PsmA1 (alpha1, HVO_1091) is the major alpha-type subunit of the 20S proteasome core particle of the halophilic archaeon Haloferax volcanii. It is a non-catalytic member of the peptidase T1A (Ntn-hydrolase) family: seven alpha1 subunits form each outer ring of the four-ring barrel, while the inner rings are formed by the beta subunit (PsmB), whose N-terminal threonine carries the proteolytic active sites. Alpha1 and beta alone assemble into an active, salt-dependent alpha1-beta proteasome with chymotrypsin-like peptidase activity that can also degrade unfolded protein substrates; with the second alpha-type subunit (alpha2, PsmC) alpha1 also forms an asymmetric alpha1-alpha2-beta proteasome. The alpha1 N terminus forms the gate that restricts substrate entry into the catalytic chamber, which in archaea is opened by the PAN AAA+ ATPases. Alpha1 is abundant throughout growth and is N-terminally acetylated and phosphorylated. Cells lacking alpha1 are viable but sensitive to hypo-osmotic and thermal stress, whereas loss of both alpha1 and alpha2 is lethal. The proteasome is cytoplasmic and degrades proteins in vivo; H. volcanii lacks ubiquitin, and the ubiquitin-like SAMP proteins have been linked to proteasomal degradation.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004175 endopeptidase activity | IDA PMID:10482525 Halophilic 20S proteasomes of the archaeon Haloferax volcani... | MODIFY | Summary: Wilson et al. (1999) purified the alpha1-beta 20S proteasome and measured peptide- and protein-hydrolyzing (endopeptidase) activity of the complex. The catalytic nucleophile is the N-terminal threonine of the beta subunit, exposed by propeptide removal; alpha1 is a non-catalytic outer-ring subunit. Reason: The experimental finding (endopeptidase activity of the alpha1-containing core particle) is sound and is not disputed. But the row asserts that alpha1 itself enables endopeptidase activity, and the same abstract places catalysis on the beta subunit's N-terminal threonine. Alpha1 has no catalytic threonine. Its contribution to the activity is the GO contributes_to relationship, which is recorded in core_functions. The activity alpha1 itself enables is structural, so the replacement is GO:0140756 structural constituent of proteasome, as in this repository's human PSMA1 review. Proposed replacements: structural constituent of proteasome Supporting Evidence: PMID:10482525 A 20S proteasome, composed of alpha(1) and beta subunits arranged in a barrel-shaped structure of four stacked rings, was purified from a halophilic archaeon Haloferax volcanii. PMID:10482525 Comparison of the beta-subunit protein sequence with the sequence deduced from the gene revealed that a 49-residue propeptide is removed to expose a highly conserved N-terminal threonine which is proposed to serve as the catalytic nucleophile |
| GO:0004175 endopeptidase activity | IDA PMID:12486053 Subunit topology of two 20S proteasomes from Haloferax volca... | MODIFY | Summary: Kaczowka and Maupin-Furlow (2003) purified alpha1-beta and alpha1-alpha2-beta proteasomes and measured their peptide-hydrolyzing activity. As above, the activity belongs to the complex; the catalytic sites are on beta. Reason: Same reasoning as the PMID:10482525 row. The activity was measured on whole core particles. The abstract says alpha1 and beta together form active proteasomes, not that alpha1 is catalytic. Alpha1 contributes to the complex's endopeptidase activity (recorded in core_functions) and itself enables a structural role in the core particle. Proposed replacements: structural constituent of proteasome Supporting Evidence: PMID:12486053 The alpha1 and beta proteins alone form active 20S proteasomes PMID:22623373 The Ξ±-type subunits form the outer rings and the Ξ²-type subunits form the two inner rings which harbor the proteolytic active sites |
| GO:0004175 endopeptidase activity | IEA GO_REF:0000117 | MODIFY | Summary: ARBA machine-learning rule assigning endopeptidase activity to proteasome subunits. Reason: Consistent with the IDA rows for the same term. Alpha subunits lack the N-terminal threonine nucleophile and contribute to, rather than enable, the endopeptidase activity of the core particle. The activity alpha1 enables is structural. Proposed replacements: structural constituent of proteasome Supporting Evidence: PMID:22623373 The Ξ±-type subunits form the outer rings and the Ξ²-type subunits form the two inner rings which harbor the proteolytic active sites |
| GO:0004298 threonine-type endopeptidase activity | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO mapping from IPR019982 (Proteasome alpha subunit, archaeal family) to threonine-type endopeptidase activity. Reason: IPR019982 is specific to archaeal alpha subunits, which have no N-terminal threonine nucleophile. Mapping it to an enabled threonine-type catalytic activity is therefore systematically wrong for every member. QuickGO lists about 786 archaeal rows of GO:0004298 made through this one mapping. The true relation is contributes_to GO:0004298, recorded in core_functions. The function alpha1 enables in its own right is structural (GO:0140756). The mapping should either be dropped or carry a contributes_to qualifier. Proposed replacements: structural constituent of proteasome Supporting Evidence: PMID:10482525 Comparison of the beta-subunit protein sequence with the sequence deduced from the gene revealed that a 49-residue propeptide is removed to expose a highly conserved N-terminal threonine which is proposed to serve as the catalytic nucleophile |
| GO:0005737 cytoplasm | IEA GO_REF:0000120 | ACCEPT | Summary: UniProt SubCell (HAMAP MF_00289) places the proteasome in the cytoplasm. Reason: Haloarchaeal 20S proteasomes are soluble cytoplasmic complexes, purified from cell lysates, that degrade intracellular proteins. Cytoplasm is the correct prokaryotic compartment; no finer location is supported. Supporting Evidence: file:HALVD/psmA1/psmA1-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm PMID:15574956 This inhibitor was highly specific for H. volcanii 20S proteasomes |
| GO:0005839 proteasome core complex | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO mapping that places alpha1 in the 20S proteasome core complex. Reason: The term is correct, since alpha1 is part of the 20S core particle, but it is less specific than the evidence supports. Alpha1 forms the outer alpha rings, which is GO:0019773 proteasome core complex, alpha-subunit complex (part_of GO:0005839). The gene already carries that term by IDA from two papers. Proposed replacements: proteasome core complex, alpha-subunit complex Supporting Evidence: PMID:12486053 the alpha1-beta proteasome was a symmetrical cylinder with alpha1 rings on each end |
| GO:0006511 ubiquitin-dependent protein catabolic process | IEA GO_REF:0000002 | REMOVE | Summary: InterPro2GO mapping from IPR000426 (Proteasome alpha-subunit, N-terminal domain) to ubiquitin-dependent protein catabolic process. Reason: GO:0006511 is defined as protein catabolism initiated by covalent attachment of ubiquitin. H. volcanii, like other archaea, has no ubiquitin and no 26S proteasome ubiquitin receptors. Its 20S core is capped by PAN ATPases, and the only protein modifiers linked to proteasomal degradation are the ubiquitin-like SAMPs. Even that link is indirect (SAMP1 conjugates accumulate in a panA psmA mutant), so no modification-dependent process term is substituted. This is a taxon-blind InterPro2GO mapping. QuickGO shows about 888 archaeal GO:0006511 rows made through IPR000426, out of 910 archaeal rows in total. The mapping should be restricted to Eukaryota. Supporting Evidence: PMID:20054389 The enhanced levels of SAMP1-conjugates in the ΞpanA ΞpsmA mutant suggest SAMP1 targets proteins for destruction by proteasomes. |
| GO:0010498 proteasomal protein catabolic process | IDA PMID:10482525 Halophilic 20S proteasomes of the archaeon Haloferax volcani... | ACCEPT | Summary: The purified alpha1-beta proteasome hydrolyzed peptides and insulin B-chain protein. Reason: Alpha1 is a structural subunit of the 20S core particle that performs proteasomal protein degradation. As the outer ring and gate, it does part of the work of the process. Protein (insulin B-chain) hydrolysis by the alpha1-beta particle supports the annotation. In vivo proteasome-dependent turnover of reporter proteins (PMID:15574956) and the growth requirement for alpha-containing core particles (PMID:18931121) corroborate it. Supporting Evidence: PMID:10482525 The alpha(1)beta-proteasome also hydrolyzed insulin B-chain protein. |
| GO:0010498 proteasomal protein catabolic process | IDA PMID:12486053 Subunit topology of two 20S proteasomes from Haloferax volca... | ACCEPT | Summary: Purified alpha1-beta and alpha1-alpha2-beta proteasomes have peptide-hydrolyzing activity. Reason: Consistent with the PMID:10482525 row; alpha1 is a constituent of both active core particle subtypes. Supporting Evidence: PMID:12486053 The alpha1 and beta proteins alone form active 20S proteasomes |
| GO:0010498 proteasomal protein catabolic process | IEA GO_REF:0000120 | ACCEPT | Summary: Combined automated (ARBA/UniRule) assignment of proteasomal protein catabolic process. Reason: Agrees with the IDA evidence for this term. Supporting Evidence: PMID:18931121 Our results demonstrate that 20S proteasomes are required for growth. |
| GO:0019773 proteasome core complex, alpha-subunit complex | IDA PMID:10482525 Halophilic 20S proteasomes of the archaeon Haloferax volcani... | ACCEPT | Summary: Alpha1 was purified as a subunit of the four-ring alpha1-beta 20S proteasome. Reason: GO:0019773 is defined as the subcomplex that forms the two outer rings of the proteasome core complex. It carries no taxon constraint (the Mus musculus mention in the definition is only an example), so it applies to archaeal core particles. Alpha1 is the outer-ring subunit. Supporting Evidence: PMID:10482525 A 20S proteasome, composed of alpha(1) and beta subunits arranged in a barrel-shaped structure of four stacked rings, was purified from a halophilic archaeon Haloferax volcanii. |
| GO:0019773 proteasome core complex, alpha-subunit complex | IDA PMID:12486053 Subunit topology of two 20S proteasomes from Haloferax volca... | ACCEPT | Summary: Cross-linking showed homo-oligomeric alpha1 rings at the ends of the alpha1-beta and alpha1-alpha2-beta proteasomes. Reason: Direct topological evidence that alpha1 forms the outer alpha rings of the core particle. Supporting Evidence: PMID:12486053 the alpha1-beta proteasome was a symmetrical cylinder with alpha1 rings on each end |
| GO:0019773 proteasome core complex, alpha-subunit complex | IEA GO_REF:0000120 | ACCEPT | Summary: Combined automated assignment of the alpha-subunit complex. Reason: Agrees with the IDA evidence for this term. Supporting Evidence: PMID:22623373 The Ξ±-type subunits form the outer rings and the Ξ²-type subunits form the two inner rings which harbor the proteolytic active sites |
| GO:0030163 protein catabolic process | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO mapping to the generic protein catabolic process. Reason: The term is correct but general. GO:0010498 proteasomal protein catabolic process is an is_a descendant, and the gene already carries it by IDA. Proposed replacements: proteasomal protein catabolic process Supporting Evidence: PMID:10482525 The alpha(1)beta-proteasome also hydrolyzed insulin B-chain protein. |
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Download this section (compressed HTML)Q: Should the InterPro2GO mappings of IPR019982 (archaeal proteasome alpha subunit) to GO:0004298 threonine-type endopeptidase activity (enables) be dropped or converted to contributes_to, given that alpha subunits lack the catalytic N-terminal threonine?
Q: Should the InterPro2GO mapping of IPR000426 (proteasome alpha N-terminal domain) to GO:0006511 ubiquitin-dependent protein catabolic process be restricted to Eukaryota, given that archaea lack ubiquitin?
Q: Does SAMP conjugation directly target substrates to the PAN-20S proteasome in H. volcanii, which would make a modification-dependent protein catabolic process term appropriate for archaeal proteasome subunits?
Experiment: Reconstitute PAN-A with alpha1-beta core particles and purified SAMP1 conjugates in vitro to test whether SAMPylation is sufficient to target a substrate for ATP-dependent degradation.
Type: in vitro reconstitution
Experiment: Compare substrate degradation by symmetric alpha1-beta and asymmetric alpha1-alpha2-beta core particles, with and without PAN-A or PAN-B, to test whether the alpha-ring composition determines activator docking or substrate selection.
Type: biochemical assay
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