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35  structures 11117  species 3  interactions 54923  sequences 75  architectures

Family: PASTA (PF03793)

Summary: PASTA domain

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PASTA domain Edit Wikipedia article

PASTA domain
PDB 1rp5 EBI.jpg
Structure the PASTA domain in a penicillin binding protein.
Symbol PASTA
Pfam PF03793
InterPro IPR005543
SCOP 1rp5
CDD cd06573

The PASTA domain is a small protein domain that can bind to beta-lactam rings found in antibiotics.[1] The domain was initially discovered in 2002 by Yeats and colleagues as a region of sequence similarity found in penicillin binding proteins and PknB-like kinases found in some bacteria. The name is an acronym derived from PBP and Serine/Threonine kinase Associated domain.


The PASTA domain adopts a structure composed of an alpha-helix followed by three beta strands. Recent structural studies show that the extracellular region of PknB that is composed of four PASTA domains shows a linear arrangement of the domains.[2]

Species distribution

PASTA domains are found in a variety of bacterial species including gram-positive firmicutes and actinobacteria.


  1. ^ Yeats C, Finn RD, Bateman A (September 2002). "The PASTA domain: a beta-lactam-binding domain". Trends Biochem. Sci. 27 (9): 438. doi:10.1016/s0968-0004(02)02164-3. PMID 12217513. 
  2. ^ Barthe P, Mukamolova GV, Roumestand C, Cohen-Gonsaud M (May 2010). "The structure of PknB extracellular PASTA domain from mycobacterium tuberculosis suggests a ligand-dependent kinase activation". Structure 18 (5): 606–15. doi:10.1016/j.str.2010.02.013. PMID 20462494. 

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PASTA domain Provide feedback

This domain is found at the C termini of several Penicillin-binding proteins and bacterial serine/threonine kinases [1]. It binds the beta-lactam stem, which implicates it in sensing D-alanyl-D-alanine - the PBP transpeptidase substrate. It is a small globular fold consisting of 3 beta-sheets and an alpha-helix. The name PASTA is derived from PBP and Serine/Threonine kinase Associated domain.

Literature references

  1. Yeats C, Finn R, Bateman A; , Trends Biochem Sci 2002;27:438-440.: The PASTA domain: a beta-lactam-binding domain. PUBMED:12217513 EPMC:12217513

  2. Yeats C, Bentley S, Bateman A; , BMC Microbiol 2003;3:3-3.: New Knowledge from Old: In silico discovery of novel protein domains in Streptomyces coelicolor. PUBMED:12625841 EPMC:12625841

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR005543

The PASTA domain is found at the C-termini of several Penicillin-binding proteins (PBP) and bacterial serine/threonine kinases. It binds the beta-lactam stem, which implicates it in sensing D-alanyl-D-alanine - the PBP transpeptidase substrate. In PknB of Mycobacterium tuberculosis (SWISSPROT), all of the extracellular portion is predicted to be made up of four PASTA domains, which strongly suggests that it is a signal-binding sensor domain. The domain has also been found in proteins involved in cell wall biosynthesis, where it is implicated in localizing the biosynthesis complex to unlinked peptidoglycan.

PASTA is a small globular fold consisting of 3 beta-sheets and an alpha-helix, with a loop region of variable length between the first and second beta-strands. The name PASTA is derived from PBP and Serine/Threonine kinase Associated domain [PUBMED:12217513].

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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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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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.

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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.

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Seed source: Yeats C
Previous IDs: none
Type: Domain
Author: Yeats C
Number in seed: 237
Number in full: 54923
Average length of the domain: 62.00 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 21.53 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.2 21.2
Trusted cut-off 21.2 21.2
Noise cut-off 21.1 21.1
Model length: 63
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
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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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There are 3 interactions for this family. More...

PASTA PBP_dimer Transpeptidase


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 PASTA domain has been found. There are 35 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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