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25  structures 1237  species 0  interactions 1783  sequences 24  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
OPM superfamily88
OPM protein1olp

Zinc dependent prokaryotic phospholipases C is a family of bacterial phospholipases C, some of which are also known as alpha toxins.

Bacillus cereus contains a monomeric phospholipase C EC (PLC) of 245 amino-acid residues. Although PLC prefers to acton 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 fromClostridium 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.


  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. PMID 2841128.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  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. PMID 2536355.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  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. PMID 1309513.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  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. PMID 2111259.
This article incorporates text from the public domain Pfam and InterPro: IPR001531

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

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 IPR029002

This domain is found in bacterial zinc-dependent phospholipase C and in eukaryotic phosphatidylinositol-glycan-specific phospholipase D.

Bacterial phospholipase C is a zinc-dependent enzyme, binding 3 zinc ions per molecule [ PUBMED:2111259 ]. This enzyme catalyses the conversion of phosphatidylcholine and water to 1,2-diacylglycerol and choline phosphate. Phosphatidylinositol-glycan-specific phospholipase D is an extracellular amphiphilic glycoprotein [ PUBMED:1606959 , PUBMED:2017684 ]. It hydrolyses the inositol phosphate linkage in proteins anchored by phosphatidylinositol glycans, releasing these proteins from the membrane.

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 S1-P1_nuclease YdjM Zn_dep_PLPC


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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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.

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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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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...


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

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
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 129
Number in full: 1783
Average length of the domain: 175 aa
Average identity of full alignment: 15 %
Average coverage of the sequence by the domain: 43.53 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild --amino -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.8 26.8
Trusted cut-off 26.8 26.8
Noise cut-off 26.7 26.7
Model length: 179
Family (HMM) version: 21
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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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 adjacent tab. More...

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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 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 sequence.

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