scholarly journals PAM-Dependent Target DNA Recognition and Cleavage by C2c1 CRISPR-Cas Endonuclease

Cell ◽  
2016 ◽  
Vol 167 (7) ◽  
pp. 1814-1828.e12 ◽  
Author(s):  
Hui Yang ◽  
Pu Gao ◽  
Kanagalaghatta R. Rajashankar ◽  
Dinshaw J. Patel
Keyword(s):  
Dna Recognition ◽  
Target Dna

scholarly journals Structural basis for DNA recognition by the transcription regulator MetR

2016 ◽  
Vol 72 (6) ◽  
pp. 417-426 ◽  
Author(s):  
Avinash S. Punekar ◽  
Jonathan Porter ◽  
Stephen B. Carr ◽  
Simon E. V. Phillips
Keyword(s):  
Molecular Level ◽  
Dna Recognition ◽  
Data Driven ◽  
Structural Basis ◽  
Methionine Biosynthesis ◽  
Dna Complexes ◽  
Winged Helix ◽  
Target Dna ◽  
Operator Sequence ◽  
Dna Complex

MetR, a LysR-type transcriptional regulator (LTTR), has been extensively studied owing to its role in the control of methionine biosynthesis in proteobacteria. A MetR homodimer binds to a 24-base-pair operator region of themetgenes and specifically recognizes the interrupted palindromic sequence 5′-TGAA-N5-TTCA-3′. Mechanistic details underlying the interaction of MetR with its target DNA at the molecular level remain unknown. In this work, the crystal structure of the DNA-binding domain (DBD) of MetR was determined at 2.16 Å resolution. MetR-DBD adopts a winged-helix–turn–helix (wHTH) motif and shares significant fold similarity with the DBD of the LTTR protein BenM. Furthermore, a data-driven macromolecular-docking strategy was used to model the structure of MetR-DBD bound to DNA, which revealed that a bent conformation of DNA is required for the recognition helix α3 and the wing loop of the wHTH motif to interact with the major and minor grooves, respectively. Comparison of the MetR-DBD–DNA complex with the crystal structures of other LTTR-DBD–DNA complexes revealed residues that may confer operator-sequence binding specificity for MetR. Taken together, the results show that MetR-DBD uses a combination of direct base-specific interactions and indirect shape recognition of the promoter to regulate the transcription ofmetgenes.

scholarly journals Key determinants of target DNA recognition by retroviral intasomes

Retrovirology ◽  
2015 ◽  
Vol 12 (1) ◽  
Author(s):  
Erik Serrao ◽  
Allison Ballandras-Colas ◽  
Peter Cherepanov ◽  
Goedele N Maertens ◽  
Alan N Engelman
Keyword(s):  
Dna Recognition ◽  
Target Dna

scholarly journals Dynamic Conformational Change Regulates the Protein-DNA Recognition: An Investigation on Binding of a Y-Family Polymerase to Its Target DNA

2014 ◽  
Vol 10 (9) ◽  
pp. e1003804 ◽  
Author(s):  
Xiakun Chu ◽  
Fei Liu ◽  
Brian A. Maxwell ◽  
Yong Wang ◽  
Zucai Suo ◽  
...  
Keyword(s):  
Conformational Change ◽  
Dna Recognition ◽  
Target Dna ◽  
Y Family

scholarly journals Structural basis for the Target DNA recognition and binding by the MYB domain of phosphate starvation response 1

FEBS Journal ◽  
2019 ◽  
Author(s):  
Meiqin Jiang ◽  
Lifang Sun ◽  
Michail N. Isupov ◽  
Jennifer A. Littlechild ◽  
Xiuling Wu ◽  
...  
Keyword(s):  
Dna Recognition ◽  
Phosphate Starvation ◽  
Structural Basis ◽  
Starvation Response ◽  
Phosphate Starvation Response ◽  
Target Dna ◽  
Myb Domain

A Cas9-guide RNA complex preorganized for target DNA recognition

Science ◽  
2015 ◽  
Vol 348 (6242) ◽  
pp. 1477-1481 ◽  
Author(s):  
F. Jiang ◽  
K. Zhou ◽  
L. Ma ◽  
S. Gressel ◽  
J. A. Doudna
Keyword(s):  
Dna Recognition ◽  
Guide Rna ◽  
Target Dna ◽  
Rna Complex

scholarly journals Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease

Nature ◽  
2014 ◽  
Vol 513 (7519) ◽  
pp. 569-573 ◽  
Author(s):  
Carolin Anders ◽  
Ole Niewoehner ◽  
Alessia Duerst ◽  
Martin Jinek
Keyword(s):  
Dna Recognition ◽  
Structural Basis ◽  
Target Dna

scholarly journals Structure of WT1 zinc fingers bound to its cognate DNA: Implications of the KTS insert

2018 ◽  
Author(s):  
Raymond K. Yengo ◽  
Elmar Nurmemmedov ◽  
Marjolein M.G.M. Thunnissen
Keyword(s):  
Crystal Structure ◽  
Transcription Factor ◽  
Amino Acid ◽  
Dna Binding ◽  
Rna Splicing ◽  
Zinc Fingers ◽  
Dna Recognition ◽  
Life Forms ◽  
Target Dna ◽  
Partner Proteins

ABSTRACTWT1 is a transcription factor with a DNA binding N-terminal domain containing four C2H2-type zinc fingers. In order to perform its role as a transcription factor, WT1 needs to specifically recognize and properly bind to its target DNA. How this is done is still not completely clear. Two of WT1’s major isoforms are distinguished by the presence or absence of a 3 amino acid insert, Lysine-Threonine-Serine (KTS) in the linker between zinc-fingers 3 and 4. This KTS insert is conserved throughout all life forms expressing WT1. The –KTS isoform, which acts as a transcription factor, binds DNA with higher affinity than the +KTS isoform, which is thought to participate in RNA splicing and interaction with partner proteins. This study was aims at elucidating the effect of the KTS insert on DNA binding. Here we present the crystal structure of WT1 zinc fingers 2-4, with and without the KTS insert, bound to the WT1 9-base pair cognate DNA sequence, refined to 1.9 Å and 2.5 Å respectively. The structures show that the +KTS isoform of WT1 recognizes DNA with the same specificity as the –KTS isoform. The only differences in the DNA bound conformation of the two isoforms are found within the linker containing the KTS, and these mainly involve the loss of the C-capping interactions thought to stabilize the complex. These structures provide the molecular detail necessary for the interpretation of the WT1 transcriptional DNA recognition and validation of its transcriptional targets.

scholarly journals Cas3 Mediated Target DNA Recognition and Cleavage is Independent of the Composition and Architecture of Cascade Surveillance Complex

2019 ◽  
Author(s):  
Siddharth Nimkar ◽  
B. Anand
Keyword(s):  
Rna Processing ◽  
Dna Recognition ◽  
Nuclease Activity ◽  
Helicase Domain ◽  
Type I ◽  
Conserved Residues ◽  
Target Dna ◽  
Evolutionarily Conserved ◽  
Single Stranded Region

ABSTRACTIn type I CRISPR-Cas system, Cas3 –a nuclease cum helicase– in cooperation with Cascade surveillance complex cleaves the target DNA. Unlike the Cascade/I-E, which is composed of five subunits, the Cascade/I-C is made of only three subunits lacking the CRISPR RNA processing enzyme Cas6, whose role is assumed by Cas5. How these differences in the composition and organisation of Cascade subunits in type I-C influences the Cas3/I-C binding and its target cleavage mechanism is poorly understood. Here, we show that Cas3/I-C is intrinsically a single-strand specific promiscuous nuclease. Apart from the helicase domain, a constellation of highly conserved residues –that are unique to type I-C– located in the uncharacterised C-terminal domain appears to influence the nuclease activity. Recruited by Cascade/I-C, the HD nuclease of Cas3/I-C nicks the single-stranded region of the nontarget strand and positions the helicase motor. Powered by ATP, the helicase motor reels in the target DNA, until it encounters the roadblock en route, which stimulates the HD nuclease. Remarkably, we show that Cas3/I-C supplants Cas3/I-E for CRISPR interference in type I-E in vivo, suggesting that the target cleavage mechanism is evolutionarily conserved between type I-C and type I-E despite the architectural difference exhibited by Cascade/I-C and Cascade/I-E.

scholarly journals Structural basis of target DNA recognition by CRISPR-Cas12k for RNA-guided DNA transposition

2021 ◽  
Author(s):  
Renjian Xiao ◽  
Shukun Wang ◽  
Ruijie Han ◽  
Zhuang Li ◽  
Clinton Gabel ◽  
...  
Keyword(s):  
Dna Recognition ◽  
Structural Basis ◽  
Structural Elements ◽  
Dna Transposition ◽  
Guide Rna ◽  
Promising Tool ◽  
Target Dna ◽  
Dna Insertion ◽  
Type V

The type V-K CRISPR-Cas system, featured by Cas12k effector with a naturally inactivated RuvC domain and associated with Tn7-like transposon for RNA-guided DNA transposition, is a promising tool for precise DNA insertion. To reveal the mechanism underlying target DNA recognition, we determined a cryo-EM structure of Cas12k from cyanobacteria Scytonema hofmanni in complex with a single guide RNA (sgRNA) and a double-stranded target DNA. Coupled with mutagenesis and in vitro DNA transposition assay, our results revealed mechanisms for the recognition of the GGTT PAM sequence and the structural elements of Cas12k critical for RNA-guided DNA transposition. These structural and mechanistic insights should aid in the development of type V-K CRISPR-transposon systems as tools for genome editing.

scholarly journals Type V CRISPR-Cas Cpf1 endonuclease employs a unique mechanism for crRNA-mediated target DNA recognition

Cell Research ◽  
2016 ◽  
Vol 26 (8) ◽  
pp. 901-913 ◽  
Author(s):  
Pu Gao ◽  
Hui Yang ◽  
Kanagalaghatta R Rajashankar ◽  
Zhiwei Huang ◽  
Dinshaw J Patel
Keyword(s):  
Dna Recognition ◽  
Target Dna ◽  
Type V ◽  
Unique Mechanism
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