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 Structural analysis of human dual-specificity phosphatase 22 complexed with a phosphotyrosine-like substrate

2015 ◽  
Vol 71 (2) ◽  
pp. 199-205 ◽  
Author(s):  
George T. Lountos ◽  
Scott Cherry ◽  
Joseph E. Tropea ◽  
David S. Waugh
Keyword(s):  
Crystal Structure ◽  
Structural Analysis ◽  
Phosphatase Activity ◽  
Small Molecule ◽  
Molecular Basis ◽  
Protein Tyrosine Phosphatases ◽  
Simple Method ◽  
Dual Specificity Phosphatase ◽  
Dual Specificity ◽  
Nitrophenyl Phosphate

4-Nitrophenyl phosphate (p-nitrophenyl phosphate, pNPP) is widely used as a small molecule phosphotyrosine-like substrate in activity assays for protein tyrosine phosphatases. It is a colorless substrate that upon hydrolysis is converted to a yellow 4-nitrophenolate ion that can be monitored by absorbance at 405 nm. Therefore, the pNPP assay has been widely adopted as a quick and simple method to assess phosphatase activity and is also commonly used in assays to screen for inhibitors. Here, the first crystal structure is presented of a dual-specificity phosphatase, human dual-specificity phosphatase 22 (DUSP22), in complex with pNPP. The structure illuminates the molecular basis for substrate binding and may also facilitate the structure-assisted development of DUSP22 inhibitors.

Conformational Studies of Triazole Based Flexible Molecules: A Comparative Analysis of Crystal Structure and Optimized Structure for DNA Binding Ability

2017 ◽  
Vol 2 (12) ◽  
pp. 3444-3451
Author(s):  
Ranjeet Kumar ◽  
Pratima Yadav ◽  
Shiv Pal ◽  
Krishnan R. Kumar ◽  
Balasubramanian Sridhar ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Comparative Analysis ◽  
Dna Binding ◽  
Binding Ability ◽  
Conformational Studies ◽  
Flexible Molecules

Crystal structure, DNA-binding ability and cytotoxic activity of platinum(II) 2,2′-dipyridylamine complexes

2004 ◽  
Vol 357 (1) ◽  
pp. 95-102 ◽  
Author(s):  
Chao Tu ◽  
Xuefeng Wu ◽  
Qin Liu ◽  
Xiaoyong Wang ◽  
Qiang Xu ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Dna Binding ◽  
Cytotoxic Activity ◽  
Binding Ability

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 Synthesis, X-ray crystal structure elucidation and Hirshfeld surface analysis of N-((4-(1H-benzo[d]imidazole-2-yl)phenyl)carbamothioyl)benzamide: investigations for elastase inhibition, antioxidant and DNA binding potentials for biological applications

RSC Advances ◽  
2020 ◽  
Vol 10 (35) ◽  
pp. 20837-20851
Author(s):  
Nasima Arshad ◽  
Mamoona Rafiq ◽  
Rabail Ujan ◽  
Aamer Saeed ◽  
Shahid I. Farooqi ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Dna Binding ◽  
Surface Analysis ◽  
Structure Elucidation ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
Biological Applications ◽  
Binding Ability ◽  
X Ray

A new compound based upon a benzimidazole thiourea moiety that has unique properties related to elastase inhibition, antioxidant and DNA binding ability has been studied.

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
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