AAA proteins

ATPases associated with diverse cellular activities

Structure of N-ethylmaleimide-sensitive factor.[1]

Identifiers
Symbol| AAA
Pfam| PF00004
Pfam clan| CL0023
InterPro| IPR003959
PROSITE| PDOC00572
SCOP2| 1nsf / SCOPe / SUPFAM
CDD| cd00009
Membranome| 74
| Available protein structures:

Pfam | structures / ECOD
PDB| RCSB PDB; PDBe; PDBj
PDBsum| structure summary

AAA (ATPases Associated with diverse cellular Activities) proteins (speak: triple-A ATPases) are a large group of protein family sharing a common conserved module of approximately 230 amino acid residues. This is a large, functionally diverse protein family belonging to the AAA+ protein superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent remodeling or translocation of macromolecules.[2][3]

AAA proteins couple chemical energy provided by ATP hydrolysis to conformational changes which are transduced into mechanical force exerted on a macromolecular substrate.[4]

AAA proteins are functionally and organizationally diverse, and vary in activity, stability, and mechanism.[4] Members of the AAA family are found in all organisms[5] and they are essential for many cellular functions. They are involved in processes such as DNA replication, protein degradation, membrane fusion, microtubule severing, peroxisome biogenesis, signal transduction and the regulation of gene expression.

## Contents

* 1 Structure
* 1.1 Classification
* 1.2 Evolutionary relationships
* 2 Quaternary structure
* 3 Molecular mechanism
* 4 Prokaryotic AAAs
* 5 Functions
* 5.1 Molecular motion
* 5.2 Targeting to multivesicular bodies
* 5.3 Proteasome functions
* 6 Human proteins containing this domain
* 6.1 AAA ATPase family (HGNC)
* 6.1.1 Torsins
* 6.2 Other
* 6.3 Pseudogenes
* 7 Further reading
* 8 References

## Structure

The AAA proteins contain two domains, an N-terminal alpha/beta domain that binds and hydrolyzes nucleotides (a Rossmann fold) and a C-terminal alpha-helical domain.[5] The N-terminal domain is 200-250 amino acids long and contains Walker A and Walker B motifs,[5] and is shared in common with other P-loop NTPases, the superfamily which includes the AAA family.[6] Most AAA proteins have additional domains that are used for oligomerization, substrate binding and/or regulation. These domains can lie N- or C-terminal to the AAA module.

### Classification

Some classes of AAA proteins have an N-terminal non-ATPase domain which is followed by either one or two AAA domains (D1 and D2). In some proteins with two AAA domains, both are evolutionarily well conserved (like in Cdc48/p97). In others, either the D2 domain (like in Pex1p and Pex6p) or the D1 domain (in Sec18p/NSF) is better conserved in evolution.

While the classical AAA family was based on motifs, the family has been expanded using structural information and is now termed the AAA family.[5]

### Evolutionary relationships

AAA proteins are divided into seven basic clades, based on secondary structure elements included within or near the core AAA fold: clamp loader, initiator, classic, superfamily III helicase, HCLR, H2-insert, and PS-II insert.[4]

## Quaternary structure

AAA ATPases assemble into oligomeric assemblies (often homo-hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that can be propagated through the assembly in order to act upon a target substrate, either translocating or remodelling the substrate.[7]

The central pore may be involved in substrate processing. In the hexameric configuration, the ATP-binding site is positioned at the interface between the subunits. Upon ATP binding and hydrolysis, AAA enzymes undergo conformational changes in the AAA-domains as well as in the N-domains. These motions can be transmitted to substrate protein.

## Molecular mechanism

ATP hydrolysis by AAA ATPases is proposed to involve nucleophilic attack on the ATP gamma-phosphate by an activated water molecule, leading to movement of the N-terminal and C-terminal AAA subdomains relative to each other. This movement allows the exertion of mechanical force, amplified by other ATPase domains within the same oligomeric structure. The additional domains in the protein allow for regulation or direction of the force towards different goals.[6]

## Prokaryotic AAAs

AAA proteins are not restricted to eukaryotes. Prokaryotes have AAA which combine chaperone with proteolytic activity, for example in ClpAPS complex, which mediates protein degradation and recognition in E. coli. The basic recognition of proteins by AAAs is thought to occur through unfolded protein domains in the substrate protein. In HslU, a bacterial ClpX/ClpY homologue of the HSP100 family of AAA proteins, the N- and C-terminal subdomains move towards each other when nucleotides are bound and hydrolysed. The terminal domains are most distant in the nucleotide-free state and closest in the ADP-bound state. Thereby the opening of the central cavity is affected.

## Functions

AAA proteins are involved in protein degradation, membrane fusion, DNA replication, microtubule dynamics, intracellular transport, transcriptional activation, protein refolding, disassembly of protein complexes and protein aggregates.[5][8]

### Molecular motion

Dyneins, one of the three major classes of motor protein, are AAA proteins which couple their ATPase activity to molecular motion along microtubules.[9]

The AAA-type ATPase Cdc48p/p97 is perhaps the best-studied AAA protein. Misfolded secretory proteins are exported from the endoplasmic reticulum (ER) and degraded by the ER-associated degradation pathway (ERAD). Nonfunctional membrane and luminal proteins are extracted from the ER and degraded in the cytosol by proteasomes. Substrate retrotranslocation and extraction is assisted by the Cdc48p(Ufd1p/Npl4p) complex on the cytosolic side of the membrane. On the cytosolic side, the substrate is ubiquitinated by ER-based E2 and E3 enzymes before degradation by the 26S proteasome.

### Targeting to multivesicular bodies

Multivesicular bodies are endosomal compartments that sort ubiquitinated membrane proteins by incorporating them into vesicles. This process involves the sequential action of three multiprotein complexes, ESCRT I to III (ESCRT standing for 'endosomal sorting complexes required for transport'). Vps4p is a AAA-type ATPase involved in this MVB sorting pathway. It had originally been identified as a ”class E” vps (vacuolar protein sorting) mutant and was subsequently shown to catalyse the dissociation of ESCRT complexes. Vps4p is anchored via Vps46p to the endosomal membrane. Vps4p assembly is assisted by the conserved Vta1p protein, which regulates its oligomerization status and ATPase activity.

### Proteasome functions

AAA proteases use the energy from ATP hydrolysis to translocate a protein inside the proteasome for degradation. Cdc48p/p97 functions as a hexameric AAA+ ATPase that provides the mechanical force necessary for substrate dislocation. Its activity is tightly regulated by ATP binding and hydrolysis, which induce conformational changes required for protein unfolding and extraction. The HbYX motif plays a crucial role in regulating this process by mediating interactions between Cdc48p/p97 and downstream effectors such as the 20S proteasome or specific cofactors (e.g., Ufd1/Npl4). This interaction facilitates substrate transfer from Cdc48p/p97 to the proteasome, ensuring efficient protein degradation.[10]

Given its pivotal role in protein homeostasis, Cdc48p/p97 has been implicated in a wide range of cellular processes beyond ERAD, including autophagy, mitochondrial quality control, and DNA repair. The dysregulation of its function, particularly through mutations affecting the ATPase domain or HbYX-mediated interactions,[11] has been linked to neurodegenerative diseases and cancer.[11]

## Human proteins containing this domain

### AAA ATPase family (HGNC)

See also: Organization:HUGO Gene Nomenclature Committee (HGNC)

AFG3L2; ATAD1; ATAD2; ATAD2B; ATAD3A; ATAD3B; ATAD3C; ATAD5; BCS1L; CHTF18; CLBP; CLPP; CLPX; FIGN; FIGNL1; FIGNL2; IQCA1; KATNA1; KATNAL1; KATNAL2; LONP1; LONP2; MDN1; NSF; NVL; ORC1; ORC4; PEX1; PEX6; PSMC1; PSMC2 (Nbla10058); PSMC3; PSMC4; PSMC5; PSMC6; RFC1; RFC2; RFC3; RFC4; RFC5; RUVBL1; RUVBL2; SPAST; SPATA5 (SPAF); SPATA5L1; SPG7; TRIP13; VCP; VPS4A; VPS4B; WRNIP1; YME1L1 (FTSH);[12]

#### Torsins

TOR1A; TOR1B; TOR2A; TOR3A; TOR4A;[13]

### Other

AK6 (CINAP);[14] CDC6;

### Pseudogenes

AFG3L1P;[15]

## Further reading

* "AAA+ proteins: diversity in function, similarity in structure". Biochemical Society Transactions 36 (Pt 1): 72–77. February 2008. doi:10.1042/BST0360072. PMID 18208389.
* "AAA+ ATPases: achieving diversity of function with conserved machinery". Traffic 8 (12): 1657–1667. December 2007. doi:10.1111/j.1600-0854.2007.00642.x. PMID 17897320.

## References

1. ↑ "Structure of the ATP-dependent oligomerization domain of N-ethylmaleimide sensitive factor complexed with ATP". Nature Structural Biology 5 (9): 803–811. September 1998. doi:10.1038/1843. PMID 9731775.
2. ↑ "Evolutionary history and higher order classification of AAA+ ATPases". Journal of Structural Biology 146 (1–2): 11–31. 2004. doi:10.1016/j.jsb.2003.10.010. PMID 15037234.
3. ↑ "Phylogenetic analysis of AAA proteins". Journal of Structural Biology 146 (1–2): 2–10. 2004. doi:10.1016/j.jsb.2003.11.020. PMID 15037233.
4. ↑ 4.0 4.1 4.2 "Evolutionary relationships and structural mechanisms of AAA+ proteins". Annual Review of Biophysics and Biomolecular Structure 35: 93–114. 2006. doi:10.1146/annurev.biophys.35.040405.101933. PMID 16689629.
5. ↑ 5.0 5.1 5.2 5.3 5.4 "AAA+ proteins: have engine, will work". Nature Reviews. Molecular Cell Biology 6 (7): 519–529. July 2005. doi:10.1038/nrm1684. PMID 16072036.
6. ↑ 6.0 6.1 "The AAA+ superfamily of functionally diverse proteins". Genome Biology 9 (4): 216. April 2008. doi:10.1186/gb-2008-9-4-216. PMID 18466635.
7. ↑ "Proteasomes and their associated ATPases: a destructive combination". Journal of Structural Biology 156 (1): 72–83. October 2006. doi:10.1016/j.jsb.2006.04.012. PMID 16919475.
8. ↑ "The AAA+ superfamily--a myriad of motions". Current Opinion in Structural Biology 17 (6): 641–652. December 2007. doi:10.1016/j.sbi.2007.09.012. PMID 18023171.
9. ↑ "Communication between the AAA+ ring and microtubule-binding domain of dynein". Biochemistry and Cell Biology 88 (1): 15–21. February 2010. doi:10.1139/o09-127. PMID 20130675.
10. ↑ "Origin and Functional Evolution of the Cdc48/p97/VCP AAA+ Protein Unfolding and Remodeling Machine". Journal of Molecular Biology 428 (9 Pt B): 1861–1869. May 2016. doi:10.1016/j.jmb.2015.11.015. PMID 26608813.
11. ↑ 11.0 11.1 "ProEnd: a comprehensive database for identifying HbYX motif-containing proteins across the tree of life". BMC Genomics 25 (1): 951. October 2024. doi:10.1186/s12864-024-10864-4. PMID 39396964.
12. ↑ "Gene group: AAA ATPases (ATAD)". HUGO Gene Nomenclature Committee. https://www.genenames.org/data/genegroup/#!/group/413.
13. ↑ "Gene group: Torsins (TOR)". HUGO Gene Nomenclature Committee. https://www.genenames.org/data/genegroup/#!/group/1831.
14. ↑ "Symbol report for AK6". HUGO Gene Nomenclature Committee. https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:49151.
15. ↑ "Symbol report for AFG3L1P". HUGO Gene Nomenclature Committee. https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:314.

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