STRAP: editor for STRuctural Alignments of Proteins

Gille, Christoph; Frömmel, Cornelius

doi:10.1093/bioinformatics/17.4.377

Cited by 206 publications

(147 citation statements)

References 9 publications

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“…Ramachandran plot for KtrAB crystals: 0% outliers, 5.94% allowed, 94.06% preferred. Model analysis was performed with PYMOL 38 , STRAP 39 , ESPrit 40 and Hollow 41 . Complementation assay.…”

Section: Methodsmentioning

confidence: 99%

The structure of the KtrAB potassium transporter

Vieira-Pires

Szöllősi

Morais-Cabral

2013

Nature

106

163

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In bacteria, archaea, fungi and plants the Trk, Ktr and HKT ion transporters are key components of osmotic regulation, pH homeostasis and resistance to drought and high salinity. These ion transporters are functionally diverse: they can function as Na + or K + channels and possibly as cation/K + symporters. They are closely related to potassium channels both at the level of the membrane protein and at the level of the cytosolic regulatory domains. Here we describe the crystal structure of a Ktr K + transporter, the KtrAB complex from Bacillus subtilis. The structure shows the dimeric membrane protein KtrB assembled with a cytosolic octameric KtrA ring bound to ATP, an activating ligand. A comparison between the structure of KtrAB-ATP and the structures of the isolated fulllength KtrA protein with ATP or ADP reveals a ligand-dependent conformational change in the octameric ring, raising new ideas about the mechanism of activation in these transporters.The Trk/Ktr/HKT superfamily of ion transporters includes the Trk, Ktr and HKT transporter families 1 . These transporters are closely related to the superfamily of tetrameric cation channels 2-4 , which includes potassium, sodium and calcium channels. The membrane proteins in both superfamilies share the same architecture 2,5-9 : four subunits or repeats, each with the TM-P loop-TM (where TM indicates transmembrane helix) structural motif first seen in the KcsA potassium channel structure 10 , assemble to form an ion pore with a 'selectivity filter' along its central axis. In addition, the cytosolic regulatory proteins of the Trk and Ktr transporters and of the MthK 11,12 and large-conductance Ca 2+ -gated (BK) K + channels [13][14][15] are RCK (regulate conductance of K+) domains.Ktr ion transporters are crucial K + transport systems in some bacteria 16,17 , with a role in resistance to osmotic stress and high salinity by mediating the early uptake of K + (refs 16, 18). The Ktr ion transporters are composed of two essential components 3,16 : a membrane protein (KtrB or KtrD) and a cytosolic regulatory protein (KtrA or KtrC). Studies with cells show that Ktr proteins 8,19 transport K + but are also permeable to Na + , and that K + transport is ATP 20 and Na + dependent 5,8,18 . Furthermore, it has been shown that truncated KtrA forms octameric rings 21,22 and that KtrB assembles as homodimers 6,21 . The structures described here clarify the molecular basis of some of these properties as well as the structural relationship between these transporters and ion channels.

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Section: Methodsmentioning

confidence: 99%

The structure of the KtrAB potassium transporter

Vieira-Pires

Szöllősi

Morais-Cabral

2013

Nature

106

163

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“…Protein surface properties were analyzed using Pymol (63). 3D structural alignment and creation of the phylogenetic tree based on this 3D alignment were done using STRAP (64). Fig.…”

Section: Methodsmentioning

confidence: 99%

Evolution of insect arylalkylamine N -acetyltransferases: Structural evidence from the yellow fever mosquito, Aedes aegypti

Han

Robinson

Ding

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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Arylalkylamine N-acetyltransferase (aaNAT) catalyzes the transacetylation from acetyl-CoA to arylalkylamines. aaNATs are involved in sclerotization and neurotransmitter inactivation in insects. Phyletic distribution analysis confirms three clusters of aaNAT-like sequences in insects: typical insect aaNAT, polyamine NAT-like aaNAT, and mosquito unique putative aaNAT (paaNAT). Here we studied three proteins: aaNAT2, aaNAT5b, and paaNAT7, each from a different cluster. aaNAT2, a protein from the typical insect aaNAT cluster, uses histamine as a substrate as well as the previously identified arylalkylamines. aaNAT5b, a protein from polyamine NAT -like aaNAT cluster, uses hydrazine and histamine as substrates. The crystal structure of aaNAT2 was determined using single-wavelength anomalous dispersion methods, and that of native aaNAT2, aaNAT5b and paaNAT7 was detected using molecular replacement techniques. All three aaNAT structures have a common fold core of GCN5-related N-acetyltransferase superfamily proteins, along with a unique structural feature: helix/helices between β3 and β4 strands. Our data provide a start toward a more comprehensive understanding of the structure-function relationship and physiology of aaNATs from the mosquito Aedes aegypti and serve as a reference for studying the aaNAT family of proteins from other insect species. The structures of three different types of aaNATs may provide targets for designing insecticides for use in mosquito control.biogenic amine | melatonin synthesis | catecholamine | insect cuticle

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“…After manual inspection for sequence quality, 31 sequences were trimmed to include only helices 1 and 2 and aligned using the ClustalW algorithm with Strap multiple sequence alignment software (52). 30 Mutations Alter ␣ Chain Binding, Autooxidation, and Hemin Loss-The evolutionarily conserved proline at position 30 in loop 1 of AHSP contacts helix G of ␣-globin at the edge of the protein-binding interface (Fig.…”

Section: Isoelectric Focusing Of 35 S-labeled Reticulocyte Extracts Tmentioning

confidence: 99%

Insights into Hemoglobin Assembly through in Vivo Mutagenesis of α-Hemoglobin Stabilizing Protein

Khandros

Mollan

et al. 2012

Journal of Biological Chemistry

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Background:The ␣-hemoglobin-stabilizing protein (AHSP) facilitates hemoglobin assembly. Results: AHSP mutations that enhance binding affinity for ␣-globin or slow its rate of autooxidation in vitro do not affect normal or stressed erythropoiesis in mice. Conclusion: AHSP exhibits robust molecular chaperone activity in vivo even when its biochemical interactions with reduced ␣-globin are perturbed. Significance: Our findings support new models for AHSP activities in vivo.

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STRAP: editor for STRuctural Alignments of Proteins

Cited by 206 publications

References 9 publications

The structure of the KtrAB potassium transporter

The structure of the KtrAB potassium transporter

Evolution of insect arylalkylamine N -acetyltransferases: Structural evidence from the yellow fever mosquito, Aedes aegypti

Insights into Hemoglobin Assembly through in Vivo Mutagenesis of α-Hemoglobin Stabilizing Protein

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