ABSTRACT
We describe a method to analyze the sequence specificity of an RNA-binding domain. The method, which we have named scaffold-independent analysis, reports on the specificity for each nucleotide position within an RNA target, uncoupled from the surrounding structural and sequence context. We expect this information to improve our understanding of protein-RNA interfaces in ssRNA binding domains (e.g., KH or RRM domains) and to be useful to the design of novel protein-RNA recognition surfaces. Our NMR binding assays using the third KH domain of the Nova-1 protein provide a proof-of-principle for the method and novel information on the specificity of this domain for its RNA targets.
Subject(s)
Antigens, Neoplasm/chemistry , Nerve Tissue Proteins/chemistry , RNA-Binding Proteins/chemistry , RNA/chemistry , Antigens, Neoplasm/metabolism , Humans , Nerve Tissue Proteins/metabolism , Neuro-Oncological Ventral Antigen , Nuclear Magnetic Resonance, Biomolecular , Protein Structure, Tertiary , RNA/metabolism , RNA-Binding Proteins/metabolismABSTRACT
Pcf11 and Clp1 are subunits of cleavage factor IA (CFIA), an essential polyadenylation factor in Saccahromyces cerevisiae. We have determined the structure of a ternary complex of Clp1 together with ATP and the Clp1-binding region of Pcf11. Clp1 contains three domains, a small N-terminal beta sandwich domain, a C-terminal domain containing a novel alpha/beta-fold and a central domain that binds ATP. The arrangement of the nucleotide binding site is similar to that observed in SIMIBI-class ATPase subunits found in other multisubunit macromolecular complexes. However, despite this similarity, nucleotide hydrolysis does not occur. The Pcf11 binding site is also located in the central domain where three highly conserved residues in Pcf11 mediate many of the protein-protein interactions. We propose that this conserved Clp1-Pcf11 interaction is responsible for maintaining a tight coupling between the Clp1 nucleotide binding subunit and the other components of the polyadenylation machinery. Moreover, we suggest that this complex represents a stabilized ATP bound form of Clp1 that requires the participation of other non-CFIA processing factors in order to initiate timely ATP hydrolysis during 3' end processing.
Subject(s)
Adenosine Triphosphate/chemistry , Models, Molecular , Saccharomyces cerevisiae Proteins/chemistry , mRNA Cleavage and Polyadenylation Factors/chemistry , Adenosine Triphosphate/metabolism , Amino Acid Sequence , Binding Sites , Crystallography, X-Ray , Molecular Sequence Data , Saccharomyces cerevisiae Proteins/metabolism , Sequence Alignment , mRNA Cleavage and Polyadenylation Factors/metabolismABSTRACT
NusA is a key regulator of bacterial transcriptional elongation, pausing, termination and antitermination, yet relatively little is known about the molecular basis of its activity in these fundamental processes. In Mycobacterium tuberculosis, NusA has been shown to bind with high affinity and specificity to BoxB-BoxA-BoxC antitermination sequences within the leader region of the single ribosomal RNA (rRNA) operon. We have determined high-resolution X-ray structures of a complex of NusA with two short oligo-ribonucleotides derived from the BoxC stem-loop motif and have characterised the interaction of NusA with a variety of RNAs derived from the antitermination region. These structures reveal the RNA bound in an extended conformation to a large interacting surface on both KH domains. Combining structural data with observed spectral and calorimetric changes, we now show that NusA binding destabilises secondary structure within rRNA antitermination sequences and propose a model where NusA functions as a chaperone for nascently forming RNA structures.
Subject(s)
Bacterial Proteins/chemistry , Mycobacterium tuberculosis/genetics , Peptide Elongation Factors/chemistry , RNA, Ribosomal/chemistry , RNA-Binding Proteins/chemistry , Transcription Factors/chemistry , Amino Acid Sequence , Base Sequence , Crystallography, X-Ray , Escherichia coli Proteins , Molecular Sequence Data , Nucleic Acid Conformation , Protein Conformation , RNA, Bacterial/chemistry , Transcriptional Elongation FactorsABSTRACT
Creatinine amidohydrolase (creatininase; EC 3.5.2.10) from Pseudomonas putida, a homohexameric enzyme with a molecular mass of 28.4 kDa per subunit, is a cyclic amidohydrolase catalysing the reversible conversion of creatinine to creatine. The enzyme plays a key role in the bacterial degradation of creatinine. The three-dimensional structure of creatininase from P.putida was determined and refined to 2.1A. The structure shows the six subunits arranged as a trimer of dimers and definitely disproves previous reports that the enzyme has an octameric quaternary structure. Each monomer consists of a central, four-stranded, parallel beta-sheet flanked by two alpha-helices on both sides of the beta-sheet. This topology is unique within the superfamily of amidohydrolases. Moreover, creatininase possesses a novel fold with no close structural relatives within the Protein Data Bank. Each creatininase monomer contains a binuclear zinc centre near the C termini of the beta-strands and the N termini of the main alpha-helices. These zinc ions indicate the location of the active site unambiguously. The active site is entirely buried and is not accessible from the solution without movement of parts of the protein. The two zinc ions are bridged by a water molecule and by an aspartate residue, which acts as a bidentate ligand. They differ from each other in the number and the spatial arrangement of their ligands. One of them is tetrahedrally and the other trigonal-bipyramidally ligated. Using two water molecules of the first coordination sphere as anchor points, a creatinine-water adduct resembling the transition state of the hydrolysation reaction was modelled into the active site. The resulting complex in combination with structural comparisons with other amidohydrolases enabled us to identify the most probable candidate for the catalytic base and to suggest a putative reaction mechanism. Surprisingly these structural comparisons revealed a similarity in the active-site arrangement between creatininase and the hydantoinase-like cyclic amidohydrolases that was unexpected, given the completely unrelated primary and tertiary structures. In particular, the zinc-bridging aspartate residue of creatininase is a spatially and functionally analogue to a carboxylated lysine residue found in dihydroorotase and the hydantoinases. Hence, creatininase and the hydantoinase-like cyclic amidohydrolases represent a further example of convergent evolution within the enzyme class of hydrolases.
Subject(s)
Amidohydrolases/chemistry , Evolution, Molecular , Protein Folding , Protein Structure, Tertiary , Pseudomonas putida/enzymology , Amidohydrolases/metabolism , Amino Acid Sequence , Binding Sites , Crystallography, X-Ray , Models, Molecular , Molecular Sequence Data , Molecular Structure , Protein Structure, Quaternary , Sequence Alignment , Substrate Specificity , Zinc/chemistryABSTRACT
Creatininase (CrnA) from Pseudomonas putida is a homohexameric heat-stable enzyme composed of 259 amino acids per subunit. The molecular weight of each monomer is 28.4 kDa. The enzyme hydrolyses creatinine to yield creatine. Crystals of this protein have been grown from ethanol/PEG 8000. They belong to the monoclinic space group P2(1), with unit-cell parameters a = 74.8, b = 95.7, c = 116.9 A, alpha = gamma = 90, beta = 103.8 degrees. The diffraction limit is 2.5 A. The self-rotation function of the native data set is consistent with a CrnA hexamer in the asymmetric unit and suggests D(3) point-group symmetry of the enzyme.