Summary: Pup-ligase protein
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Pup-ligase protein Provide feedback
Pupylation is a novel protein modification system found in some bacteria . 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 . It has been suggested that these proteins are related to gamma-glutamyl-cysteine synthetases .
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
External database links
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].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Biological process||modification-dependent protein catabolic process (GO:0019941)|
|proteasomal protein catabolic process (GO:0010498)|
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This clan represents a superfamily of carboxylate-amine/ammonia ligases  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 8 members:Amidoligase_2 ATP-gua_Ptrans DUF2126 GCS GCS2 Gln-synt_C Glu_cys_ligase Pup_ligase
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
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- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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Curation and family details
|Seed source:||Pfam-B_3042 (release 6.5)|
|Previous IDs:||DUF245; Proteosome_20S;|
|Author:||Mifsud W, Bateman A|
|Number in seed:||131|
|Number in full:||4584|
|Average length of the domain:||435.90 aa|
|Average identity of full alignment:||59 %|
|Average coverage of the sequence by the domain:||88.99 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||11|
|Download:||download the raw HMM for this family|
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There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 6 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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