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7  structures 1115  species 0  interactions 2597  sequences 4  architectures

Family: Pup_ligase (PF03136)

Summary: Pup-ligase protein

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The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

Pup-ligase protein Provide feedback

Pupylation is a novel protein modification system found in some bacteria [1]. This family of proteins are the enzyme that can conjugate proteins of the Pup family to lysine residues in target proteins marking them for degradation. The archetypal protein in this family is PafA (proteasome accessory factor) from Mycobacterium tuberculosis [2]. It has been suggested that these proteins are related to gamma-glutamyl-cysteine synthetases [1].

Literature references

  1. Iyer LM, Burroughs AM, Aravind L;, Biol Direct. 2008;3:45.: Unraveling the biochemistry and provenance of pupylation: a prokaryotic analog of ubiquitination. PUBMED:18980670 EPMC:18980670

  2. Pearce MJ, Mintseris J, Ferreyra J, Gygi SP, Darwin KH;, Science. 2008;322:1104-1107.: Ubiquitin-like protein involved in the proteasome pathway of Mycobacterium tuberculosis. PUBMED:18832610 EPMC:18832610

This tab holds annotation information from the InterPro database.

InterPro entry IPR004347

Pupylation is a novel protein modification system found in some bacteria [ PUBMED:18980670 ]. This entry represents two related groups of proteins involved in this system. Pup ligases, such as PafA, conjugate the prokaryotic ubiquitin-like protein Pup to lysine residues in target proteins, marking them for degradation [ PUBMED:18832610 ]. Pup deamidases, such as PafD, catalyse the deamidation of the Pup C-terminal glutamine to glutamate, thereby rendering the protein competent for conjugation [ PUBMED:19448618 ]. It has been suggested that proteins in this entry are related to gamma-glutamyl-cysteine synthetases [ PUBMED:18980670 ].

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 GCS (CL0286), which has the following description:

This clan represents a superfamily of carboxylate-amine/ammonia ligases [1] that includes Gamma-Glutamylcysteine synthetase (gamma-GCS) and glutamine synthetase (GS). Gamma-Glutamylcysteine synthetase (gamma-GCS) catalyses the first step in the de novo biosynthesis of glutathione.

The clan contains the following 9 members:

Amidoligase_2 ATP-gua_Ptrans DUF2126 GatB_N GCS GCS2 Gln-synt_C Glu_cys_ligase Pup_ligase


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.

Representative proteomes UniProt
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Representative proteomes UniProt

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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.

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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.

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: Pfam-B_3042 (release 6.5)
Previous IDs: DUF245; Proteosome_20S;
Type: Family
Sequence Ontology: SO:0100021
Author: Mifsud W , Bateman A
Number in seed: 108
Number in full: 2597
Average length of the domain: 436.70 aa
Average identity of full alignment: 48 %
Average coverage of the sequence by the domain: 91.07 %

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 46.1 29.0
Noise cut-off 23.2 23.1
Model length: 440
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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The tree shows the occurrence of this domain across different species. 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 Pup_ligase domain has been found. There are 7 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
P9WNU7 View 3D Structure Click here
P9WNU9 View 3D Structure Click here