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613  structures 9093  species 0  interactions 185093  sequences 2605  architectures

Family: DEAD (PF00270)

Summary: DEAD/DEAH box helicase

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DEAD box Edit Wikipedia article

DEAD/DEAH box helicase
PDB 1qva EBI.jpg
Structure of the amino terminal domain of yeast initiation factor 4A. PDB 1qva[1]
Pfam clanCL0023

DEAD box proteins are involved in an assortment of metabolic processes that typically involve RNAs, but in some cases also other nucleic acids.[2] They are highly conserved in nine motifs and can be found in most prokaryotes and eukaryotes, but not all. Many organisms, including humans, contain DEAD-box (SF2) helicases, which are involved in RNA metabolism.[3]

DEAD box family

DEAD box proteins were first brought to attention in the late 1980s in a study that looked at a group of NTP binding sites that were similar in sequence to the eIF4A RNA helicase sequence.[4] The results of this study showed that these proteins (p68, SrmB, MSS116, vasa, PL10, mammalian eIF4A, yeast eIF4A) involved in RNA metabolism had several common elements.[5] There were nine common sequences found to be conserved amongst the studied species, which is an important criterion of the DEAD box family.[5]

The nine conserved motif from the N-terminal to the C-terminal are named as follows: Q-motif, motif 1, motif 1a, motif 1b, motif II, motif III, motif IV, motif V, and motif VI, as shown in the figure. Motif II is also known as the Walker B motif and contains the amino acid sequence D-E-A-D (asp-glu-ala-asp), which gave this family of proteins the name “DEAD box”.[5] Motif 1, motif II, the Q motif, and motif VI are all needed for ATP binding and hydrolysis, while motifs, 1a, 1b, III, IV, and V may be involved in intramolecular rearrangements and RNA interaction.[6]

Related families

The DEAH and SKI2 families have had proteins that have been identified to be related to the DEAD box family.[7][8][9] These two relatives have a few particularly unique motifs[which?] that are conserved within their own family.[10]

DEAD box, DEAH, and the SKI2 families are collectively referred to as DExD/H proteins.[10] It is thought that each family has a specific role in RNA metabolism, for example both DEAD box and DEAH box proteins NTPase activities become stimulated by RNA, but DEAD box proteins use ATP and DEAH does not.[6]

Biological functions

DEAD box proteins are considered to be RNA helicases and many have been found to be required in cellular processes such as RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.[10][11][12]

Pre-mRNA splicing

Pre-mRNA splicing requires rearrangements of five large RNP complexes, which are snRNPs U1, U2, U4, U5, and U6. DEAD box proteins are helicases that perform unwinding in an energy dependent approach and are able to perform these snRNP rearrangements in a quick and efficient manner.[13] There are three DEAD box proteins in the yeast system, Sub2, Prp28, and Prp5, and have been proven to be required for in vivo splicing.[13] Prp5 has been shown to assist in a conformational rearrangement of U2 snRNA, which makes the branch point recognition sequence of U2 available to bind the branch point sequence.[14] Prp28 may have a role in recognizing the 5’ splice site and does not display RNA helicase activity, suggesting that other factors must be present in order to activate Prp28.[15] DExD/H proteins have also been found to be required components in pre- mRNA splicing, in particular the DEAH proteins, Prp2, Prp16, Prp22, Prp43, and Brr213.[16] As shown in the figure, DEAD box proteins are needed in the initial steps of spliceosome formation, while DEAH box proteins are indirectly required for the transesterifications, release of the mRNA, and recycling of the spliceosome complex9.

The role of DEAD box proteins in pre-mRNA splicing. The orange text represents the DEAD box proteins.

Translation initiation

The eIF4A translation initiation factor was the first DEAD box protein found to have a RNA dependent ATPase activity. It has been proposed that this abundant protein helps in unwinding the secondary structure in the 5'-untranslated region.[17] This can inhibit the scanning process of the small ribosomal subunit, if not unwound.[17] Ded1 is another DEAD box protein that is also needed for translation initiation, but its exact role in this process is still obscure.[18] Vasa, a DEAD box protein highly related to Ded1 plays a part in translation initiation by interacting with eukaryotic initiation factor 2 (eIF2).[19]

See also


  1. ^ Johnson, E. R.; McKay, D. B. (1999). "Crystallographic structure of the amino terminal domain of yeast initiation factor 4A, a representative DEAD-box RNA helicase". RNA. 5 (12): 1526–1534. doi:10.1017/S1355838299991410. PMC 1369875. PMID 10606264.
  2. ^ Takashi Kikuma; Masaya Ohtsu; Takahiko Utsugi; Shoko Koga; Kohji Okuhara; Toshihiko Eki; Fumihiro Fujimori; Yasufumi Murakami (March 2004). "Dbp9p, a Member of the DEAD Box Protein Family, Exhibits DNA Helicase Activity". J. Biol. Chem. 279 (20): 20692–20698. doi:10.1074/jbc.M400231200. PMID 15028736.
  3. ^ Heung LJ, Del Poeta M (March 2005). "Unlocking the DEAD-box: a key to cryptococcal virulence?". J. Clin. Invest. 115 (3): 593–5. doi:10.1172/JCI24508. PMC 1052016. PMID 15765144.
  4. ^ Gorbalenya AE, Koonin EV, Donchenko AP, Blinov VM (June 1989). "Two related superfamilies of putative helicases involved in replication, recombination, repair and expression of DNA and RNA genomes". Nucleic Acids Res. 17 (12): 4713–30. doi:10.1093/nar/17.12.4713. PMC 318027. PMID 2546125.
  5. ^ a b c Linder, P.; Lasko, P. F.; Ashburner, M.; Leroy, P.; Nielsen, P. J.; Nishi, K.; Schnier, J.; Slonimski, P. P. (1989). "Birth of the D-E-A-D box". Nature. 337 (6203): 121–122. Bibcode:1989Natur.337..121L. doi:10.1038/337121a0. PMID 2563148. S2CID 13529955.
  6. ^ a b Tanner NK, Cordin O, Banroques J, Doère M, Linder P (January 2003). "The Q motif: a newly identified motif in DEAD box helicases may regulate ATP binding and hydrolysis". Mol. Cell. 11 (1): 127–38. doi:10.1016/S1097-2765(03)00006-6. PMID 12535527.
  7. ^ Tanaka N, Schwer B (July 2005). "Characterization of the NTPase, RNA-binding, and RNA helicase activities of the DEAH-box splicing factor Prp22". Biochemistry. 44 (28): 9795–803. doi:10.1021/bi050407m. PMID 16008364.
  8. ^ Xu J, Wu H, Zhang C, Cao Y, Wang L, Zeng L, Ye X, Wu Q, Dai J, Xie Y, Mao Y (2002). "Identification of a novel human DDX40gene, a new member of the DEAH-box protein family". J. Hum. Genet. 47 (12): 681–3. doi:10.1007/s100380200104. PMID 12522690.
  9. ^ Wang L, Lewis MS, Johnson AW (August 2005). "Domain interactions within the Ski2/3/8 complex and between the Ski complex and Ski7p". RNA. 11 (8): 1291–302. doi:10.1261/rna.2060405. PMC 1370812. PMID 16043509.
  10. ^ a b c de la Cruz J, Kressler D, Linder P (May 1999). "Unwinding RNA in Saccharomyces cerevisiae: DEAD-box proteins and related families". Trends Biochem. Sci. 24 (5): 192–8. doi:10.1016/S0968-0004(99)01376-6. PMID 10322435.
  11. ^ Aubourg S, Kreis M, Lecharny A (January 1999). "The DEAD box RNA helicase family in Arabidopsis thaliana". Nucleic Acids Res. 27 (2): 628–36. doi:10.1093/nar/27.2.628. PMC 148225. PMID 9862990.
  12. ^ Staley JP, Guthrie C (February 1998). "Mechanical devices of the spliceosome: motors, clocks, springs, and things". Cell. 92 (3): 315–26. doi:10.1016/S0092-8674(00)80925-3. PMID 9476892. S2CID 6208113.
  13. ^ a b Linder P (2006). "Dead-box proteins: a family affair—active and passive players in RNP-remodeling". Nucleic Acids Res. 34 (15): 4168–80. doi:10.1093/nar/gkl468. PMC 1616962. PMID 16936318.
  14. ^ Ghetti A, Company M, Abelson J (April 1995). "Specificity of Prp24 binding to RNA: a role for Prp24 in the dynamic interaction of U4 and U6 snRNAs". RNA. 1 (2): 132–45. PMC 1369067. PMID 7585243.
  15. ^ Strauss EJ, Guthrie C (August 1994). "PRP28, a 'DEAD-box' protein, is required for the first step of mRNA splicing in vitro". Nucleic Acids Res. 22 (15): 3187–93. doi:10.1093/nar/22.15.3187. PMC 310295. PMID 7520570.
  16. ^ Silverman E, Edwalds-Gilbert G, Lin RJ (July 2003). "DExD/H-box proteins and their partners: helping RNA helicases unwind". Gene. 312: 1–16. doi:10.1016/S0378-1119(03)00626-7. PMID 12909336.
  17. ^ a b Sonenberg N (1988). Cap-binding proteins of eukaryotic messenger RNA: functions in initiation and control of translation. Prog. Nucleic Acid Res. Mol. Biol. Progress in Nucleic Acid Research and Molecular Biology. 35. pp. 173–207. doi:10.1016/S0079-6603(08)60614-5. ISBN 978-0-12-540035-0. PMID 3065823.
  18. ^ Berthelot K, Muldoon M, Rajkowitsch L, Hughes J, McCarthy JE (February 2004). "Dynamics and processivity of 40S ribosome scanning on mRNA in yeast". Mol. Microbiol. 51 (4): 987–1001. doi:10.1046/j.1365-2958.2003.03898.x. PMID 14763975.
  19. ^ Carrera P, Johnstone O, Nakamura A, Casanova J, Jäckle H, Lasko P (January 2000). "VASA mediates translation through interaction with a Drosophila yIF2 homolog". Mol. Cell. 5 (1): 181–7. doi:10.1016/S1097-2765(00)80414-1. hdl:11858/00-001M-0000-0012-F80E-6. PMID 10678180.

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.

DEAD/DEAH box helicase Provide feedback

Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.

Literature references

  1. de la Cruz J, Kressler D, Linder P; , Trends Biochem Sci 1999;24:192-198.: Unwinding RNA in Saccharomyces cerevisiae: DEAD-box proteins and related families. PUBMED:10322435 EPMC:10322435

  2. Aubourg S, Kreis M, Lecharny A; , Nucleic Acids Res 1999;27:628-636.: The DEAD box RNA helicase family in Arabidopsis thaliana. PUBMED:9862990 EPMC:9862990

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR011545

Proteins with this domain include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression [ PUBMED:16935882 , PUBMED:20941364 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

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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 245 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 BrxC_BrxD BrxL_ATPase 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 DEAD DEAD_2 divDNAB DLIC DNA_pack_C DNA_pack_N DNA_pol3_delta DNA_pol3_delta2 DnaB_C dNK DO-GTPase1 DO-GTPase2 DUF1611 DUF2075 DUF2326 DUF2478 DUF257 DUF2813 DUF3584 DUF463 DUF4914 DUF5906 DUF6079 DUF815 DUF835 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 GpA_ATPase GpA_nuclease GTP_EFTU Gtr1_RagA Guanylate_kin GvpD_P-loop HDA2-3 Helicase_C Helicase_C_2 Helicase_C_4 Helicase_RecD HerA_C Herpes_Helicase Herpes_ori_bp Herpes_TK HydF_dimer HydF_tetramer Hydin_ADK IIGP IPPT IPT iSTAND IstB_IS21 KAP_NTPase KdpD Kinase-PPPase Kinesin KTI12 LAP1_C 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 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_GTPase RhoGAP_pG1_pG2 RHSP RNA12 RNA_helicase Roc RsgA_GTPase RuvB_N SbcC_Walker_B SecA_DEAD Senescence Septin Sigma54_activ_2 Sigma54_activat SKI SMC_N SNF2-rel_dom SpoIVA_ATPase Spore_III_AA SRP54 SRPRB SulA Sulfotransfer_1 Sulfotransfer_2 Sulfotransfer_3 Sulfotransfer_4 Sulfotransfer_5 Sulphotransf SWI2_SNF2 T2SSE T4SS-DNA_transf TerL_ATPase Terminase_3 Terminase_6N Thymidylate_kin TIP49 TK TmcA_N 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


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...

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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...


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.

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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: Published_alignment
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , Bruskiewich R , Sonnhammer ELL
Number in seed: 181
Number in full: 185093
Average length of the domain: 169.90 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 21.82 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.0 24.1
Trusted cut-off 26.0 24.1
Noise cut-off 25.9 24.0
Model length: 176
Family (HMM) version: 32
Download: download the raw HMM for this family

Species distribution

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Colour assignments

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


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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 DEAD domain has been found. There are 613 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
A0A096MIX2 View 3D Structure Click here
A0A096Q9L0 View 3D Structure Click here
A0A096RF51 View 3D Structure Click here
A0A096RQJ0 View 3D Structure Click here
A0A0B4J303 View 3D Structure Click here
A0A0G2JZH9 View 3D Structure Click here
A0A0G2JZQ1 View 3D Structure Click here
A0A0G2K0E0 View 3D Structure Click here
A0A0G2K4S4 View 3D Structure Click here
A0A0G2K719 View 3D Structure Click here
A0A0G2K744 View 3D Structure Click here
A0A0G2K9N3 View 3D Structure Click here
A0A0G2QC02 View 3D Structure Click here
A0A0K1H3C4 View 3D Structure Click here
A0A0N4SVP8 View 3D Structure Click here
A0A0P0VNY0 View 3D Structure Click here
A0A0P0VQJ4 View 3D Structure Click here
A0A0P0W309 View 3D Structure Click here
A0A0P0WAF3 View 3D Structure Click here
A0A0P0X9X6 View 3D Structure Click here
A0A0P0XCD9 View 3D Structure Click here
A0A0P0XV93 View 3D Structure Click here
A0A0P0Y5Y3 View 3D Structure Click here
A0A0P0Y964 View 3D Structure Click here
A0A0R0EP03 View 3D Structure Click here
A0A0R0ETL8 View 3D Structure Click here
A0A0R0ETU0 View 3D Structure Click here
A0A0R0F600 View 3D Structure Click here
A0A0R0FN75 View 3D Structure Click here
A0A0R0FUV4 View 3D Structure Click here
A0A0R0FWV1 View 3D Structure Click here
A0A0R0G126 View 3D Structure Click here
A0A0R0GBB6 View 3D Structure Click here
A0A0R0GBU8 View 3D Structure Click here
A0A0R0GJA7 View 3D Structure Click here
A0A0R0H501 View 3D Structure Click here
A0A0R0HJR0 View 3D Structure Click here
A0A0R0HL42 View 3D Structure Click here
A0A0R0I0S6 View 3D Structure Click here
A0A0R0I8N6 View 3D Structure Click here