scholarly journals Determinants of HMGB Proteins Required To Promote RAG1/2-Recombination Signal Sequence Complex Assembly and Catalysis during V(D)J Recombination

2005 ◽  
Vol 25 (11) ◽  
pp. 4413-4425 ◽  
Author(s):  
Yan Dai ◽  
Ben Wong ◽  
Yi-Meng Yen ◽  
Marjorie A. Oettinger ◽  
Jongbum Kwon ◽  
...  
Keyword(s):  
Dna Binding ◽  
Signal Sequence ◽  
Recombination Signal Sequence ◽  
Dna Complexes ◽  
Recombination Signal ◽  
Dna Binding Domains ◽  
Naked Dna ◽  
Binding Domains ◽  
Dna Binding And Bending ◽  
Hmgb Proteins

ABSTRACT Efficient assembly of RAG1/2-recombination signal sequence (RSS) DNA complexes that are competent for V(D)J cleavage requires the presence of the nonspecific DNA binding and bending protein HMGB1 or HMGB2. We find that either of the two minimal DNA binding domains of HMGB1 is effective in assembling RAG1/2-RSS complexes on naked DNA and stimulating V(D)J cleavage but that both domains are required for efficient activity when the RSS is incorporated into a nucleosome. The single-domain HMGB protein from Saccharomyces cerevisiae, Nhp6A, efficiently assembles RAG1/2 complexes on naked DNA; however, these complexes are minimally competent for V(D)J cleavage. Nhp6A forms much more stable DNA complexes than HMGB1, and a variety of mutations that destabilize Nhp6A binding to bent microcircular DNA promote increased V(D)J cleavage. One of the two DNA bending wedges on Nhp6A and the analogous phenylalanine wedge at the DNA exit site of HMGB1 domain A were found to be essential for promoting RAG1/2-RSS complex formation. Because the phenylalanine wedge is required for specific recognition of DNA kinks, we propose that HMGB proteins facilitate RAG1/2-RSS interactions by recognizing a distorted DNA structure induced by RAG1/2 binding. The resulting complex must be sufficiently dynamic to enable the series of RAG1/2-mediated chemical reactions on the DNA.

Biochemical and Immunological Characterization of the DNA Binding Protein (RBP-Jx) to Mouse Jx Recombination Signal Sequence

1992 ◽  
Vol 112 (3) ◽  
pp. 314-320 ◽  
Author(s):  
Yasushi Hamaguchi ◽  
Yoshiki Yamamoto ◽  
Hiroko Iwanari ◽  
Shingo Maruyama ◽  
Takahisa Furukawa ◽  
...  
Keyword(s):  
Dna Binding ◽  
Signal Sequence ◽  
Binding Protein ◽  
Dna Binding Protein ◽  
Recombination Signal Sequence ◽  
Immunological Characterization ◽  
Recombination Signal

Crystals of ternary protein–DNA complexes composed of DNA-binding domains of c-Myb or v-Myb, C/EBPα or C/EBPβ andtom-1A promoter fragment

2001 ◽  
Vol 57 (11) ◽  
pp. 1655-1658 ◽  
Author(s):  
Tahir H. Tahirov ◽  
Motoko Sasaki ◽  
Taiko Inoue-Bungo ◽  
Atsushi Fujikawa ◽  
Ko Sato ◽  
...  
Keyword(s):  
Dna Binding ◽  
Dna Complexes ◽  
Promoter Fragment ◽  
Dna Binding Domains ◽  
Binding Domains

Heteronuclear Strategies for the Assignment of Larger protein/DNA complexes: Application to the 37 kDa trp Represser-Operator Complex

1997 ◽  
Author(s):  
M.J. Revington ◽  
W. Lee
Keyword(s):  
Dna Binding ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Nmr Studies ◽  
Dna Complexes ◽  
Dna Binding Domains ◽  
Binding Domains

The sequence-specific DNA binding function of many proteins is recognized as one of the central mechanisms of regulating transcription and DNA replication and repair. The ability of these proteins to select a short (usually 10 to 20 basepair) sequence out of the entire genome with which to form a stable complex is a prime example of molecular recognition. Atomic resolution structural studies using NMR and X-ray crystallography have emerged as essential techniques in understanding the basis of specificity and stability in these systems. While NMR studies of small DNA-binding domains of proteins have become almost routine (see Kaptein, 1993 for a review) relatively few NMR studies of protein-DNA complexes have been reported. These include the lac repressor headpiece complex (Chuprina et al., 1993). the Antennapedia homeodomain complex (Billetere et al., 1993), the GATA-1 complex (Omichinski et al., 1993). and the Myb DNA binding domain complex (Ogata et al., 1993); all of these complexes are smaller than 20 kDa. In most cases, size limitations have meant that only the DNA binding domain of the protein in complex with a single binding element have been studied. In vivo, however, most DNA binding proteins are much larger than these domains and often function as oligomers. The decrease in quality and increase in complexity of spectra as the molecular weight of the sample increases, limits the number of systems amenable to study using NMR and influences the decision to focus on single domains of multidomain proteins. However, since many DNA-binding proteins are regulated by the binding of ligands, other proteins or phosphorylation, often at sites distal from the DNA-binding domain, it is preferable to study as much of the intact protein as possible in order to characterize allosteric and regulatory mechanisms (Pabo and Sauer, 1992). E. coli trp repressor is a 25 kDa homodimer that regulates operons involved in tryptophan biosynthesis. The dimer is one of the smallest intact proteins that binds sequence specifically to DNA and whose affinity is modulated by an effector (L-tryptophan).

scholarly journals Mechanistic Heterogeneity in Site Recognition by the Structurally Homologous DNA-binding Domains of the ETS Family Transcription Factors Ets-1 and PU.1

2014 ◽  
Vol 289 (31) ◽  
pp. 21605-21616 ◽  
Author(s):  
Shuo Wang ◽  
Miles H. Linde ◽  
Manoj Munde ◽  
Victor D. Carvalho ◽  
W. David Wilson ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Ets Family ◽  
Site Recognition

scholarly journals Protein Kinase A Signaling Pathway Regulates Transcriptional Activity of SAF-1 by Unmasking Its DNA-binding Domains

2003 ◽  
Vol 278 (25) ◽  
pp. 22586-22595 ◽  
Author(s):  
Alpana Ray ◽  
Papiya Ray ◽  
Nicole Guthrie ◽  
Arvind Shakya ◽  
Deepak Kumar ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Dna Binding ◽  
Protein Kinase A ◽  
Signaling Pathway ◽  
Transcriptional Activity ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Kinase A

scholarly journals Role of Papillomavirus E1 Initiator Dimerization in DNA Replication

2005 ◽  
Vol 79 (13) ◽  
pp. 8661-8664 ◽  
Author(s):  
Stephen Schuck ◽  
Arne Stenlund
Keyword(s):  
Dna Replication ◽  
Dna Binding ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Severe Effect ◽  
Origin Of Dna Replication ◽  
Initiation Of Dna Replication

ABSTRACT Viral initiator proteins are polypeptides that form oligomeric complexes on the origin of DNA replication (ori). These complexes carry out a multitude of functions related to initiation of DNA replication, and although many of these functions have been characterized biochemically, little is understood about how the complexes are assembled. Here we demonstrate that loss of one particular interaction, the dimerization between E1 DNA binding domains, has a severe effect on DNA replication in vivo but has surprisingly modest effects on most individual biochemical activities in vitro. We conclude that the dimer interaction is primarily required for initial recognition of ori.

scholarly journals Cdc13 N-Terminal Dimerization, DNA Binding, and Telomere Length Regulation

2010 ◽  
Vol 30 (22) ◽  
pp. 5325-5334 ◽  
Author(s):  
Meghan T. Mitchell ◽  
Jasmine S. Smith ◽  
Mark Mason ◽  
Sandy Harper ◽  
David W. Speicher ◽  
...  
Keyword(s):  
Dna Binding ◽  
Telomere Length ◽  
Functional Characterization ◽  
Point Mutations ◽  
Telomeric Dna ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Length Regulation ◽  
Telomere Length Regulation

ABSTRACT The essential yeast protein Cdc13 facilitates chromosome end replication by recruiting telomerase to telomeres, and together with its interacting partners Stn1 and Ten1, it protects chromosome ends from nucleolytic attack, thus contributing to genome integrity. Although Cdc13 has been studied extensively, the precise role of its N-terminal domain (Cdc13N) in telomere length regulation remains unclear. Here we present a structural, biochemical, and functional characterization of Cdc13N. The structure reveals that this domain comprises an oligonucleotide/oligosaccharide binding (OB) fold and is involved in Cdc13 dimerization. Biochemical data show that Cdc13N weakly binds long, single-stranded, telomeric DNA in a fashion that is directly dependent on domain oligomerization. When introduced into full-length Cdc13 in vivo, point mutations that prevented Cdc13N dimerization or DNA binding caused telomere shortening or lengthening, respectively. The multiple DNA binding domains and dimeric nature of Cdc13 offer unique insights into how it coordinates the recruitment and regulation of telomerase access to the telomeres.

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