Cloning and characterization of HARP/SMARCAL1: a prokaryotic HepA-related SNF2 helicase protein from human and mouse

Genomics. 2000 May 1;65(3):274-82. doi: 10.1006/geno.2000.6174.


The SNF2 gene family consists of a large group of proteins involved in transcriptional regulation, maintenance of chromosome integrity, and various aspects of DNA repair. We cloned a novel SNF2 family human cDNA, with sequence identity to the Escherichia coli RNA polymerase-binding protein HepA and named the human hepA-related protein (HHARP/SMARCAL1). In addition, the mouse ortholog (Mharp/Smarcal1) was cloned, and the Caenorhabditis elegans ortholog (CEHARP) was identified in the GenBank database. Phylogenetic analysis indicates that the HARP proteins share a high level of sequence similarity to the seven motif helicase core region (SNF2 domain) with identifiable orthologs in other eukaryotic species, except for yeast. Purified His-tagged HARP/SMARCAL1 protein exhibits single-stranded DNA-dependent ATPase activity, consistent with it being a member of the SNF2 family of proteins. Both the human and the mouse genes consist of 17 exons and 16 introns. The human gene maps to chromosome 2q34-q36, and the mouse gene is localized to the syntenic region of chromosome 1 (between markers Gls and Acrg). HARP/SMARCAL1 transcripts are ubiquitously expressed in human and mouse tissues, with testis presenting the highest levels of mRNA expression in humans.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • ATP-Binding Cassette Transporters*
  • Adenosine Triphosphatases / metabolism
  • Amino Acid Motifs
  • Amino Acid Sequence
  • Animals
  • Bacterial Proteins / chemistry
  • Bacterial Proteins / genetics*
  • Bacterial Proteins / metabolism
  • Chromosome Mapping
  • Cloning, Molecular
  • DNA Helicases / chemistry
  • DNA Helicases / genetics*
  • DNA Helicases / metabolism
  • DNA, Complementary / genetics
  • DNA-Binding Proteins / chemistry
  • DNA-Binding Proteins / genetics*
  • DNA-Binding Proteins / metabolism
  • Humans
  • Mice
  • Molecular Sequence Data
  • Nuclear Proteins*
  • Phylogeny
  • Prokaryotic Cells
  • Protein Structure, Tertiary
  • RNA, Messenger / metabolism
  • Sequence Alignment
  • Transcription Factors / chemistry
  • Transcription Factors / genetics*
  • Transcription Factors / metabolism


  • ATP-Binding Cassette Transporters
  • Bacterial Proteins
  • DNA, Complementary
  • DNA-Binding Proteins
  • Nuclear Proteins
  • RNA, Messenger
  • SMARCA1 protein, human
  • SMARCA2 protein, human
  • Smarca2 protein, mouse
  • Transcription Factors
  • hepA protein, Anabaena
  • SMARCAL1 protein, human
  • Smarcal1 protein, mouse
  • Adenosine Triphosphatases
  • SMARCA4 protein, human
  • Smarca4 protein, mouse
  • DNA Helicases

Associated data

  • GENBANK/AF082179
  • GENBANK/AF209773
  • GENBANK/AF210833
  • GENBANK/AF210834
  • GENBANK/AF210835
  • GENBANK/AF210836
  • GENBANK/AF210837
  • GENBANK/AF210838
  • GENBANK/AF210839
  • GENBANK/AF210840
  • GENBANK/AF210841
  • GENBANK/AF210842