Databases in Protein Crystallography

Kleywegt, Gerard J.; Jones, T. Alwyn

doi:10.1107/s0907444998007100

Cited by 506 publications

(435 citation statements)

References 63 publications

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“…Bond lengths for the thioester sulfur were derived from TOPPIX01 (33) in the Cambridge Structural Database. Atom names for the 4′ phosphopantetheine, stearate and decanoate heavy atoms were taken from the residues PNS, STE, and DKA, respectively, in the HIC-UP small molecule library (34). Protons were numbered according to the attached heavy atom, and an additional designator (1, 2, or 3) was appended to specify prochiral and methyl protons.…”

Section: Xplor Model Buildingmentioning

confidence: 99%

Solution Structures of Spinach Acyl Carrier Protein with Decanoate and Stearate^,

2006

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Acyl carrier protein (ACP) is a cofactor in a variety of biosynthetic pathways, including fatty acid metabolism. Thus it is of interest to determine structures of physiologically relevant ACP-fatty acid complexes. We report here the NMR solution structures of spinach ACP with decanoate (10:0-ACP) and stearate (18:0-ACP) attached to the 4′ phosphopantetheine prosthetic group. The protein in the fatty acid complexes adopts a single conformer, unlike apo-and holo-ACP, which interconvert in solution between two major conformers. The protein component of both 10:0-and 18:0-ACP adopts the four-helix bundle topology characteristic of ACP, and a fatty acid binding cavity was identified in both structures. Portions of the protein close in space to the fatty acid and the 4′ phosphopantetheine were identified using filtered/edited NOESY experiments. A docking protocol was used to generate protein structures containing bound fatty acid for 10:0-and 18:0-ACP. In both cases, the predominant structure contained fatty acid bound down the center of the helical bundle, in agreement with the location of the fatty acid binding pockets. These structures demonstrate the conformational flexibility of spinach-ACP and suggest how the protein changes to accommodate its myriad binding partners.Acyl carrier proteins participate in a wide variety of biosynthetic processes, including the synthesis of fatty acids (1), toxins (2), oligosaccharides (3,4), polyketides (5,6), biotin (7), and depsipeptides (8). They ferry small molecules between enzymes involved in biosynthesis by covalent linkage as a thioester to the thiol group of 4′-phosphopantetheine ( Figure 1). This prosthetic group is attached by a post-translational modification to a serine (S38 in spinach ACP 1 ) in the middle a conserved Asp-Ser-Leu (DSL) sequence. Whereas the sequences of different acyl carrier proteins are divergent, they share a similar four-helix bundle topology and often can be interchanged with full activity in reactions in vitro. This prompts the question: are ACPs simply passive molecules that constantly present their cargo to enzymes, or do protein-protein and protein-ligand interactions affect the utility of ACP as an enzyme substrate?One well-studied biosynthetic process involving ACP is the desaturation of the fatty acid stearate by the enzyme stearoyl-ACP Δ 9 -desaturase (Δ9D). This enzyme, in a reaction dependent on O 2 and reducing-equivalent, acts on ACP with an attached stearate (18:0-ACP) † This work was supported by the National Institutes of Health Grants R01 GM-50853 to B.G.F. and R01 GM-58667 to J.L.M. NMR data were collected at the National Magnetic Resonance Facility at Madison (NMRFAM), which is supported by grants from the NIH Center for Research Resources Biomedical Research Technology Program (P41 RR-02301) and the National Institutes of General Medical Sciences (P41 GM-GM66326) with additional instrumentation purchased with funds from the University of Wisconsin, the NSF Biological Instrumentation Program, the NIH Shared Instrumentat...

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Section: Xplor Model Buildingmentioning

confidence: 99%

Solution Structures of Spinach Acyl Carrier Protein with Decanoate and Stearate^,

2006

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“…31 Similarly, there are numerous databases that allow searching of the PDB for compounds present in protein-ligand complexes. [32][33][34][35] Unfortunately, these databases lack the ability to globally compare an active site identifi ed for a novel protein against the entire structural database, irrespective of the identity of the bound ligand, to determine the relative similarity in the sequence and structure of the active sites.…”

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confidence: 99%

Comparison of protein active site structures for functional annotation of proteins and drug design

et al. 2006

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Rapid and accurate functional assignment of novel proteins is increasing in importance, given the completion of numerous genome sequencing projects and the vastly expanding list of unannotated proteins. Traditionally, global primary‐sequence and structure comparisons have been used to determine putative function. These approaches, however, do not emphasize similarities in active site configurations that are fundamental to a protein's activity and highly conserved relative to the global and more variable structural features. The Comparison of Protein Active Site Structures (CPASS) database and software enable the comparison of experimentally identified ligand‐binding sites to infer biological function and aid in drug discovery. The CPASS database comprises the ligand‐defined active sites identified in the protein data bank, where the CPASS program compares these ligand‐defined active sites to determine sequence and structural similarity without maintaining sequence connectivity. CPASS will compare any set of ligand‐defined protein active sites, irrespective of the identity of the bound ligand. Proteins 2006. © 2006 Wiley‐Liss, Inc.

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“…Numerous groups have tried to make high-quality small molecules derived from PDB more easily accessible through online resources such as PDBsum [6], HIC-up [7] or MSD [8]. Nevertheless, these datasets are still riddled with errors and/or missing information.…”

Section: Introductionmentioning

confidence: 99%

A complete small molecule dataset from the protein data bank

Feldman¹,

Snyder²,

Ticoll³

et al. 2006

FEBS Letters

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A complete set of 6300 small molecule ligands was extracted from the protein data bank, and deposited online in PubChem as data source 'SMID'. This set's major improvement over prior methods is the inclusion of cyclic polypeptides and branched polysaccharides, including an unambiguous nomenclature, in addition to normal monomeric ligands. Only the best available example of each ligand structure is retained, and an additional dataset is maintained containing co-ordinates for all examples of each structure. Attempts are made to correct ambiguous atomic elements and other common errors, and a perception algorithm was used to determine bond order and aromaticity when no other information was available.

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Databases in Protein Crystallography

Abstract: Applications of structural databases in the protein crystallographic structure determination process are reviewed, using mostly examples from work carried out by the authors. Four application areas are discussed: model building, model re®nement, model validation and model analysis.

Cited by 506 publications

References 63 publications

Solution Structures of Spinach Acyl Carrier Protein with Decanoate and Stearate^,

Solution Structures of Spinach Acyl Carrier Protein with Decanoate and Stearate^,

Comparison of protein active site structures for functional annotation of proteins and drug design

A complete small molecule dataset from the protein data bank

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Databases in Protein Crystallography

Abstract: Applications of structural databases in the protein crystallographic structure determination process are reviewed, using mostly examples from work carried out by the authors. Four application areas are discussed: model building, model re®nement, model validation and model analysis.

Cited by 506 publications

References 63 publications

Solution Structures of Spinach Acyl Carrier Protein with Decanoate and Stearate,

Solution Structures of Spinach Acyl Carrier Protein with Decanoate and Stearate,

Comparison of protein active site structures for functional annotation of proteins and drug design

A complete small molecule dataset from the protein data bank

Contact Info

Product

Resources

About

Solution Structures of Spinach Acyl Carrier Protein with Decanoate and Stearate^,

Solution Structures of Spinach Acyl Carrier Protein with Decanoate and Stearate^,