Schultz et al. (1998) Proc. Natl. Acad. Sci. USA 95, 5857-5864
Letunic et al. (2012) Nucleic Acids Res , doi:10.1093/nar/gkr931

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HELICc helicase superfamily c-terminal domain

SMART accession number:	SM00490
Description:
Interpro abstract (IPR001650):	Helicases have been classified in 5 superfamilies (SF1-SF5). For the two largest groups, commonly referred to as SF1 and SF2, a total of seven characteristic motifs has been identified [(PUBMED:2546125)]. These two superfamilies encompass a large number of DNA and RNA helicases from archaea, eubacteria, eukaryotes and viruses. This entry represents the C-terminal domain found in proteins belonging to the helicase superfamilies 1 and 2. Included in this group is the eukaryotic translation initiation factor 4A (eIF4A), a member of the DEA(D/H)-box RNA helicase family. The structure of the carboxyl-terminal domain of eIF4A has been determined; it has a parallel alpha-beta topology that superimposes, with minor variations, on the structures and conserved motifs of the equivalent domain in other, distantly related helicases [(PUBMED:11087862)].
GO function:	helicase activity (GO:0004386), ATP binding (GO:0005524), nucleic acid binding (GO:0003676)
Family alignment:	View or CHROMA formatCLUSTALW formatMSF formatFASTA formatPIR format

There are 36933 HELICc domains in 36715 proteins in SMART's nrdb database.

Click on the following links for more information.

• Evolution (species in which this domain is found)

• Click on to expand nodes. To display all proteins with a HELICc domain in a specific node, click on it.

  This tree shows only several representative species. The complete taxonomic breakdown of all proteins with HELICc domain is also avaliable.

  Useful shortcuts: Expand all nodes or Collapse tree
  Go to specific node: Anopheles gambiae, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae, Takifugu rubripes

• Literature (relevant references for this domain)

• Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.

  • Bork P, Koonin EV
  • An expanding family of helicases within the 'DEAD/H' superfamily.
  • Nucleic Acids Res. 1993; 21: 751-2
• Disease (disease genes where sequence variants are found in this domain)

• SwissProt sequences and OMIM curated human diseases associated with missense mutations within the HELICc domain.

  Protein	Disease
  Transcriptional regulator ATRX (P46100) (SMART)	OMIM:300032: Alpha-thalassemia/mental retardation syndrome OMIM:301040: Juberg-Marsidi syndrome OMIM:309590: Sutherland-Haan syndrome OMIM:309470: Smith-Fineman-Myers syndrome OMIM:309580:

• Metabolism (metabolic pathways involving proteins which contain this domain)

• Click the image to view the interactive version of the map in iPath

  % proteins involved KEGG pathway ID Description 42.40 map00500 Starch and sucrose metabolism 42.40 map00790 Folate biosynthesis 8.69 map00230 Purine metabolism 5.69 map03090 Type II secretion system 0.52 map04310 Wnt signaling pathway 0.10 map00970 Aminoacyl-tRNA biosynthesis 0.10 map03020 RNA polymerase 0.10 map00330 Arginine and proline metabolism This information is based on mapping of SMART genomic protein database to KEGG orthologous groups. Percentage points are related to the number of proteins with HELICc domain which could be assigned to a KEGG orthologous group, and not all proteins containing HELICc domain. Please note that proteins can be included in multiple pathways, ie. the numbers above will not always add up to 100%.

• Structure (3D structures containing this domain)

• 3D Structures of HELICc domains in PDB

  PDB code	Main view	Title
  1c4o		Crystal structure of the dna nucleotide excision repair enzyme uvrb from thermus thermophilus
  1d2m		Uvrb protein of thermus thermophilus hb8; a nucleotide excision repair enzyme
  1d9x		Crystal structure of the dna repair protein uvrb
  1d9z		Crystal structure of the dna repair protein uvrb in complex with atp
  1fuk		Crystal structure of the carboxy terminal domain of yeast eif4a
  1fuu		Yeast initiation factor 4a
  1gm5		Structure of recg bound to three-way dna junction
  1hv8		Crystal structure of a dead box protein from the hyperthermophile methanococcus jannaschii
  1jr6		Solution structure of an engineered arginine-rich subdomain of the hepatitis c virus ns3 rna helicase
  1onb		Solution structure of an engineered arginine-rich subdomain of the hepatitis c virus ns3 rna helicase
  1oyw		Structure of the recq catalytic core
  1oyy		Structure of the recq catalytic core bound to atp-gamma-s
  1s2m		Crystal structure of the dead box protein dhh1p
  1t5i		Crystal structure of the c-terminal domain of uap56
  1t5l		Crystal structure of the dna repair protein uvrb point mutant y96a revealing a novel fold for domain 2
  1wp9		Crystal structure of pyrococcus furiosus hef helicase domain
  1xti		Structure of wildtype human uap56
  1xtj		Structure of human uap56 in complex with adp
  1xtk		Structure of decd to dead mutation of human uap56
  1yks		Crystal structure of yellow fever virus ns3 helicase
  1ymf		Crystal structure of yellow fever virus ns3 helicase complexed with adp
  1z3i		Structure of the swi2/snf2 chromatin remodeling domain of eukaryotic rad54
  1z5z		Sulfolobus solfataricus swi2/snf2 atpase c-terminal domain
  1z63		Sulfolobus solfataricus swi2/snf2 atpase core in complex with dsdna
  1z6a		Sulfolobus solfataricus swi2/snf2 atpase core domain
  2bhr		Dengue virus rna helicase
  2bmf		Dengue virus rna helicase at 2.4a
  2d7d		Structural insights into the cryptic dna dependent atp-ase activity of uvrb
  2db3		Structural basis for rna unwinding by the dead-box protein drosophila vasa
  2eyq		Crystal structure of escherichia coli transcription-repair coupling factor
  2fdc		Structural basis of dna damage recognition and processing by uvrb: crystal structure of a uvrb/dna complex
  2fwr		Structure of archaeoglobus fulgidis xpb
  2fzl		Structure of c-terminal domain of archaeoglobus fulgidus xpb
  2hjv		Structure of the second domain (residues 207-368) of the bacillus subtilis yxin protein
  2hxy		Crystal structure of human apo-eif4aiii
  2hyi		Structure of the human exon junction complex with a trapped dead-box helicase bound to rna
  2i4i		Crystal structure of human dead-box rna helicase ddx3x
  2j0q		The crystal structure of the exon junction complex at 3.2 a resolution
  2j0s		The crystal structure of the exon junction complex at 2.2 a resolution
  2j0u		The crystal structure of eif4aiii-barentsz complex at 3.0 a resolution
  2jgn		Ddx3 helicase domain
  2kbf		Solution structure of carboxyl-terminal domain of dbp5p
  2nmv		Damage detection by the uvrabc pathway: crystal structure of uvrb bound to fluorescein-adducted dna
  2oca		The crystal structure of t4 uvsw
  2p6n		Human dead-box rna helicase ddx41, helicase domain
  2p6r		Crystal structure of superfamily 2 helicase hel308 in complex with unwound dna
  2p6u		Apo structure of the hel308 superfamily 2 helicase
  2qeq		Crystal structure of kunjin virus ns3 helicase
  2rb4		Crystal structure of the helicase domain of human ddx25 rna helicase
  2v1x		Crystal structure of human recq-like dna helicase
  2v6i		Kokobera virus helicase
  2v6j		Kokobera virus helicase: mutant met47thr
  2v8o		Structure of the murray valley encephalitis virus rna helicase to 1.9a resolution
  2va8		Dna repair helicase hel308
  2vso		Crystal structure of a translation initiation complex
  2vsx		Crystal structure of a translation initiation complex
  2wax		Structure of the human ddx6 c-terminal domain in complex with an edc3-fdf peptide
  2way		Structure of the human ddx6 c-terminal domain in complex with an edc3-fdf peptide
  2z0m		Crystal structure of hypothetical atp-dependent rna helicase from sulfolobus tokodaii
  2z83		Crystal structure of catalytic domain of japanese encephalitis virus ns3 helicase/nucleoside triphosphatase at a resolution 1.8
  2zj2		Archaeal dna helicase hjm apo state in form 1
  2zj5		Archaeal dna helicase hjm complexed with adp in form 1
  2zj8		Archaeal dna helicase hjm apo state in form 2
  2zja		Archaeal dna helicase hjm complexed with amppcp in form 2
  2zu6		Crystal structure of the eif4a-pdcd4 complex
  3dmq		Crystal structure of rapa, a swi2/snf2 protein that recycles rna polymerase during transcription
  3eaq		Novel dimerization motif in the dead box rna helicase hera form 2, complete dimer, symmetric
  3ear		Novel dimerization motif in the dead box rna helicase hera: form 1, partial dimer
  3eas		Novel dimerization motif in the dead box rna helicase hera: form 1, complete dimer, asymmetric
  3eiq		Crystal structure of pdcd4-eif4a
  3ews		Human dead-box rna-helicase ddx19 in complex with adp
  3ex7		The crystal structure of ejc in its transition state
  3fho		Structure of s. pombe dbp5
  3fht		Crystal structure of human dbp5 in complex with amppnp and rna
  3fmp		Crystal structure of the nucleoporin nup214 in complex with the dead-box helicase ddx19
  3g0h		Human dead-box rna helicase ddx19, in complex with an atp- analogue and rna
  3gfp		Structure of the c-terminal domain of the dead-box protein dbp5
  3i32		Dimeric structure of a hera helicase fragment including the c-terminal reca domain, the dimerization domain, and the rna binding domain
  3i5x		Structure of mss116p bound to ssrna and amp-pnp
  3i5y		Structure of mss116p bound to ssrna containing a single 5- bru and amp-pnp
  3i61		Structure of mss116p bound to ssrna and adp-beryllium fluoride
  3i62		Structure of mss116p bound to ssrna and adp-aluminum fluoride

• Links (links to other resources describing this domain)

• PFAM	helicase_C
  INTERPRO	IPR001650

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