Solution NMR Structure of Ribosome-binding Factor A (RbfA), A Cold-shock Adaptation Protein from Escherichia coli

Huang, Yuanpeng Janet; Swapna, G.V.T.; Rajan, P.K.; Ke, Haiping; Xia, Bing; Shukla, Kamlesh Kumar; Inouye, Masayori; Montelione, Gaetano T.

doi:10.1016/s0022-2836(03)00061-5

Cited by 77 publications

(89 citation statements)

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“…In its unassigned form, an NOE restraint gives the information that two nuclei are approximately d Å apart (1.8 ≤ d ≤ 6) but not the identity of the two nuclei (in the primary sequence). Automated methods can be used to quickly obtain resonance assignments, but automated NOE assignment typically requires hours to weeks, since NOE assignment often sits in a tight inner loop of structure refinement (e.g., aria [Nilges et al, 1997], candid [Herrmann et al, 2002], auto-structure [Huang et al, 2003], and psad [Juszewski et al, 2004]). Furthermore, it is not uncommon to need manual intervention (e.g., to assign side-chain NOEs [Clore, 2000]) to obtain enough distance restraints (in conjunction with a priori restraints such as bond angles and bond lengths) to compute an accurate NMR structure.…”

Section: Wang Et Almentioning

confidence: 99%

A Polynomial-Time Algorithm for De Novo Protein Backbone Structure Determination from Nuclear Magnetic Resonance Data

Wang

Mettu

Donald

2006

Journal of Computational Biology

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We describe an efficient algorithm for protein backbone structure determination from solution Nuclear Magnetic Resonance (NMR) data. A key feature of our algorithm is that it finds the conformation and orientation of secondary structure elements as well as the global fold in polynomial time. This is the first polynomial-time algorithm for de novo high-resolution biomacromolecular structure determination using experimentally recorded data from either NMR spectroscopy or X-ray crystallography. Previous algorithmic formulations of this problem focused on using local distance restraints from NMR (e.g., nuclear Overhauser effect [NOE] restraints) to determine protein structure. This approach has been shown to be NP-hard, essentially due to the local nature of the constraints. In practice, approaches such as molecular dynamics and simulated annealing, which lack both combinatorial precision and guarantees on running time and solution quality, are used routinely for structure determination. We show that residual dipolar coupling (RDC) data, which gives global restraints on the orientation of internuclear bond vectors, can be used in conjunction with very sparse NOE data to obtain a polynomial-time algorithm for structure determination. Furthermore, an implementation of our algorithm has been applied to six different real biological NMR data sets recorded for three proteins. Our algorithm is combinatorially precise, polynomialtime, and uses much less NMR data to produce results that are as good or better than previous approaches in terms of accuracy of the computed structure as well as running time.

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Section: Wang Et Almentioning

confidence: 99%

A Polynomial-Time Algorithm for De Novo Protein Backbone Structure Determination from Nuclear Magnetic Resonance Data

Wang

Mettu

Donald

2006

Journal of Computational Biology

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“…A search for structural homologs [49] revealed that the N-terminal domain is similar to ribosomal binding factor A (RbfA) [50,51], which contains a type II KH RNAbinding fold (Z score of 3-4). However, the structural similarity probably does not carry over to function.…”

Section: Page 7 12/12/06mentioning

confidence: 99%

NMR structure of the N-terminal domain of the replication initiator protein DnaA

Lowery

Chandonia

Kim

et al. 2007

J Struct Funct Genomics

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DnaA is an essential component in the initiation of bacterial chromosomal replication. DnaA binds to a series of 9 base pair repeats leading to oligomerization, recruitment of the DnaBC helicase, and the assembly of the replication fork machinery. The structure of the N-terminal domain (residues 1 -100) of DnaA from Mycoplasma genitalium was determined by NMR spectroscopy. The backbone r.m.s.d. for the first 86 residues was 0.6 +/-0.2 Å based on 742 NOE, 50 hydrogen bond, 46 backbone angle, and 88 residual dipolar coupling restraints. Ultracentrifugation studies revealed that the domain is monomeric in solution. Features on the protein surface include a hydrophobic cleft flanked by several negative residues on one side, and positive residues on the other. A negatively charged ridge is present on the opposite face of the protein. These surfaces may be important sites of interaction with other proteins involved in the replication process. Together, the structure and NMR assignments should facilitate the design of new experiments to probe the protein-protein interactions essential for the initiation of DNA replication.Keywords: replication, DnaB, DiaA, ATPase, initiation Page 2 12/12/06The bacterial protein DnaA plays a central role in the initiation of chromosomal replication and is involved in the activation and repression of several genes, including its own gene (dnaA) in E.coli. Replication begins with the formation of oligomers of DnaA on recognition sites at the origin of replication (OriC). The DnaA complex unwinds and opens several AT-rich segments of doublestranded DNA within the origin and stabilizes the resulting single-strands. DnaA then recruits the DnaB helicase with help from DnaC to form the "prepriming complex" [1]. After priming of the singlestranded DNA, replication occurs by the action of DNA Polymerase III. ATP hydrolysis acts as the switch between active (ATP-bound) and inactive (ADP-bound) forms of DnaA. Initiation begins only with the ATP-bound form (for reviews see [2][3][4] , as well as domain IV bound to DNA [8] showed that domain III resembles other members of the AAA+ family of ATPases, and that domain IV adopts a helix-turn-helix DNA-binding fold. In contrast, the secondary structure of domain I has been predicted based on multiple sequence alignments [5,9,10], however, little is known about its tertiary structure.DnaA recognizes five high affinity 9 base pair sites as well as several lower affinity 6 base pair sites within OriC via the C-terminal helix-turn-helix DNA-binding domain (domain IV) [11,12]. In addition to direct binding, the formation of oligomers containing 20 to 30 molecules of DnaA at the origin has been demonstrated by electron microscopy [13,14]. The mechanism of oligomer formation has been studied extensively [3,15], but the nature of the complex remains poorly understood.Replacement of the dimerization domain of the lambda cI repressor with the N-terminal domain of DnaA resulted in a functional chimeric protein, suggesting direct interactions between the N-terminal ...

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“…Uniformly (U) 13 C, 15 N-labeled yqbG was cloned, expressed, and purified by following standard protocols. Briefly, the full-length gene from Bacillus subtilis was cloned into a pET21 (Novagen) derivative, yielding the plasmid pSR215-21.3.…”

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confidence: 99%

“…7 Assignments were obtained for 100% of the assignable backbone (excluding the N-terminal NH 3 ϩ , the Pro 15 N and the 13 CЈ shifts) and 13 Table I). Stereospecific assignments were obtained for 55% of the ␤-methylene groups exhibiting nondegenerated proton chemical shifts and for 80% of the Val and Leu isopropyl moieties (Table I).…”

mentioning

confidence: 99%

“…In addition, backbone dihedral angle constraints were derived from chemical shifts as described 10 for residues located in globally well-defined helices I-V (Table I). The programs CYANA 11,12 and AUTOSTRUCTURE 13 were used in parallel to automatically assign long-range NOEs. Coinciding assignments ("consensus assignments") were retained and established the starting point for manual completion of iterative NOE assignment, peak picking, and structure calculation.…”

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NMR structure of protein yqbG from Bacillus subtilis reveals a novel α‐helical protein fold

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Solution NMR Structure of Ribosome-binding Factor A (RbfA), A Cold-shock Adaptation Protein from Escherichia coli

Cited by 77 publications

References 50 publications

A Polynomial-Time Algorithm for De Novo Protein Backbone Structure Determination from Nuclear Magnetic Resonance Data

A Polynomial-Time Algorithm for De Novo Protein Backbone Structure Determination from Nuclear Magnetic Resonance Data

NMR structure of the N-terminal domain of the replication initiator protein DnaA

NMR structure of protein yqbG from Bacillus subtilis reveals a novel α‐helical protein fold

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