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78  structures 3542  species 0  interactions 5210  sequences 21  architectures

Family: Peptidase_S66 (PF02016)

Summary: LD-carboxypeptidase N-terminal domain

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LD-carboxypeptidase N-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 IPR040449

This entry includes proteins belonging to the MEROPS peptidase family S66, such as muramoyl-tetrapeptide carboxypeptidase and the microcin c7 self-immunity protein SWISSPROT .

Muramoyl-tetrapeptide carboxypeptidase, also known as 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. This activity has a role in murein recycling [ PUBMED:10428950 , PUBMED:18535144 ].

The structure of Pseudomonas aeruginosa LD-carboxypeptidase showed that the enzyme consists of an N-terminal beta-sheet and a C-terminal beta-barrel domain [ PUBMED:16162494 ]. This entry represents the N-terminal domain.

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 Glutaminase_I (CL0014), which has the following description:

Most members of this clan are glutaminase enzymes. This superfamily is shown to be related in [1]. The clan also contains the DJ-1/PfpI family that includes the peptidase PfpI that has a catalytic Cys-His-Glu triad that differs from the class I GAT Cys-His-Glu triad.

The clan contains the following 18 members:

ABC_transp_aux BPL_N Catalase_C DJ-1_PfpI DUF4159 GATase GATase1_like GATase_3 GATase_5 Glyco_hydro_42M HTS LBP_M Peptidase_C26 Peptidase_S51 Peptidase_S66 SNO ThiJ_like ThuA


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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Representative proteomes UniProt

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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.

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: Swiss-Prot
Previous IDs: UPF0094; Peptidase_U61;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , Studholme DJ
Number in seed: 256
Number in full: 5210
Average length of the domain: 118.20 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 36.73 %

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 25.0 25.0
Trusted cut-off 25.0 25.0
Noise cut-off 24.9 24.7
Model length: 119
Family (HMM) version: 17
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_S66 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