CaspR: a web server for automated molecular replacement using homology modelling

Claude, Jean‐Baptiste; Suhre, Karsten; Notredame, Cédric; Claverie, Jean‐Michel; Abergel, Chantal

doi:10.1093/nar/gkh400

Cited by 85 publications

(76 citation statements)

References 14 publications

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“…Attempts to solve the structure using the AMoRe molecular-replacement method (17) and multiple anomalous dispersion failed. Eventually, the crystal structure of the unliganded ePL kinase 1 was solved with the web tool CaspR, which executes an optimized molecularreplacement procedure using a combination of stand-alone software programs (6). The ePL kinase 1 sequence and three search models, ePL kinase 2 (Protein Data Bank [PDB] code 1TD2; 30% identity), sheep PL kinase (PDB code 1LHP; 30% identity), and 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate kinase from Salmonella enterica serovar Typhimurium (PDB code 1JXH; 27% identity), were first used to derive multiple structure-sequence alignments with the program T-Coffee (18), followed by homology model building with the program MODELLER (21).…”

Section: Methodsmentioning

confidence: 99%

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Crystal Structure of Pyridoxal Kinase from the Escherichia coli pdxK Gene: Implications for the Classification of Pyridoxal Kinases

et al. 2006

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The pdxK and pdxY genes have been found to code for pyridoxal kinases, enzymes involved in the pyridoxal phosphate salvage pathway. Two pyridoxal kinase structures have recently been published, including Escherichia coli pyridoxal kinase 2 (ePL kinase 2) and sheep pyridoxal kinase, products of the pdxY and pdxK genes, respectively. We now report the crystal structure of E. coli pyridoxal kinase 1 (ePL kinase 1), encoded by a pdxK gene, and an isoform of ePL kinase 2. The structures were determined in the unliganded and binary complexes with either MgATP or pyridoxal to 2.1-, 2.6-, and 3.2-Å resolutions, respectively. The active site of ePL kinase 1 does not show significant conformational change upon binding of either pyridoxal or MgATP. Like sheep PL kinase, ePL kinase 1 exhibits a sequential random mechanism. Unlike sheep pyridoxal kinase, ePL kinase 1 may not tolerate wide variation in the size and chemical nature of the 4 substituent on the substrate. This is the result of differences in a key residue at position 59 on a loop (loop II) that partially forms the active site. Residue 59, which is His in ePL kinase 1, interacts with the formyl group at C-4 of pyridoxal and may also determine if residues from another loop (loop I) can fill the active site in the absence of the substrate. Both loop I and loop II are suggested to play significant roles in the functions of PL kinases.Pyridoxal 5Ј-phosphate (PLP) serves as a cofactor for many enzymes involved in amino acid and sugar metabolism. In many bacteria and plants, PLP is synthesized by a de novo pathway, but most cells rely on a nutritional source of vitamin B 6 , i.e., pyridoxine (PN), pyridoxal (PL), and pyridoxamine (PM) (24). Most cell types have a salvage pathway for reutilizing the PL liberated during protein turnover (27). The salvage pathway involves an ATP-dependent pyridoxal kinase that phosphorylates PL, PN, and PM by transferring the terminal phosphate of ATP to the 5Ј-hydroxyl group of these substrates. The product of PN and PM phosphorylation is converted to PLP by pyridoxine 5Ј-phosphate oxidase, which is also expressed in most cells. The PL kinases that have been purified and studied show activity with PN and PM, in addition to PL, and are often referred to as PL/PN/PM kinases (14, 15). For brevity, we will refer to these enzymes as PL kinases with the understanding that many of them exhibit considerable activity with PN and PM.PL kinase has been purified from bacterial, plant, and mammalian sources, and evidence suggests that most organisms contain a single PL kinase, coded by a pdxK gene. However, studies with Escherichia coli mutants that were blocked in the de novo biosynthetic pathway and with an inactivated pdxK gene, which codes for E. coli pyridoxal kinase 1 (ePL kinase 1), were still able to grow on pyridoxal (26). A search for a gene that expressed a protein that had PL kinase activity in E. coli led to the discovery of the pdxY gene (26). The E. coli protein ePL kinase 2, expressed by this gene, was shown to have some PL kinase act...

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Section: Methodsmentioning

confidence: 99%

“…In many bacteria and plants, PLP is synthesized by a de novo pathway, but most cells rely on a nutritional source of vitamin B 6 , i.e., pyridoxine (PN), pyridoxal (PL), and pyridoxamine (PM) (24). Most cell types have a salvage pathway for reutilizing the PL liberated during protein turnover (27).…”

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confidence: 99%

Crystal Structure of Pyridoxal Kinase from the Escherichia coli pdxK Gene: Implications for the Classification of Pyridoxal Kinases

et al. 2006

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“…Solution of the 3D structure was achieved through molecular-replacement techniques, using the webserver CASPR (http://www.igs.cnrs-mrs.fr/Caspr2/) [63]. The crystal structure of At-2/2HbO (PDB code 2XYK) was used as the search model.…”

Section: Crystallization and Data Collectionmentioning

confidence: 99%

Structural flexibility of the heme cavity in the cold‐adapted truncated hemoglobin from the Antarctic marine bacterium Pseudoalteromonas haloplanktis TAC125

et al. 2015

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*These authors contributed equally to this workTruncated hemoglobins build one of the three branches of the globin protein superfamily. They display a characteristic two-on-two a-helical sandwich fold and are clustered into three groups (I, II and III) based on distinct structural features. Truncated hemoglobins are present in eubacteria, cyanobacteria, protozoa and plants. Here we present a structural, spectroscopic and molecular dynamics characterization of a group-II truncated hemoglobin, encoded by the PSHAa0030 gene from Pseudoalteromonas haloplanktis TAC125 (Ph-2/2HbO), a cold-adapted Antarctic marine bacterium hosting one flavohemoglobin and three distinct truncated hemoglobins. The Ph-2/2HbO aquo-met crystal structure (at 2.21A resolution) shows typical features of group-II truncated hemoglobins, namely the twoon-two a-helical sandwich fold, a helix Φ preceding the proximal helix F, and a heme distal-site hydrogen-bonded network that includes water molecules and several distal-site residues, including His(58)CD1. Analysis of Ph-2/2HbO by electron paramagnetic resonance, resonance Raman and electronic absorption spectra, under varied solution conditions, shows that Ph-2/2HbO can access diverse heme ligation states. Among these, detection of a low-spin heme hexa-coordinated species suggests that residue Tyr(42)B10 can undergo large conformational changes in order to act as the sixth heme-Fe ligand. Altogether, the results show that Ph-2/2HbO maintains the general structural features of group-II truncated hemoglobins but displays enhanced conformational flexibility in the proximity of the heme cavity, a property probably related to the functional challenges, such as low Abbreviations 5c, penta-coordinated heme state; 6c, hexa-coordinated heme state; At-2/2HbO, TrHbII from Agrobacterium tumefaciens; Ath-2/2HbO,

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“…At least three other groups are also involved in the development of advanced and publicly available MR pipelines, including CaspR (Claude et al, 2004), MrBUMP (Keegan & Winn, 2008) and BALBES (Long et al, 2008). Interesting attempts have also been made to go beyond the 'rigid search model' and generate search models using normal-mode analysis (Suhre & Sanejouand, 2004;Jeong et al 2006).…”

Section: Introductionmentioning

confidence: 99%

The JCSG MR pipeline: optimized alignments, multiple models and parallel searches

Schwarzenbacher

Godzik

Jaroszewski

2007

Acta Crystallogr D Biol Cryst

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The success rate of molecular replacement (MR) falls considerably when search models share less than 35% sequence identity with their templates, but can be improved significantly by using fold-recognition methods combined with exhaustive MR searches. Models based on alignments calculated with fold-recognition algorithms are more accurate than models based on conventional alignment methods such as FASTA or BLAST, which are still widely used for MR. In addition, by designing MR pipelines that integrate phasing and automated refinement and allow parallel processing of such calculations, one can effectively increase the success rate of MR. Here, updated results from the JCSG MR pipeline are presented, which to date has solved 33 MR structures with less than 35% sequence identity to the closest homologue of known structure. By using difficult MR problems as examples, it is demonstrated that successful MR phasing is possible even in cases where the similarity between the model and the template can only be detected with fold-recognition algorithms. In the first step, several search models are built based on all homologues found in the PDB by fold-recognition algorithms. The models resulting from this process are used in parallel MR searches with different combinations of input parameters of the MR phasing algorithm. The putative solutions are subjected to rigid-body and restrained crystallographic refinement and ranked based on the final values of free R factor, figure of merit and deviations from ideal geometry. Finally, crystal packing and electron-density maps are checked to identify the correct solution. If this procedure does not yield a solution with interpretable electron-density maps, then even more alternative models are prepared. The structurally variable regions of a protein family are identified based on alignments of sequences and known structures from that family and appropriate trimmings of the models are proposed. All combinations of these trimmings are applied to the search models and the resulting set of models is used in the MR pipeline. It is estimated that with the improvements in model building and exhaustive parallel searches with existing phasing algorithms, MR can be successful for more than 50% of recognizable homologues of known structures below the threshold of 35% sequence identity. This implies that about one-third of the proteins in a typical bacterial proteome are potential MR targets.

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CaspR: a web server for automated molecular replacement using homology modelling

Cited by 85 publications

References 14 publications

Crystal Structure of Pyridoxal Kinase from the Escherichia coli pdxK Gene: Implications for the Classification of Pyridoxal Kinases

Crystal Structure of Pyridoxal Kinase from the Escherichia coli pdxK Gene: Implications for the Classification of Pyridoxal Kinases

Structural flexibility of the heme cavity in the cold‐adapted truncated hemoglobin from the Antarctic marine bacterium Pseudoalteromonas haloplanktis TAC125

The JCSG MR pipeline: optimized alignments, multiple models and parallel searches

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