scholarly journals Crystal structure of the DdrB/ssDNA complex from Deinococcus radiodurans reveals a DNA binding surface involving higher-order oligomeric states

2013 ◽  
Vol 41 (21) ◽  
pp. 9934-9944 ◽  
Author(s):  
Seiji N. Sugiman-Marangos ◽  
John K. Peel ◽  
Yoni M. Weiss ◽  
Rodolfo Ghirlando ◽  
Murray S. Junop
Keyword(s):  
Crystal Structure ◽  
Dna Binding ◽  
Deinococcus Radiodurans ◽  
Higher Order ◽  
Binding Surface

scholarly journals Structural and Functional Basis for an EBNA1 Hexameric Ring in Epstein-Barr Virus Episome Maintenance

2017 ◽  
Vol 91 (19) ◽  
Author(s):  
Julianna S. Deakyne ◽  
Kimberly A. Malecka ◽  
Troy E. Messick ◽  
Paul M. Lieberman
Keyword(s):  
Crystal Structure ◽  
Dna Binding ◽  
Complex Formation ◽  
Epstein Barr Virus ◽  
Higher Order ◽  
Order Complex ◽  
Barr Virus ◽  
Naturally Occurring ◽  
Epstein Barr

ABSTRACT Epstein-Barr virus (EBV) establishes a stable latent infection that can persist for the life of the host. EBNA1 is required for the replication, maintenance, and segregation of the latent episome, but the structural features of EBNA1 that confer each of these functions are not completely understood. Here, we have solved the X-ray crystal structure of an EBNA1 DNA-binding domain (DBD) and discovered a novel hexameric ring oligomeric form. The oligomeric interface pivoted around residue T585 as a joint that links and stabilizes higher-order EBNA1 complexes. Substitution mutations around the interface destabilized higher-order complex formation and altered the cooperative DNA-binding properties of EBNA1. Mutations had both positive and negative effects on EBNA1-dependent DNA replication and episome maintenance with OriP. We found that one naturally occurring polymorphism in the oligomer interface (T585P) had greater cooperative DNA binding in vitro, minor defects in DNA replication, and pronounced defects in episome maintenance. The T585P mutant was compromised for binding to OriP in vivo as well as for assembling the origin recognition complex subunit 2 (ORC2) and trimethylated histone 3 lysine 4 (H3K4me3) at OriP. The T585P mutant was also compromised for forming stable subnuclear foci in living cells. These findings reveal a novel oligomeric structure of EBNA1 with an interface subject to naturally occurring polymorphisms that modulate EBNA1 functional properties. We propose that EBNA1 dimers can assemble into higher-order oligomeric structures important for diverse functions of EBNA1. IMPORTANCE Epstein-Barr virus is a human gammaherpesvirus that is causally associated with various cancers. Carcinogenic properties are linked to the ability of the virus to persist in the latent form for the lifetime of the host. EBNA1 is a sequence-specific DNA-binding protein that is consistently expressed in EBV tumors and is the only viral protein required to maintain the viral episome during latency. The structural and biochemical mechanisms by which EBNA1 allows the long-term persistence of the EBV genome are currently unclear. Here, we have solved the crystal structure of an EBNA1 hexameric ring and characterized key residues in the interface required for higher-order complex formation and long-term plasmid maintenance.

scholarly journals Crystal structure and DNA-binding analysis of RecO from Deinococcus radiodurans

2005 ◽  
Vol 24 (5) ◽  
pp. 906-918 ◽  
Author(s):  
Ingar Leiros ◽  
Joanna Timmins ◽  
David R Hall ◽  
Sean McSweeney
Keyword(s):  
Crystal Structure ◽  
Dna Binding ◽  
Deinococcus Radiodurans ◽  
Binding Analysis

scholarly journals Crystal Structure of the SarS Protein from Staphylococcus aureus

2003 ◽  
Vol 185 (14) ◽  
pp. 4219-4225 ◽  
Author(s):  
Ronggui Li ◽  
Adhar C. Manna ◽  
Shaodong Dai ◽  
Ambrose L. Cheung ◽  
Gongyi Zhang
Keyword(s):  
Crystal Structure ◽  
Staphylococcus Aureus ◽  
Dna Binding ◽  
Efflux Pump ◽  
Sequence Similarity ◽  
Protein Family ◽  
Proper Function ◽  
Regulation Mechanism ◽  
Winged Helix ◽  
Binding Surface

ABSTRACT The expression of virulence determinants in Staphylococcus aureus is controlled by global regulatory loci (e.g., sarA and agr). One of these determinants, protein A (spa), is activated by sarS, which encodes a 250-residue DNA-binding protein. Genetic analysis indicated that the agr locus likely mediates spa repression by suppressing the transcription of sarS. Contrary to SarA and SarR, which require homodimer formation for proper function, SarS is unusual within the SarA protein family in that it contains two homologous halves, with each half sharing sequence similarity to SarA and SarR. Here we report the 2.2 Å resolution X-ray crystal structure of the SarS protein. SarS has folds similar to those of SarR and, quite plausibly, the native SarA structure. Two typical winged-helix DNA-binding domains are connected by a well-ordered loop. The interactions between the two domains are extensive and conserved. The putative DNA-binding surface is highly positively charged. In contrast, negatively charged patches are located opposite to the DNA-binding surface. Furthermore, sequence alignment and structural comparison revealed that MarR has folds similar to those of SarR and SarS. Members of the MarR protein family have previously been implicated in the negative regulation of an efflux pump involved in multiple antibiotic resistance in many gram-negative species. We propose that MarR also belongs to the winged-helix protein family and has a similar mode of DNA binding as SarR and SarS and possibly the entire SarA protein family member. Based on the structural differences of SarR, SarS, and MarR, we further classified these winged-helix proteins to three subfamilies, SarA, SarS, and MarR. Finally, a possible transcription regulation mechanism is proposed.

scholarly journals Crystal structure of chromo barrel domain of RBBP1

2018 ◽  
Author(s):  
Ming Lei ◽  
Yue Feng ◽  
Mengqi Zhou ◽  
Yuan Yang ◽  
Peter Loppnau ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Structural Analysis ◽  
Dna Binding ◽  
Surface Charge ◽  
Gene Transcription ◽  
Molecular Basis ◽  
Binding Ability ◽  
Histone Binding ◽  
Multidomain Protein ◽  
Binding Surface

AbstractRBBP1 is a retinoblastoma protein (pRb) binding protein acting as a repressor of gene transcription. RBBP1 is a multidomain protein including a chromo barrel domain, and its chromo barrel domain has been reported to recognize histone H4K20me3 weakly, and this binding is enhanced by the simultaneous binding of DNA. However, the molecular basis of this DNA-mediated histone binding by the chromo barrel domain of RBBP1 is unclear. Here we attempted to co-crystallize the chromo barrel domain of RBBP1 with either a histone H4K20me3 peptide alone or with both a histone H4K20me3 peptide and DNA, but only solved the peptide/DNA unbound crystal structure. Our structural analysis indicates that RBBP1 could interact with histone H4K20me3 similar to other histone binding chromo barrel domains, and the surface charge representation analysis of the chromo barrel domain of RBBP1 suggests that the chromo barrel domain of RBBP1 does not have a typical DNA binding surface, indicating that it might not bind to DNA. Consistently, our ITC assays also showed that DNA does not significantly enhance the histone binding ability of the chromo barrel domain of RBBP1.

scholarly journals Crystal Structure ofDeinococcus radioduransRecQ Helicase Catalytic Core Domain: The Interdomain Flexibility

2014 ◽  
Vol 2014 ◽  
pp. 1-8 ◽  
Author(s):  
Sheng-Chia Chen ◽  
Chi-Hung Huang ◽  
Chia Shin Yang ◽  
Tzong-Der Way ◽  
Ming-Chung Chang ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Deinococcus Radiodurans ◽  
Domain Architecture ◽  
Genome Integrity ◽  
Catalytic Core Domain ◽  
Catalytic Core ◽  
Core Domain ◽  
Winged Helix ◽  
Dna Helicases ◽  
E Coli

RecQ DNA helicases are key enzymes in the maintenance of genome integrity, and they have functions in DNA replication, recombination, and repair. In contrast to most RecQs, RecQ fromDeinococcus radiodurans(DrRecQ) possesses an unusual domain architecture that is crucial for its remarkable ability to repair DNA. Here, we determined the crystal structures of the DrRecQ helicase catalytic core and its ADP-bound form, revealing interdomain flexibility in its first RecA-like and winged-helix (WH) domains. Additionally, the WH domain of DrRecQ is positioned in a different orientation from that of theE. coliRecQ (EcRecQ). These results suggest that the orientation of the protein during DNA-binding is significantly different when comparing DrRecQ and EcRecQ.

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