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78  structures 3568  species 0  interactions 5259  sequences 21  architectures

Family: Peptidase_S66C (PF17676)

Summary: LD-carboxypeptidase C-terminal domain

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LD-carboxypeptidase C-terminal domain Provide feedback

Muramoyl-tetrapeptide carboxypeptidase hydrolyses a peptide bond between a di-basic amino acid and the C-terminal D-alanine in the tetrapeptide moiety in peptidoglycan. This cleaves the bond between an L- and a D-amino acid. The function of this activity is in murein recycling. This family also includes the microcin c7 self-immunity protein Q47511. This family corresponds to Merops family S66.

Literature references

  1. Gonzalez-Pastor JE, San Millan JL, Castilla MA, Moreno F; , J Bacteriol 1995;177:7131-7140.: Structure and organization of plasmid genes required to produce the translation inhibitor microcin C7. PUBMED:8522520 EPMC:8522520

  2. Guijarro JI, Gonzalez-Pastor JE, Baleux F, San Millan JL, Castilla MA, Rico M, Moreno F, Delepierre M; , J Biol Chem 1995;270:23520-23532.: Chemical structure and translation inhibition studies of the antibiotic microcin C7. PUBMED:7559516 EPMC:7559516

  3. Templin MF, Ursinus A, Holtje JV; , EMBO J 1999;18:4108-4117.: A defect in cell wall recycling triggers autolysis during the stationary growth phase of Escherichia coli. PUBMED:10428950 EPMC:10428950

  4. Korza HJ, Bochtler M; , J Biol Chem 2005; [Epub ahead of print]: P. aeruginosa LD-carboxypeptidase: A serine peptidase with a Ser-His-Glu triad and a nucleophilic elbow. PUBMED:16162494 EPMC:16162494

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR040921

This entry represents the C-terminal domain of the LD-carboxypeptidase A. Muramoyl-tetrapeptide carboxypeptidase or LD-carboxypeptidase A hydrolyses a peptide bond between a di-basic amino acid and the C-terminal D-alanine in the tetrapeptide moiety in peptidoglycan. This cleaves the bond between an L- and a D-amino acid. The function of this activity is in murein recycling [ PUBMED:10428950 , PUBMED:18535144 ]. Proteins containing this domain also include the microcin c7 self-immunity protein SWISSPROT [ PUBMED:8522520 ] and microcin immunity protein MccF [ PUBMED:22516613 ].

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 Leu-IlvD (CL0364), which has the following description:

Superfamily includes LeuD-like, IlvD/EDD C-terminal domain-like, and AF0055-like families.

The clan contains the following 10 members:

Aconitase_2_N Aconitase_C CPSase_sm_chain Cyclase DUF126 DUF2172 PA PEP-utilizers Peptidase_S66C RraA-like


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.

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...


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: SwissProt
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , Studholme DJ
Number in seed: 242
Number in full: 5259
Average length of the domain: 117.40 aa
Average identity of full alignment: 28 %
Average coverage of the sequence by the domain: 36.71 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.7 23.7
Trusted cut-off 24.3 23.9
Noise cut-off 23.1 23.3
Model length: 123
Family (HMM) version: 3
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 Peptidase_S66C domain has been found. There are 78 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
P76008 View 3D Structure Click here