and P1-nuclease families.

The clan contains the following 5 members:

DUF2227 DUF4184 DUF457 S1-P1_nuclease Zn_dep_PLPC

Alignments

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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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
(152)
Full
(1056)
Representative proteomes NCBI
(1095)
Meta
(36)
RP15
(119)
RP35
(194)
RP55
(221)
RP75
(245)
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Format an alignment

  Seed
(152)
Full
(1056)
Representative proteomes NCBI
(1095)
Meta
(36)
RP15
(119)
RP35
(194)
RP55
(221)
RP75
(245)
Alignment:
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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
(152)
Full
(1056)
Representative proteomes NCBI
(1095)
Meta
(36)
RP15
(119)
RP35
(194)
RP55
(221)
RP75
(245)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

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.

Note: You can also download the data file for the tree.

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_1401 (release 3.0)
Previous IDs: none
Type: Domain
Author: Bateman A
Number in seed: 152
Number in full: 1056
Average length of the domain: 178.70 aa
Average identity of full alignment: 16 %
Average coverage of the sequence by the domain: 56.63 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild --amino -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.6 21.6
Trusted cut-off 21.6 21.6
Noise cut-off 21.5 21.5
Model length: 164
Family (HMM) version: 13
Download: download the raw HMM for this family

Species distribution

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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 Zn_dep_PLPC domain has been found. There are 25 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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