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604  structures 8523  species 0  interactions 38873  sequences 274  architectures

Family: AAA_2 (PF07724)

Summary: AAA domain (Cdc48 subfamily)

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "AAA proteins". More...

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

AAA domain (Cdc48 subfamily) Provide feedback

This Pfam entry includes some of the AAA proteins not detected by the PF00004 model.

Literature references

  1. Confalonieri F, Duguet M; , Bioessays 1995;17:639-650.: A 200-amino acid ATPase module in search of a basic function. PUBMED:7646486 EPMC:7646486

  2. Neuwald AF, Aravind L, Spouge JL, Koonin EV; , Genome Res 1999;9:27-43.: AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. PUBMED:9927482 EPMC:9927482


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003959

AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport. Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors [ PUBMED:17201069 ].

AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [ PUBMED:15037233 , PUBMED:16828312 ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades [ PUBMED:15037233 ].

They assemble into oligomeric assemblies (often 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 act upon a target substrate, either translocating or remodelling it [ PUBMED:16919475 ].

They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) [ PUBMED:17201069 ].

The functional variety seen between AAA ATPases is in part due to their extensive number of accessory domains and factors, and to their variable organisation within oligomeric assemblies, in addition to changes in key functional residues within the ATPase domain itself.

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 P-loop_NTPase (CL0023), which has the following description:

AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes [2].

The clan contains the following 243 members:

6PF2K AAA AAA-ATPase_like AAA_10 AAA_11 AAA_12 AAA_13 AAA_14 AAA_15 AAA_16 AAA_17 AAA_18 AAA_19 AAA_2 AAA_21 AAA_22 AAA_23 AAA_24 AAA_25 AAA_26 AAA_27 AAA_28 AAA_29 AAA_3 AAA_30 AAA_31 AAA_32 AAA_33 AAA_34 AAA_35 AAA_5 AAA_6 AAA_7 AAA_8 AAA_9 AAA_PrkA ABC_ATPase ABC_tran ABC_tran_Xtn Adeno_IVa2 Adenylsucc_synt ADK AFG1_ATPase AIG1 APS_kinase Arf ArsA_ATPase ATP-synt_ab ATP_bind_1 ATP_bind_2 ATPase ATPase_2 Bac_DnaA BCA_ABC_TP_C Beta-Casp bpMoxR Cas_Csn2 Cas_St_Csn2 CbiA CBP_BcsQ CDC73_C CENP-M CFTR_R CLP1_P CMS1 CoaE CobA_CobO_BtuR CobU cobW CPT CSM2 CTP_synth_N Cytidylate_kin Cytidylate_kin2 DAP3 DBINO DEAD DEAD_2 DLIC DNA_pack_C DNA_pack_N DNA_pol3_delta DNA_pol3_delta2 DnaB_C dNK DO-GTPase1 DO-GTPase2 DUF1611 DUF1726 DUF2075 DUF2326 DUF2478 DUF257 DUF2791 DUF2813 DUF3584 DUF463 DUF5906 DUF6079 DUF815 DUF853 DUF87 DUF927 Dynamin_N Dynein_heavy Elong_Iki1 ELP6 ERCC3_RAD25_C Exonuc_V_gamma FeoB_N Fer4_NifH Flavi_DEAD FTHFS FtsK_SpoIIIE G-alpha Gal-3-0_sulfotr GBP GBP_C GTP_EFTU Gtr1_RagA Guanylate_kin GvpD HDA2-3 Helicase_C Helicase_C_2 Helicase_C_4 Helicase_RecD Herpes_Helicase Herpes_ori_bp Herpes_TK HSA HydF_dimer HydF_tetramer Hydin_ADK IIGP IPPT IPT iSTAND IstB_IS21 KAP_NTPase KdpD Kinase-PPPase Kinesin KTI12 LAP1C Lon_2 LpxK MCM MeaB MEDS Mg_chelatase Microtub_bd MipZ MMR_HSR1 MMR_HSR1_C MobB MukB Mur_ligase_M MutS_V Myosin_head NACHT NAT_N NB-ARC NOG1 NTPase_1 NTPase_P4 OPA1_C ORC3_N P-loop_TraG ParA Parvo_NS1 PAXNEB PduV-EutP PhoH PIF1 Ploopntkinase1 Ploopntkinase2 Ploopntkinase3 Podovirus_Gp16 Polyoma_lg_T_C Pox_A32 PPK2 PPV_E1_C PRK PSY3 Rad17 Rad51 Ras RecA ResIII RHD3 RhoGAP_pG1_pG2 RHSP RNA12 RNA_helicase Roc RsgA_GTPase RuvB_N SbcCD_C SecA_DEAD Septin Sigma54_activ_2 Sigma54_activat SKI SMC_N SNF2-rel_dom Spore_III_AA Spore_IV_A SRP54 SRPRB SulA Sulfotransfer_1 Sulfotransfer_2 Sulfotransfer_3 Sulfotransfer_4 Sulfotransfer_5 Sulphotransf SWI2_SNF2 T2SSE T4SS-DNA_transf Terminase_1 Terminase_3 Terminase_6N Terminase_GpA Thymidylate_kin TIP49 TK TniB Torsin TraG-D_C tRNA_lig_kinase TrwB_AAD_bind TsaE UvrB UvrD-helicase UvrD_C UvrD_C_2 Viral_helicase1 VirC1 VirE YqeC Zeta_toxin Zot

Alignments

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...

View options

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.

  Seed
(138)
Full
(38873)
Representative proteomes UniProt
(175362)
RP15
(5615)
RP35
(19093)
RP55
(38032)
RP75
(63881)
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PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(138)
Full
(38873)
Representative proteomes UniProt
(175362)
RP15
(5615)
RP35
(19093)
RP55
(38032)
RP75
(63881)
Alignment:
Format:
Order:
Sequence:
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Download options

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.

  Seed
(138)
Full
(38873)
Representative proteomes UniProt
(175362)
RP15
(5615)
RP35
(19093)
RP55
(38032)
RP75
(63881)
Raw Stockholm Download   Download   Download   Download   Download   Download    
Gzipped Download   Download   Download   Download   Download   Download    

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...

Trees

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: PfamB-40 (Release 14.0)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Studholme DJ
Number in seed: 138
Number in full: 38873
Average length of the domain: 173.20 aa
Average identity of full alignment: 37 %
Average coverage of the sequence by the domain: 26.06 %

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 20.6 20.6
Trusted cut-off 20.6 20.6
Noise cut-off 20.5 20.5
Model length: 171
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
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Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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Structures

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 AAA_2 domain has been found. There are 604 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
A0A0B4LID7 View 3D Structure Click here
A0A0G2KJF1 View 3D Structure Click here
A0A0N7KFF5 View 3D Structure Click here
A0A0N7KFI2 View 3D Structure Click here
A0A0P0VHW9 View 3D Structure Click here
A0A0P0WPU2 View 3D Structure Click here
A0A0R0GIY4 View 3D Structure Click here
A0A0R0HUU5 View 3D Structure Click here
A0A0R0IX14 View 3D Structure Click here
A0A0R0JI83 View 3D Structure Click here
A0A0R0K0U9 View 3D Structure Click here
A0A0R0K9F8 View 3D Structure Click here
A0A0R0L7V5 View 3D Structure Click here
A0A140KXW9 View 3D Structure Click here
A0A1D6EC46 View 3D Structure Click here
A0A1D6G7E2 View 3D Structure Click here
A0A1D6H2L6 View 3D Structure Click here
A0A1D6H4P1 View 3D Structure Click here
A0A1D6H9K3 View 3D Structure Click here
A0A1D6HD70 View 3D Structure Click here
A0A1D6HX28 View 3D Structure Click here
A0A1D6K5Y7 View 3D Structure Click here
A0A1D6MA59 View 3D Structure Click here
A0A1D6Q3F7 View 3D Structure Click here
A0A1D8PTP9 View 3D Structure Click here
A0A1P8B5U7 View 3D Structure Click here
A0A368UHH5 View 3D Structure Click here
A0A381MP32 View 3D Structure Click here
A4HWA6 View 3D Structure Click here
A4I4I4 View 3D Structure Click here
A4I5J7 View 3D Structure Click here
C0PDC7 View 3D Structure Click here
C0PFV4 View 3D Structure Click here
C0PFZ0 View 3D Structure Click here
E7F9J1 View 3D Structure Click here
E7FBK2 View 3D Structure Click here
F4IGZ2 View 3D Structure Click here
F4JVJ1 View 3D Structure Click here
F4K7F6 View 3D Structure Click here
I1JU82 View 3D Structure Click here
I1JXP9 View 3D Structure Click here
I1JXT1 View 3D Structure Click here
I1JYR4 View 3D Structure Click here
I1K6S6 View 3D Structure Click here
I1KAS9 View 3D Structure Click here
I1KBU6 View 3D Structure Click here
I1KBY3 View 3D Structure Click here
I1KD00 View 3D Structure Click here
I1KP32 View 3D Structure Click here
I1L3L8 View 3D Structure Click here
I1LMS2 View 3D Structure Click here
I1MQ99 View 3D Structure Click here
I1MZZ3 View 3D Structure Click here
I1N4I0 View 3D Structure Click here
I1N6A2 View 3D Structure Click here
I1NID3 View 3D Structure Click here
K7M813 View 3D Structure Click here
K7TSX2 View 3D Structure Click here
K7VD78 View 3D Structure Click here
O74402 View 3D Structure Click here
O76031 View 3D Structure Click here
O94641 View 3D Structure Click here
P0A6H1 View 3D Structure Click here
P0A6H5 View 3D Structure Click here
P0ABH9 View 3D Structure Click here
P31539 View 3D Structure Click here
P33416 View 3D Structure Click here
P38323 View 3D Structure Click here
P42730 View 3D Structure Click here
P42762 View 3D Structure Click here
P63284 View 3D Structure Click here
P90788 View 3D Structure Click here
P9WPB9 View 3D Structure Click here
P9WPC9 View 3D Structure Click here
P9WPD1 View 3D Structure Click here
Q0E3C8 View 3D Structure Click here
Q25823 View 3D Structure Click here
Q2FV74 View 3D Structure Click here
Q2FW45 View 3D Structure Click here
Q2FXQ7 View 3D Structure Click here
Q2FZ28 View 3D Structure Click here
Q2FZS8 View 3D Structure Click here
Q2G0P5 View 3D Structure Click here
Q2QVG9 View 3D Structure Click here
Q4CLP1 View 3D Structure Click here
Q4CRW0 View 3D Structure Click here
Q4DEP1 View 3D Structure Click here
Q4DRN5 View 3D Structure Click here
Q4DRN5 View 3D Structure Click here
Q4DTH5 View 3D Structure Click here
Q4E408 View 3D Structure Click here
Q4E408 View 3D Structure Click here
Q53LY0 View 3D Structure Click here
Q53N47 View 3D Structure Click here
Q54EV3 View 3D Structure Click here
Q54I27 View 3D Structure Click here
Q54IQ2 View 3D Structure Click here
Q5N8G6 View 3D Structure Click here
Q5U2U0 View 3D Structure Click here
Q60649 View 3D Structure Click here
Q65XY4 View 3D Structure Click here
Q66GN9 View 3D Structure Click here
Q6F2Y7 View 3D Structure Click here
Q6H795 View 3D Structure Click here
Q75GT3 View 3D Structure Click here
Q7F9I1 View 3D Structure Click here
Q7XL03 View 3D Structure Click here
Q8I0E1 View 3D Structure Click here
Q8I0E1 View 3D Structure Click here
Q8I377 View 3D Structure Click here
Q8IB03 View 3D Structure Click here
Q8IIJ8 View 3D Structure Click here
Q8IM28 View 3D Structure Click here
Q8VYJ7 View 3D Structure Click here
Q96UX5 View 3D Structure Click here
Q9FHH2 View 3D Structure Click here
Q9FI56 View 3D Structure Click here
Q9FK07 View 3D Structure Click here
Q9H078 View 3D Structure Click here
Q9JHS4 View 3D Structure Click here
Q9LF37 View 3D Structure Click here
Q9SXJ7 View 3D Structure Click here
Q9WTT2 View 3D Structure Click here