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953  structures 7034  species 0  interactions 42218  sequences 116  architectures

Family: Transpeptidase (PF00905)

Summary: Penicillin binding protein transpeptidase domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Penicillin binding proteins". More...

Penicillin binding proteins Edit Wikipedia article

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.

Penicillin binding protein transpeptidase domain Provide feedback

The active site serine (residue 337 in P14677) is conserved in all members of this family.

Literature references

  1. Pares S, Mouz N, Petillot Y, Hakenbeck R, Dideberg O , Nat Struct Biol 1996;3:284-289.: X-ray structure of Streptococcus pneumoniae PBP2x, a primary penicillin target enzyme. PUBMED:8605631 EPMC:8605631


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001460

This signature identifies a large group of proteins, which include:

  • Beta-lactamase precursor ( EC , penicillinase)
  • Peptidoglycan synthetase ftsI ( EC , peptidoglycan glycosyltransferase 3)
  • Methicillin resistance mecR1 protein
  • Methicillin resistance blaR1 protein

The large number of penicillin binding proteins, which are represented in this group of sequences, are responsible for the final stages of peptidoglycan biosynthesis for cell wall formation. The proteins synthesise cross-linked peptidoglycan from lipid intermediates, and contain a penicillin-sensitive transpeptidase carboxy-terminal domain. The active site serine (residue 337 in SWISSPROT ) is conserved in all members of this family [ PUBMED:8605631 ].

MecR1 and BlaR1 are metallopeptidases belonging to MEROPS peptidase family M56, clan M-. BlaR1 and MecR1 cleave their cognate transcriptional repressors BlaI and MecI, respectively, activating the synthesis of MecA.

MecR1 is present in Staphylococcus aureus and Staphylococcus sciuri, whereas BlaR1 (also known as BlaR, PenR1, or PenJ) has been found in Bacillus licheniformis, Staphylococcus epidermidis, Staphylococcus haemolyticus, and several S. aureus strains. These proteins are either plasmid-encoded, chromosomal, or transposon-mediated. MecR1/BlaR1 proteins are made up by homologous N-terminal 330-residue transmembrane metallopeptidase domains linked to extracellular 260-residue homologous PBP-like penicillin sensor moieties.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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 Beta-lactamase (CL0013), which has the following description:

This superfamily contains proteins that have a beta-lactamase fold. This includes beta-lactamases as well as Dala-Dala carboxypeptidases and glutaminases.

The clan contains the following 6 members:

Beta-lactamase Beta-lactamase2 Glutaminase Peptidase_S11 Peptidase_S13 Transpeptidase

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

View options

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
(40)
Full
(42218)
Representative proteomes UniProt
(230193)
RP15
(5017)
RP35
(20287)
RP55
(44420)
RP75
(77636)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(40)
Full
(42218)
Representative proteomes UniProt
(230193)
RP15
(5017)
RP35
(20287)
RP55
(44420)
RP75
(77636)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

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
(40)
Full
(42218)
Representative proteomes UniProt
(230193)
RP15
(5017)
RP35
(20287)
RP55
(44420)
RP75
(77636)
Raw Stockholm Download   Download   Download   Download   Download   Download    
Gzipped 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.

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: Bateman A & Pfam-B_726 (Release 8.0)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , Finn RD
Number in seed: 40
Number in full: 42218
Average length of the domain: 287.9 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 42.48 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.1 22.1
Trusted cut-off 22.1 22.1
Noise cut-off 22.0 22.0
Model length: 306
Family (HMM) version: 25
Download: download the raw HMM for this family

Species distribution

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

Selections

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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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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 Transpeptidase domain has been found. There are 953 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
A0A077ZF37 View 3D Structure Click here
A0A077ZHE1 View 3D Structure Click here
A0A077ZLG1 View 3D Structure Click here
A0A0H3GIH5 View 3D Structure Click here
A0A0H3GN85 View 3D Structure Click here
A0A0H3GTX1 View 3D Structure Click here
A0A0H3GVC7 View 3D Structure Click here
A0A0H3GY10 View 3D Structure Click here
A0A0H3GZF1 View 3D Structure Click here
A0A0H3H1G6 View 3D Structure Click here
A0PZT1 View 3D Structure Click here
A0QNG3 View 3D Structure Click here
A0R022 View 3D Structure Click here
A0R7G2 View 3D Structure Click here
A5I6G4 View 3D Structure Click here
B8H0A0 View 3D Structure Click here
G3XCV7 View 3D Structure Click here
G3XCV9 View 3D Structure Click here
G3XD31 View 3D Structure Click here
G3XD46 View 3D Structure Click here
I6YGX2 View 3D Structure Click here
K0EFL6 View 3D Structure Click here
K0EGI4 View 3D Structure Click here
K0ETW9 View 3D Structure Click here
K0EWB3 View 3D Structure Click here
K0EXV7 View 3D Structure Click here
K0F8Y9 View 3D Structure Click here
K0FEN4 View 3D Structure Click here
L0T911 View 3D Structure Click here
O25319 View 3D Structure Click here
O26078 View 3D Structure Click here
O26085 View 3D Structure Click here
O32032 View 3D Structure Click here
O33346 View 3D Structure Click here
O66874 View 3D Structure Click here
P02918 View 3D Structure Click here
P02919 View 3D Structure Click here
P0A0U9 View 3D Structure Click here
P0A0Z6 View 3D Structure Click here
P0A3M6 View 3D Structure Click here