Browse
Submit Data
Databases
API
Help

Dataset Information

17 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Structure of the RecQ C-terminal domain of human Bloom syndrome protein.

ABSTRACT: Bloom syndrome is a rare genetic disorder characterized by genomic instability and cancer predisposition. The disease is caused by mutations of the Bloom syndrome protein (BLM). Here we report the crystal structure of a RecQ C-terminal (RQC) domain from human BLM. The structure reveals three novel features of BLM RQC which distinguish it from the previous structures of the Werner syndrome protein (WRN) and RECQ1. First, BLM RQC lacks an aromatic residue at the tip of the ?-wing, a key element of the RecQ-family helicases used for DNA-strand separation. Second, a BLM-specific insertion between the N-terminal helices exhibits a looping-out structure that extends at right angles to the ?-wing. Deletion mutagenesis of this insertion interfered with binding to Holliday junction. Third, the C-terminal region of BLM RQC adopts an extended structure running along the domain surface, which may facilitate the spatial positioning of an HRDC domain in the full-length protein.

SUBMITTER: Kim SY

PROVIDER: S-EPMC6505963 | biostudies-literature | 2013 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Structure of the RecQ C-terminal domain of human Bloom syndrome protein.

Kim Sun-Yong SY Hakoshima Toshio T Kitano Ken K

Scientific reports 20131121

Bloom syndrome is a rare genetic disorder characterized by genomic instability and cancer predisposition. The disease is caused by mutations of the Bloom syndrome protein (BLM). Here we report the crystal structure of a RecQ C-terminal (RQC) domain from human BLM. The structure reveals three novel features of BLM RQC which distinguish it from the previous structures of the Werner syndrome protein (WRN) and RECQ1. First, BLM RQC lacks an aromatic residue at the tip of the β-wing, a key element of ...[more]

PMID: 24257077

Similar Datasets

Recognition and Unfolding of c-MYC and Telomeric G-Quadruplex DNAs by the RecQ C-Terminal Domain of Human Bloom Syndrome Helicase.

Project description:G-quadruplex (G4) is a noncanonical DNA secondary structure formed by Hoogsteen base pairing. It is recognized by various DNA helicases involved in DNA metabolism processes such as replication and transcription. Human Bloom syndrome protein (BLM), one of five human RecQ helicases, is a G4 helicase. While several studies revealed the mechanism of G4 binding and unfolding by the conserved RecQ C-terminal (RQC) domain of BLM, how RQC recognizes different G4 topologies is still unclear. Here, we investigated the interaction of Myc-22(14/23T) G4 from the c-Myc promoter and hTelo G4 from the telomeric sequence with RQC. Myc-22(14/23T) and hTelo form parallel and (3+1) hybrid topologies, respectively. Our circular dichroism (CD) spectroscopy data indicate that RQC can partially unfold the parallel G4, even with a short 3' overhang, while it can only partially unfold the (3+1) hybrid G4 with a 3' overhang of 6 nucleotides or longer. We found that the intrinsic thermal stability of G4 does not determine RQC-induced G4 unfolding by comparing T m of G4s. We also showed that both parallel and (3+1) hybrid G4s bind to the β-wing region of RQC. Thermodynamic analysis using isothermal titration calorimetry (ITC) showed that all interactions were endothermic and entropically driven. We suggest that RQC partially unfolds the parallel G4 more efficiently than the (3+1) hybrid G4 and binds to various G4 structures using its β-wing region. By this information, our research provides new insights into the influence of G4 structure on DNA metabolic processes involving BLM.

| S-EPMC7315595 | biostudies-literature

Structure and function of the regulatory HRDC domain from human Bloom syndrome protein.

Project description:The helicase and RNaseD C-terminal (HRDC) domain, conserved among members of the RecQ helicase family, regulates helicase activity by virtue of variations in its surface residues. The HRDC domain of Bloom syndrome protein (BLM) is known as a critical determinant of the dissolution function of double Holliday junctions by the BLM-Topoisomerase III? complex. In this study, we determined the solution structure of the human BLM HRDC domain and characterized its DNA-binding activity. The BLM HRDC domain consists of five ?-helices with a hydrophobic 3(10)-helical loop between helices 1 and 2 and an extended acidic surface comprising residues in helices 3-5. The BLM HRDC domain preferentially binds to ssDNA, though with a markedly low binding affinity (K(d) ?100 ?M). NMR chemical shift perturbation studies suggested that the critical DNA-binding residues of the BLM HRDC domain are located in the hydrophobic loop and the N-terminus of helix 2. Interestingly, the isolated BLM HRDC domain had quite different DNA-binding modes between ssDNA and Holliday junctions in electrophoretic mobility shift assay experiments. Based on its surface charge separation and DNA-binding properties, we suggest that the HRDC domain of BLM may be adapted for a unique function among RecQ helicases--that of bridging protein and DNA interactions.

| S-EPMC2995041 | biostudies-literature

Structure and function of the regulatory C-terminal HRDC domain from Deinococcus radiodurans RecQ.

Project description:RecQ helicases are critical for maintaining genome integrity in organisms ranging from bacteria to humans by participating in a complex network of DNA metabolic pathways. Their diverse cellular functions require specialization and coordination of multiple protein domains that integrate catalytic functions with DNA-protein and protein-protein interactions. The RecQ helicase from Deinococcus radiodurans (DrRecQ) is unusual among RecQ family members in that it has evolved to utilize three 'Helicase and RNaseD C-terminal' (HRDC) domains to regulate its activity. In this report, we describe the high-resolution structure of the C-terminal-most HRDC domain of DrRecQ. The structure reveals unusual electrostatic surface features that distinguish it from other HRDC domains. Mutation of individual residues in these regions affects the DNA binding affinity of DrRecQ and its ability to unwind a partial duplex DNA substrate. Taken together, the results suggest the unusual electrostatic surface features of the DrRecQ HRDC domain may be important for inter-domain interactions that regulate structure-specific DNA binding and help direct DrRecQ to specific recombination/repair sites.

| S-EPMC2396406 | biostudies-literature

Residues in the RecQ C-terminal Domain of the Human Werner Syndrome Helicase Are Involved in Unwinding G-quadruplex DNA.

Project description:The structural and biophysical properties typically associated with G-quadruplex (G4) structures render them a significant block for DNA replication, which must be overcome for cell division to occur. The Werner syndrome protein (WRN) is a RecQ family helicase that has been implicated in the efficient processing of G4 DNA structures. The aim of this study was to identify the residues of WRN involved in the binding and ATPase-driven unwinding of G4 DNA. Using a c-Myc G4 DNA model sequence and recombinant WRN, we have determined that the RecQ-C-terminal (RQC) domain of WRN imparts a 2-fold preference for binding to G4 DNA relative to non-G4 DNA substrates. NMR studies identified residues involved specifically in interactions with G4 DNA. Three of the amino acids in the WRN RQC domain that exhibited the largest G4-specific changes in NMR signal were then mutated alone or in combination. Mutating individual residues implicated in G4 binding had a modest effect on WRN binding to DNA, decreasing the preference for G4 substrates by ∼25%. Mutating two G4-interacting residues (T1024G and T1086G) abrogated preferential binding of WRN to G4 DNA. Very modest decreases in G4 DNA-stimulated ATPase activity were observed for the mutant enzymes. Most strikingly, G4 unwinding by WRN was inhibited ∼50% for all three point mutants and >90% for the WRN double mutant (T1024G/T1086G) relative to normal B-form dsDNA substrates. Our work has helped to identify residues in the WRN RQC domain that are involved specifically in the interaction with G4 DNA.

| S-EPMC5336152 | biostudies-literature

The C-terminal domain of the Bloom syndrome DNA helicase is essential for genomic stability.

Project description:BACKGROUND:Bloom syndrome is a rare cancer-prone disorder in which the cells of affected persons have a high frequency of somatic mutation and genomic instability. Bloom syndrome cells have a distinctive high frequency of sister chromatid exchange and quadriradial formation. BLM, the protein altered in BS, is a member of the RecQ DNA helicase family, whose members share an average of 40% identity in the helicase domain and have divergent N-terminal and C-terminal flanking regions of variable lengths. The BLM DNA helicase has been shown to localize to the ND10 (nuclear domain 10) or PML (promyelocytic leukemia) nuclear bodies, where it associates with TOPIIIalpha, and to the nucleolus. RESULTS:This report demonstrates that the N-terminal domain of BLM is responsible for localization of the protein to the nuclear bodies, while the C-terminal domain directs the protein to the nucleolus. Deletions of the N-terminal domain of BLM have little effect on sister chromatid exchange frequency and chromosome stability as compared to helicase and C-terminal mutations which can increase SCE frequency and chromosome abnormalities. CONCLUSION:The helicase activity and the C-terminal domain of BLM are critical for maintaining genomic stability as measured by the sister chromatid exchange assay. The localization of BLM into the nucleolus by the C-terminal domain appears to be more important to genomic stability than localization in the nuclear bodies.

| S-EPMC35277 | biostudies-literature

Evolution of the RECQ family of helicases: A drosophila homolog, Dmblm, is similar to the human bloom syndrome gene.

Project description:Several eukaryotic homologs of the Escherichia coli RecQ DNA helicase have been found. These include the human BLM gene, whose mutation results in Bloom syndrome, and the human WRN gene, whose mutation leads to Werner syndrome resembling premature aging. We cloned a Drosophila melanogaster homolog of the RECQ helicase family, Dmblm (Drosophila melanogaster Bloom), which encodes a putative 1487-amino-acid protein. Phylogenetic and dot plot analyses for the RECQ family, including 10 eukaryotic and 3 prokaryotic genes, indicate Dmblm is most closely related to the Homo sapiens BLM gene, suggesting functional similarity. Also, we found that Dmblm cDNA partially rescued the sensitivity to methyl methanesulfonate of Saccharomyces cerevisiae sgs1 mutant, demonstrating the presence of a functional similarity between Dmblm and SGS1. Our analyses identify four possible subfamilies in the RECQ family: (1) the BLM subgroup (H. sapiens Bloom, D. melanogaster Dmblm, and Caenorhabditis elegans T04A11.6); (2) the yeast RECQ subgroup (S. cerevisiae SGS1 and Schizosaccharomyces pombe rqh1/rad12); (3) the RECQL/Q1 subgroup (H. sapiens RECQL/Q1 and C. elegans K02F3.1); and (4) the WRN subgroup (H. sapiens Werner and C. elegans F18C5.2). This result may indicate that metazoans hold at least three RECQ genes, each of which may have a different function, and that multiple RECQ genes diverged with the generation of multicellular organisms. We propose that invertebrates such as nematodes and insects are useful as model systems of human genetic diseases.

| S-EPMC1460517 | biostudies-other

Solution NMR structure of the N-terminal domain of the human DEK protein.

Project description:The human DEK protein has a long-standing association with carcinogenesis since the DEK gene was originally identified in the t(6:9) chromosomal translocation in a subtype of patients with acute myelogenous leukemia (AML). Recent studies have partly unveiled DEK's cellular functions including apoptosis inhibition in primary cells as well as cancer cells, determination of 3' splice site of transcribed RNA, and suppression of transcription initiation by polymerase II. It has been previously shown that the N-terminal region of DEK, spanning residues 68-226, confers important in vitro and in vivo functions of DEK, which include double-stranded DNA (ds-DNA) binding, introduction of constrained positive supercoils into closed dsDNA, and apoptosis inhibition. In this paper, we describe the three-dimensional structure of the N-terminal domain of DEK (DEKntd) as determined using solution NMR. The C-terminal part of DEKntd, which contains a putative DNA-binding motif (SAF/SAP motif), folds into a helix-loop-helix structure. Interestingly, the N-terminal part of DEKntd shows a very similar structure to the C-terminal part, although the N-terminal and the C-terminal part differ distinctively in their amino acid sequences. As a consequence, the structure of DEKntd has a pseudo twofold plane symmetry. In addition, we tested dsDNA binding of DEKntd by monitoring changes of NMR chemical shifts upon addition of dsDNAs. We found that not only the C-terminal part containing the SAF/SAP motif but the N-terminal part is also involved in DEKntd's dsDNA binding. Our study illustrates a new structural variant and reveals novel dsDNA-binding properties for proteins containing the SAP/SAF motif.

| S-EPMC2222715 | biostudies-literature

Solution NMR structure of the C-terminal domain of the human protein DEK.

Project description:The chromatin-associated protein DEK was first identified as a fusion protein in patients with a subtype of acute myelogenous leukemia. It has since become associated with diverse human ailments ranging from cancers to autoimmune diseases. Despite much research effort, the biochemical basis for these clinical connections has yet to be explained. We have identified a structural domain in the C-terminal region of DEK [DEK(309-375)]. DEK(309-375) implies clinical importance because it can reverse the characteristic abnormal DNA-mutagen sensitivity in fibroblasts from ataxia-telangiectasia (A-T) patients. We determined the solution structure of DEK(309-375) by nuclear magnetic resonance spectroscopy, and found it to be structurally homologous to the E2F/DP transcription factor family. On the basis of this homology, we tested whether DEK(309-375) could bind DNA and identified the DNA-interacting surface. DEK presents a hydrophobic surface on the side opposite the DNA-interacting surface. The structure of the C-terminal region of DEK provides insights into the protein function of DEK.

| S-EPMC2279821 | biostudies-literature

Structure and function of the C-terminal PABC domain of human poly(A)-binding protein.

Project description:We have determined the solution structure of the C-terminal quarter of human poly(A)-binding protein (hPABP). The protein fragment contains a protein domain, PABC [for poly(A)-binding protein C-terminal domain], which is also found associated with the HECT family of ubiquitin ligases. By using peptides derived from PABP interacting protein (Paip) 1, Paip2, and eRF3, we show that PABC functions as a peptide binding domain. We use chemical shift perturbation analysis to identify the peptide binding site in PABC and the major elements involved in peptide recognition. From comparative sequence analysis of PABC-binding peptides, we formulate a preliminary PABC consensus sequence and identify human ataxin-2, the protein responsible for type 2 spinocerebellar ataxia (SCA2), as a potential PABC ligand.

| S-EPMC31848 | biostudies-literature

Insights into the RecQ helicase mechanism revealed by the structure of the helicase domain of human RECQL5.

Project description:RecQ helicases are important maintainers of genome integrity with distinct roles in almost every cellular process requiring access to DNA. RECQL5 is one of five human RecQ proteins and is particularly versatile in this regard, forming protein complexes with a diverse set of cellular partners in order to coordinate its helicase activity to various processes including replication, recombination and DNA repair. In this study, we have determined crystal structures of the core helicase domain of RECQL5 both with and without the nucleotide ADP in two distinctly different ('Open' and 'Closed') conformations. Small angle X-ray scattering studies show that the 'Open' form of the protein predominates in solution and we discuss implications of this with regards to the RECQL5 mechanism and conformational changes. We have measured the ATPase, helicase and DNA binding properties of various RECQL5 constructs and variants and discuss the role of these regions and residues in the various RECQL5 activities. Finally, we have performed a systematic comparison of the RECQL5 structures with other RecQ family structures and based on these comparisons we have constructed a model for the mechano-chemical cycle of the common catalytic core of these helicases.

| S-EPMC5397160 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data