Secondary literature sources for the R3H domain

For each of the hand selected primary papers associated with the R3H domain, 100 neighbouring papers are retrieved from PubMed. If one of these neighbouring papers is referenced by more than two primary papers, it is shown in the table below.

An adeno-associated virus (AAV) initiator protein, Rep78, catalyzes thecleavage and ligation of single-stranded AAV ori DNA.

Smith RH, Kotin RM
J Virol. 2000; 74: 3122-9

The Rep78 protein of adeno-associated virus (AAV) contains amino acidsequence motifs common to rolling-circle replication (RCR) initiatorproteins. In this report, we describe RCR initiator-like activities ofRep78. We demonstrate that a maltose-binding protein (MBP)-Rep78 fusionprotein can catalyze the cleavage and ligation of single-stranded DNAsubstrates derived from the AAV origin of replication. Rep-mediatedsingle-stranded DNA cleavage was strictly dependent on the presence ofcertain divalent cations (e.g., Mn(2+) or Mg(2+)) but did not require thepresence of a nucleoside triphosphate cofactor. Electrophoretic mobilityshift assays demonstrated that binding of single-stranded DNA by MBP-Rep78was influenced by the length of the substrate as well as the presence ofpotential single-stranded cis-acting sequence elements. Site-directedmutagenesis was used to examine the role of specific tyrosine residueswithin a conserved RCR motif (motif 3) of Rep78. Replacement of Tyr-156with phenylalanine abolished the ability of MBP-Rep78 to mediate thecleavage and ligation of single-stranded DNA substrates but not theability to stably bind single-stranded DNA. The cleaving-joining activityof Rep78 is consistent with the mechanism of replicative intermediatedimer resolution proposed for the autonomous parvoviruses and may haveimplications for targeted integration of recombinant AAV vectors.

The Drosophila melanogaster BTB proteins bric a brac bind DNA through acomposite DNA binding domain containing a pipsqueak and an AT-Hook motif.

Lours C, Bardot O, Godt D, Laski FA, Couderc JL
Nucleic Acids Res. 2003; 31: 5389-98

The bric a brac (bab) locus is composed of two paralogous genes, bab1 andbab2, in Drosophila melanogaster. Bab1 and Bab2 are nuclear proteins thatcontain a broad complex, tramtrack, bric a brac/poxviruses and zinc-finger(BTB/POZ) domain. Many BTB/POZ proteins are transcriptional regulators ofwhich the majority contain C(2)H(2) zinc-finger motifs. There is nodetectable zinc-finger motif in either Bab protein. However, they sharethe Bab conserved domain (BabCD) that is highly conserved between Bab1 andBab2, and the Bab proteins of several other species, e.g. Anophelesgambiae, Apis mellifera and Drosophila virilis. Here we show that Bab2binds to several discrete sites on polytene chromosomes including the bablocus, and that the BabCD of both Bab1 and Bab2 binds in vitro to thecis-regulatory regions of bab1 and bab2. Our results indicate that theBabCD binds to A/T-rich regions and that its optimum binding sites containTA or TAA repeats. The BabCD is a composite DNA binding domain with a psqmotif and an AT-Hook motif; both motifs are required for DNA bindingactivity. Structural similarities suggest that the BabCD may bind to DNAin a similar manner as some prokaryotic recombinases.

The single-stranded DNA-binding proteins, Puralpha, Purbeta, and MSY1specifically interact with an exon 3-derived mouse vascular smooth musclealpha-actin messenger RNA sequence.

Kelm RJ Jr, Elder PK, Getz MJ
J Biol Chem. 1999; 274: 38268-75

Amino acids 44-53 of mouse vascular smooth muscle alpha-actin are encodedby a region of exon 3 that bears structural similarity to an essentialMCAT enhancer element in the 5' promoter of the gene. The single-strandedDNA-binding proteins, Puralpha, Purbeta, and MSY1, interact with eachother and with opposite strands of the enhancer to repress transcriptionin fibroblasts (Sun, S., Stoflet, E. S., Cogan, J. G., Strauch, A. R., andGetz, M. J. (1995) Mol. Cell. Biol. 15, 2429-2436; Kelm, R. J., Jr.,Cogan, J. G., Elder, P. K., Strauch, A. R., and Getz, M. J. (1999) J.Biol. Chem. 274, 14238-14245). In this study, we employed both recombinantand fibroblast-derived proteins to demonstrate that all three proteinsspecifically interact with the mRNA counterpart of the exon 3 sequence incell-free binding assays. When placed in the 5'-untranslated region of areporter mRNA, the exon 3-derived sequence suppressed mRNA translation intransfected fibroblasts. Translational efficiency was restored bymutations that impaired mRNA binding of Puralpha, Purbeta, and MSY1,implying that these proteins can also participate in messengerribonucleoprotein formation in living cells. Additionally, primarystructure determinants required for interaction of Purbeta withsingle-stranded DNA, mRNA, and protein ligands were mapped by deletionmutagenesis. These experiments reveal highly specific protein-mRNAinteractions that are potentially important in regulating expression ofthe vascular smooth muscle alpha-actin gene in fibroblasts.

Y box-binding protein-1 binds preferentially to single-stranded nucleicacids and exhibits 3'-->5' exonuclease activity.

Izumi H, Imamura T, Nagatani G, Ise T, Murakami T, Uramoto H, Torigoe T, Ishiguchi H, Yoshida Y, Nomoto M, Okamoto T, Uchiumi T, Kuwano M, Funa K, Kohno K
Nucleic Acids Res. 2001; 29: 1200-7

We have previously shown that Y box-binding protein-1 (YB-1) bindspreferentially to cisplatin-modified Y box sequences. Based on structuraland biochemical data, we predicted that this protein binds single-strandednucleic acids. In the present study we confirmed the prediction and alsodiscovered some unexpected functional features of YB-1. We found that thecold shock domain of the protein is necessary but not sufficient fordouble-stranded DNA binding while the C-tail domain interacts with bothsingle-stranded DNA and RNA independently of the cold shock domain. In anin vitro translation system the C-tail domain of the protein inhibitedtranslation but the cold shock domain did not. Both in vitro pull-down andin vivo co-immunoprecipitation assays revealed that YB-1 can form ahomodimer. Deletion analysis mapped the C-tail domain of the protein asthe region of homodimerization. We also characterized an intrinsic 3'-->5'DNA exonuclease activity of the protein. The region between residues 51and 205 of its 324-amino acid extent is required for full exonucleaseactivity. Our findings suggest that YB-1 functions in regulating DNA/RNAtransactions and that these actions involve different domains.

Insights into nonspecific binding of homeodomains from a structure ofMATalpha2 bound to DNA.

Aishima J, Wolberger C
Proteins. 2003; 51: 544-51

The 2.1-A resolution crystal structure of the MATalpha2 homeodomain boundto DNA reveals the unexpected presence of two nonspecifically bound alpha2homeodomains, in addition to the two alpha2 homeodomains bound tocanonical alpha2 binding sites. One of the extra homeodomains makes fewbase-specific contacts, while the other extra homeodomain binds to DNA ina previously unobserved manner. This unusually bound homeodomain isrotated on the DNA, making possible major groove contacts by side-chainsthat normally do not contact the DNA. This alternate docking may representone way in which homeodomains sample nonspecific DNA sequences.