POSA: a user-driven, interactive multiple protein structure alignment server

Li, Zhanwen; Natarajan, Padmaja; Ye, Yuzhen; Hrabe, Thomas; Godzik, Adam

doi:10.1093/nar/gku394

Cited by 61 publications

(46 citation statements)

References 19 publications

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“…In the initial view, PDBFlex provides a visualization of all set of coordinates in the same relative position, as identified by structural superposition. The rotations of structures in individual windows can also be synchronized, similarly to an option implemented in on our POSA server ( 16 ). The user has the option to turn on synchronized rotation of all structure views to investigate large differences between compared structures in a cluster.…”

Section: Using Pdbflexmentioning

confidence: 99%

PDBFlex: exploring flexibility in protein structures

Hrabe

Sedova

et al. 2015

Nucleic Acids Res

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The PDBFlex database, available freely and with no login requirements at http://pdbflex.org, provides information on flexibility of protein structures as revealed by the analysis of variations between depositions of different structural models of the same protein in the Protein Data Bank (PDB). PDBFlex collects information on all instances of such depositions, identifying them by a 95% sequence identity threshold, performs analysis of their structural differences and clusters them according to their structural similarities for easy analysis. The PDBFlex contains tools and viewers enabling in-depth examination of structural variability including: 2D-scaling visualization of RMSD distances between structures of the same protein, graphs of average local RMSD in the aligned structures of protein chains, graphical presentation of differences in secondary structure and observed structural disorder (unresolved residues), difference distance maps between all sets of coordinates and 3D views of individual structures and simulated transitions between different conformations, the latter displayed using JSMol visualization software.

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Section: Using Pdbflexmentioning

confidence: 99%

PDBFlex: exploring flexibility in protein structures

Hrabe

Sedova

et al. 2015

Nucleic Acids Res

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“…APBS (Baker et al, 2001) and PDB2PQR (Dolinsky et al, 2007) in PyMOL were used to calculate the surface electrostatic potential map. Cealign in PyMOL and the POSA server (Li et al, 2014) were used for structure alignment and to calculate the root-mean-square deviation (r.m.s.d.). jF obs j À jF calc j = P hkl jF obs j.…”

Section: Sequence and Structure Analysismentioning

confidence: 99%

Structural basis for DNA recognition by the transcription regulator MetR

Punekar

Porter

Carr

et al. 2016

Acta Crystallogr F Struct Biol Commun

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MetR, a LysR-type transcriptional regulator (LTTR), has been extensively studied owing to its role in the control of methionine biosynthesis in proteobacteria. A MetR homodimer binds to a 24-base-pair operator region of the met genes and specifically recognizes the interrupted palindromic sequence 5'-TGAA-N5-TTCA-3'. Mechanistic details underlying the interaction of MetR with its target DNA at the molecular level remain unknown. In this work, the crystal structure of the DNA-binding domain (DBD) of MetR was determined at 2.16 Å resolution. MetR-DBD adopts a winged-helix-turn-helix (wHTH) motif and shares significant fold similarity with the DBD of the LTTR protein BenM. Furthermore, a data-driven macromolecular-docking strategy was used to model the structure of MetR-DBD bound to DNA, which revealed that a bent conformation of DNA is required for the recognition helix α3 and the wing loop of the wHTH motif to interact with the major and minor grooves, respectively. Comparison of the MetR-DBD-DNA complex with the crystal structures of other LTTR-DBD-DNA complexes revealed residues that may confer operator-sequence binding specificity for MetR. Taken together, the results show that MetR-DBD uses a combination of direct base-specific interactions and indirect shape recognition of the promoter to regulate the transcription of met genes.

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“…These structural variations have previously been suggested to account for the great variability in substrate specificity across the members of this superfamily (Lima et al, 1997), but conclusive evidence for this hypothesis has not yet been obtained. These differences are also reflected in the structure-based phylogenetic tree constructed using the POSA server (Li et al, 2014), which showed a common origin for all of the HINT homologues (chosen for the present study), which thus formed a single clade (Fig. 6).…”

Section: Figurementioning

confidence: 76%

Crystal structure of HINT fromHelicobacter pylori

et al. 2016

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Proteins belonging to the histidine triad (HIT) superfamily bind nucleotides and use the histidine triad motif to carry out dinucleotidyl hydrolase, nucleotidyltransferase and phosphoramidite hydrolase activities. Five different branches of this superfamily are known to exist. Defects in these proteins in humans are linked to many diseases such as ataxia, diseases of RNA metabolism and cell-cycle regulation, and various types of cancer. The histidine triad nucleotide protein (HINT) is nearly identical to proteins that have been classified as protein kinase C-interacting proteins (PKCIs), which also have the ability to bind and inhibit protein kinase C. The structure of HINT, which exists as a homodimer, is highly conserved from humans to bacteria and shares homology with the product of fragile histidine triad protein (FHit), a tumour suppressor gene of this superfamily. Here, the structure of HINT from Helicobacter pylori (HpHINT) in complex with AMP is reported at a resolution of 3 Å. The final model has R and Rfree values of 26 and 28%, respectively, with good electron density. Structural comparison with previously reported homologues and phylogenetic analysis shows H. pylori HINT to be the smallest among them, and suggests that it branched out separately during the course of evolution. Overall, this structure has contributed to a better understanding of this protein across the animal kingdom.

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POSA: a user-driven, interactive multiple protein structure alignment server

Cited by 61 publications

References 19 publications

PDBFlex: exploring flexibility in protein structures

PDBFlex: exploring flexibility in protein structures

Structural basis for DNA recognition by the transcription regulator MetR

Crystal structure of HINT fromHelicobacter pylori

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