Subsystem: Proteasome archaeal

This subsystem's description is:

(by AO) This SS captures a prokaryotic version of self-compartmentalized proteasome, both archaeal core:
1. alpha-a Proteasome subunit alpha (EC 3.4.25.1), archaeal
2. beta-a Proteasome subunit beta (EC 3.4.25.1), archaeal
3 PAN-a Proteasome-activating AAA-ATPase (PAN), archaeal

and bacterial core:
alpha-b Proteasome subunit alpha (EC 3.4.25.1), bacterial
beta-b Proteasome subunit beta (EC 3.4.25.1), bacterial
PAN-b Bacterial proteasome-activating AAA-ATPase (PAN)

Bacterial proteasome component also includes recently discovered pupylation system (analog of ubiquitinylation in eukaryotes).
Pup Prokaryotic ubiquitin-like protein Pup
PafA Pup ligase PafA, possible component of postulated heterodimer PafA-PafA'
Pup ligase PafA' paralog, possible component of postulated heterodimer PafA-PafA'

For more information, please check out the description and the additional notes tabs, below

Literature ReferencesUbiquitin-like protein involved in the proteasome pathway of Mycobacterium tuberculosis. Pearce MJ Science (New York, N.Y.) 2008 Nov 1418832610
Evolution of proteasomal ATPases. Wollenberg K Molecular biology and evolution 2001 Jun11371584
An archaebacterial ATPase, homologous to ATPases in the eukaryotic 26 S proteasome, activates protein breakdown by 20 S proteasomes. Zwickl P The Journal of biological chemistry 1999 Sep 1010473546
Unraveling the biochemistry and provenance of pupylation: a prokaryotic analog of ubiquitination. Iyer LM Biology direct 2008 Nov 318980670
Characterization of the proteasome accessory factor (paf) operon in Mycobacterium tuberculosis. Festa RA Journal of bacteriology 2007 Apr17277063
DiagramFunctional RolesSubsystem SpreadsheetDescriptionAdditional Notes 

Showing colors for genome: Sulfolobus acidocaldarius DSM 639 ( 330779.3 ), variant code 2

This diagram is not scaled.


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Taxonomy Pattern 
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Domain
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active
*alpha*beta*PANPupPafAPafA'
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(by AO) This SS captures a prokaryotic version of self-compartmentalized proteasome, both archaeal core:
1. alpha-a Proteasome subunit alpha (EC 3.4.25.1), archaeal
2. beta-a Proteasome subunit beta (EC 3.4.25.1), archaeal
3 PAN-a Proteasome-activating AAA-ATPase (PAN), archaeal

and bacterial core:
alpha-b Proteasome subunit alpha (EC 3.4.25.1), bacterial
beta-b Proteasome subunit beta (EC 3.4.25.1), bacterial
PAN-b Bacterial proteasome-activating AAA-ATPase (PAN)

Bacterial proteasome component also includes recently discovered pupylation system (analog of ubiquitinylation in eukaryotes).
Pup Prokaryotic ubiquitin-like protein Pup
PafA Pup ligase PafA, possible component of postulated heterodimer PafA-PafA'
Pup ligase PafA' paralog, possible component of postulated heterodimer PafA-PafA'
Wollenberg, K., and Swaffield, J. C. 2001. Evolution of proteasomal ATPases. Mol. Biol. Evol. 18: 962-974. PMID: 11371584

Zwickl, P., Ng, D., Woo, K. M., Klenk, H.-P., and Goldberg, A. L. 1999. An archaebacterial ATPase, homologous to ATPases in the eukaryotic 26 S proteasome, activates protein breakdown by 20 S proteasomes. J. Biol. Chem. 274: 26008-260014. PMID: 10473546

VeronikaV has suggested that the bacterial proteins similar to proteasome-activating AAA-ATPase (PAN) play that role. This is also suggested by UniProt. I am concerned that these proteins are also found in Bacteria that lack the genes for the alpha and beta subunits, hence the role would be moot. The chromosomal clustering of these, and a few other proteins seems clear, but there is also limited phylogenetic distribution of these in the Bacteria.

This subsystem is built by gjo.
Comments by AndreiO (temporarily took over the subsystem to curate bacterial components)
Key insights to pupylation, teh role of PafA etc are coming from the following papers:
1: Iyer LM, Burroughs AM, Aravind L.
Unraveling the biochemistry and provenance of pupylation: a prokaryotic analog of
ubiquitination.
Biol Direct. 2008 Nov 3;3:45.
PMID: 18980670 [PubMed - in process]

2: Pearce MJ, Mintseris J, Ferreyra J, Gygi SP, Darwin KH.
Ubiquitin-like protein involved in the proteasome pathway of Mycobacterium
tuberculosis.
Science. 2008 Nov 14;322(5904):1104-7. Epub 2008 Oct 2.
PMID: 18832610 [PubMed - indexed for MEDLINE]

3: Festa RA, Pearce MJ, Darwin KH.
Characterization of the proteasome accessory factor (paf) operon in Mycobacterium
tuberculosis.
J Bacteriol. 2007 Apr;189(8):3044-50. Epub 2007 Feb 2.
PMID: 17277063 [PubMed - indexed for MEDLINE]

A number of issues remain:
- Is it true that PafA )Pup ligase) is a heterodimer? It was proposed in #1 based on persistence of two paralogs (in this susbystem they will be PafA and PafA'). Interestingly in M. tuberculosis these two paralogs are separated on the chromosome.
- Some Pup proteisn end with Q (others with E) and need to be deamidated. What is teh deamodase gene?
- Is the DeoR family regulator clustered consistetly with proteasome components involved in its regulation?
- what is the role of pupylation in Coryne and Bifido? (see more examples in #1)