scholarly journals The crystal structure of ribosomal protein S4 reveals a two-domain molecule with an extensive RNA-binding surface: one domain shows structural homology to the ETS DNA-binding motif

1998 ◽  
Vol 17 (16) ◽  
pp. 4545-4558 ◽  
Author(s):  
C. Davies
Keyword(s):  
Crystal Structure ◽  
Dna Binding ◽  
Ribosomal Protein ◽  
Rna Binding ◽  
Binding Motif ◽  
Structural Homology ◽  
Binding Surface ◽  
Ribosomal Protein S4

scholarly journals Crystal structure and functional characterization of the human RBM25 PWI domain and its flanking basic region

2013 ◽  
Vol 450 (1) ◽  
pp. 85-94 ◽  
Author(s):  
Deshun Gong ◽  
Fan Yang ◽  
Fudong Li ◽  
Dandan Qian ◽  
Minhao Wu ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Alternative Splicing ◽  
Nucleic Acid ◽  
Rna Binding ◽  
Functional Characterization ◽  
Binding Motif ◽  
Nucleic Acid Binding ◽  
Binding Surface ◽  
Basic Region

Human RBM25 (RNA-binding motif protein 25) is a novel splicing factor that contains a PWI domain, a newly identified RNA/DNA-binding domain, and regulates Bcl-x pre-mRNA alternative splicing. The flanking basic region has been suggested to serve as a co-operative partner of the PWI domain in the binding of nucleic acids, but the structure of this basic region is unknown. In the present paper, we report the crystal structure of the RBM25 PWI domain and its flanking basic region. The PWI domain is revealed to comprise a conserved four-helix bundle, and the flanking basic region forms two α-helices and associates with helix H4 of the PWI domain. These interactions promote directly the formation of an enlarged nucleic-acid-binding platform. Structure-guided mutagenesis reveals a positively charged nucleic-acid-binding surface in the RBM25 PWI domain that is entirely different from that in the SRm160 PWI domain. Furthermore, we show that the promotion of the pro-apoptotic Bcl-xS isoform expression by RBM25 is facilitated by the PWI domain in vivo. Thus the present study suggests that the PWI domain plays an important role in the regulation of Bcl-x pre-mRNA alternative splicing.

scholarly journals Crystal structure of prokaryotic ribosomal protein L9: a bi-lobed RNA-binding protein.

1994 ◽  
Vol 13 (1) ◽  
pp. 205-212 ◽  
Author(s):  
D.W. Hoffman ◽  
C. Davies ◽  
S.E. Gerchman ◽  
J.H. Kycia ◽  
S.J. Porter ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Ribosomal Protein ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Ribosomal Protein L9

scholarly journals Ribosomal protein L7a binds RNA through two distinct RNA-binding domains

2004 ◽  
Vol 385 (1) ◽  
pp. 289-299 ◽  
Author(s):  
Giulia RUSSO ◽  
Monica CUCCURESE ◽  
Gianluca MONTI ◽  
Annapina RUSSO ◽  
Angela AMORESANO ◽  
...  
Keyword(s):  
Ribosomal Protein ◽  
Rna Binding ◽  
Limited Proteolysis ◽  
Ribosomal Subunit ◽  
The Other ◽  
Protein Domain ◽  
Binding Motif ◽  
Nucleic Acid Binding ◽  
Binding Domains ◽  
Rna Binding Domains

The human ribosomal protein L7a is a component of the major ribosomal subunit. We previously identified three nuclear-localization-competent domains within L7a, and demonstrated that the domain defined by aa (amino acids) 52–100 is necessary, although not sufficient, to target the L7a protein to the nucleoli. We now demonstrate that L7a interacts in vitro with a presumably G-rich RNA structure, which has yet to be defined. We also demonstrate that the L7a protein contains two RNA-binding domains: one encompassing aa 52–100 (RNAB1) and the other encompassing aa 101–161 (RNAB2). RNAB1 does not contain any known nucleic-acid-binding motif, and may thus represent a new class of such motifs. On the other hand, a specific region of RNAB2 is highly conserved in several other protein components of the ribonucleoprotein complex. We have investigated the topology of the L7a–RNA complex using a recombinant form of the protein domain that encompasses residues 101–161 and a 30mer poly(G) oligonucleotide. Limited proteolysis and cross-linking experiments, and mass spectral analyses of the recombinant protein domain and its complex with poly(G) revealed the RNA-binding region.

The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes

2003 ◽  
Vol 10 (12) ◽  
pp. 1026-1032 ◽  
Author(s):  
Ji-Joon Song ◽  
Jidong Liu ◽  
Niraj H Tolia ◽  
Jonathan Schneiderman ◽  
Stephanie K Smith ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Rna Binding ◽  
Binding Motif ◽  
Paz Domain

scholarly journals The Contribution of Ribosomal Protein S1 to the Structure and Function of Qβ Replicase

Acta Naturae ◽  
2017 ◽  
Vol 9 (4) ◽  
pp. 26-30
Author(s):  
Z. Sh. Kutlubaeva ◽  
Е. V. Chetverina ◽  
A. B. Chetverin
Keyword(s):  
Crystal Structure ◽  
Ribosomal Protein ◽  
Rna Binding ◽  
Structure And Function ◽  
Ribosomal Protein S1 ◽  
Bacterial Ribosome ◽  
New Findings ◽  
Replicase Complex ◽  
And Function ◽  
Fixed Structure

The high resolution crystal structure of bacterial ribosome was determined more than 10 years ago; however, it contains no information on the structure of the largest ribosomal protein, S1. This unusual protein comprises six flexibly linked domains; therefore, it lacks a fixed structure and this prevents the formation of crystals. Besides being a component of the ribosome, protein S1 also serves as one of the four subunits of Q replicase, the RNA-directed RNA polymerase of bacteriophage Q. In each case, the role of this RNA-binding protein has been thought to consist in holding the template close to the active site of the enzyme. In recent years, a breakthrough was made in studies of protein S1 within Q replicase. This includes the discovery of its paradoxical ability to displace RNA from the replicase complex and determining the crystal structure of its fragment capable of performing this function. The new findings call for a re-examination of the contribution of protein S1 to the structure and function of the ribosome.

scholarly journals 1.55 Å resolution X-ray crystal structure of Rv3902c fromMycobacterium tuberculosis

2014 ◽  
Vol 70 (4) ◽  
pp. 414-417 ◽  
Author(s):  
Bharat G. Reddy ◽  
Derek B. Moates ◽  
Heung-Bok Kim ◽  
Todd J. Green ◽  
Chang-Yub Kim ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Mycobacterium Tuberculosis ◽  
Main Chain ◽  
Binding Pocket ◽  
Bacterial Pathogenesis ◽  
Crystallographic Structure ◽  
Binding Motif ◽  
Structural Homology ◽  
X Ray ◽  
Β Sheets

The crystallographic structure of theMycobacterium tuberculosis(TB) protein Rv3902c (176 residues; molecular mass of 19.8 kDa) was determined at 1.55 Å resolution. The function of Rv3902c is unknown, although several TB genes involved in bacterial pathogenesis are expressed from the operon containing the Rv3902c gene. The unique structural fold of Rv3902c contains two domains, each consisting of antiparallel β-sheets and α-helices, creating a hand-like binding motif with a small binding pocket in the palm. Structural homology searches reveal that Rv3902c has an overall structure similar to that of theSalmonellavirulence-factor chaperone InvB, with an r.m.s.d. for main-chain atoms of 2.3 Å along an aligned domain.

scholarly journals Crystal Structure of the Hyperthermophilic Archaeal DNA-Binding Protein Sso10b2 at a Resolution of 1.85 Angstroms

2003 ◽  
Vol 185 (14) ◽  
pp. 4066-4073 ◽  
Author(s):  
Chia-Cheng Chou ◽  
Ting-Wan Lin ◽  
Chin-Yu Chen ◽  
Andrew H.-J. Wang
Keyword(s):  
Crystal Structure ◽  
Dna Binding ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Binding Protein ◽  
Diffraction Method ◽  
Dna Binding Protein ◽  
Nucleic Acid Binding ◽  
Structure Topology ◽  
Acid Protein

ABSTRACT The crystal structure of a small, basic DNA binding protein, Sso10b2, from the thermoacidophilic archaeon Sulfolobus solfataricus was determined by the Zn multiwavelength anomalous diffraction method and refined to 1.85 Å resolution. The 89-amino-acid protein adopts a βαβαββ topology. The structure is similar to that of Sso10b1 (also called Alba) from the same organism. However, Sso10b2 contains an arginine-rich loop RDRRR motif, which may play an important role in nucleic acid binding. There are two independent Sso10b2 proteins in the asymmetric unit, and a plausible stable dimer could be deduced from the crystal structure. Topology comparison revealed that Sso10b2 is similar to several RNA-binding proteins, including IF3-C, YhhP, and DNase I. Models of the Sso10b2 dimer bound to either B-DNA or A-DNA have been constructed.

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