scholarly journals Crystal Structures of SlyA Protein, a Master Virulence Regulator ofSalmonella, in Free and DNA-bound States

2011 ◽  
Vol 286 (25) ◽  
pp. 22178-22185 ◽  
Author(s):  
Kyle T. Dolan ◽  
Erica M. Duguid ◽  
Chuan He
Keyword(s):  
Crystal Structures ◽  
Bound States ◽  
Protein A ◽  
Virulence Regulator

scholarly journals New crystal structures of adenylate kinase fromStreptococcus pneumoniaeD39 in two conformations

2014 ◽  
Vol 70 (11) ◽  
pp. 1468-1471
Author(s):  
Trung Thanh Thach ◽  
Sangho Lee
Keyword(s):  
Crystal Structures ◽  
Adenylate Kinase ◽  
Bound States ◽  
Critical Role ◽  
Unit Cell ◽  
Unit Cell Parameters ◽  
Space Group ◽  
Cell Parameters ◽  
Ligand Free ◽  
Adenylate Kinases

Adenylate kinases (AdKs; EC 2.7.3.4) play a critical role in intercellular homeostasis by the interconversion of ATP and AMP to two ADP molecules. Crystal structures of adenylate kinase fromStreptococcus pneumoniaeD39 (SpAdK) have recently been determined using ligand-free and inhibitor-bound crystals belonging to space groupsP21andP1, respectively. Here, new crystal structures of SpAdK in ligand-free and inhibitor-bound states determined at 1.96 and 1.65 Å resolution, respectively, are reported. The new ligand-free crystal belonged to space groupC2, with unit-cell parametersa= 73.5,b= 54.3,c= 62.7 Å, β = 118.8°. The new ligand-free structure revealed an open conformation that differed from the previously determined conformation, with an r.m.s.d on Cαatoms of 1.4 Å. The new crystal of the complex with the two-substrate-mimicking inhibitorP1,P5-bis(adenosine-5′-)pentaphosphate (Ap5A) belonged to space groupP1, with unit-cell parametersa= 53.9,b= 62.3,c= 63.0 Å, α = 101.9, β = 112.6, γ = 89.9°. Despite belonging to the same space group as the previously reported crystal, the new Ap5A-bound crystal contains four molecules in the asymmetric unit, compared with two in the previous crystal, and shows slightly different lattice contacts. These results demonstrate that SpAdK can crystallize promiscuously in different forms and that the open structure is flexible in conformation.

scholarly journals Crystal Structures of S100A6 in the Ca2+-Free and Ca2+-Bound States

Structure ◽  
2002 ◽  
Vol 10 (4) ◽  
pp. 557-567 ◽  
Author(s):  
Ludovic R. Otterbein ◽  
Jolanta Kordowska ◽  
Carlos Witte-Hoffmann ◽  
C.-L.Albert Wang ◽  
Roberto Dominguez
Keyword(s):  
Crystal Structures ◽  
Bound States

scholarly journals Identification and characterization of two drug-like fragments that bind to the same cryptic binding pocket of Burkholderia pseudomallei DsbA

2021 ◽  
Author(s):  
Guillaume A. Petit ◽  
Biswarajan Mohanty ◽  
Róisín M. McMahon ◽  
Stefan Nebl ◽  
David H. Hilko ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Binding Affinity ◽  
Disulfide Bond ◽  
Burkholderia Pseudomallei ◽  
Protein A ◽  
Binding Pocket ◽  
New Drugs ◽  
Nmr Studies ◽  
Small Surface ◽  
Starting Point

AbstractDiSulfide Bond forming proteins (DSB) play a crucial role in the pathogenicity of many Gram-negative bacteria. Disulfide bond protein A (DsbA) catalyzes the formation of disulfide bonds necessary for the activity and stability of multiple substrate proteins, including many virulence factors. Hence, DsbA is an attractive target for the development of new drugs to combat bacterial infections. Here, we identified two fragments - 1 (bromophenoxy propanamide) and 2 (4-methoxy-N-phenylbenzenesulfonamide), that bind to the DsbA from the pathogenic bacterium Burkholderia pseudomallei, the causative agent of melioidosis. Crystal structures of the oxidized B. pseudomallei DsbA (termed BpsDsbA) co-crystallized with 1 or 2 suggests that both fragments bind to a hydrophobic pocket that is formed by a change in the side chain orientation of tyrosine 110. This conformational change opens a “cryptic” pocket that is not evident in the apo-protein structure. This binding location was supported by 2D-NMR studies which identified a chemical shift perturbation of the tyrosine 110 backbone amide resonance of more than 0.05 ppm upon addition of 2 mM of fragment 1 and over 0.04 ppm upon addition of 1 mM of fragment 2. Although binding was detected by both X-ray crystallography and NMR, the binding affinity (KD) for both fragments was low (above 2 mM), suggesting weak interactions with BpsDsbA. This conclusion is also supported by the modelled crystal structures which ascribe partial occupancy to the ligands in the cryptic binding pocket. Small fragments such as 1 and 2 are not expected to have high binding affinity due to their size and the relatively small surface area that can be involved in intermolecular interactions. However, their simplicity makes them ideal for functionalization and optimization. Identification of the binding sites of 1 and 2 to BpsDsbA could provide a starting point for the development of more potent novel antimicrobial compounds that target DsbA and bacterial virulence.SynopsisDescribes the binding properties of two drug-like fragments to a conformationally dynamic site in the disulfide-bond forming protein A from Burkholderia pseudomallei.

Crystal structures of free and antagonist-bound states of human α9 nicotinic receptor extracellular domain

2014 ◽  
Vol 21 (11) ◽  
pp. 976-980 ◽  
Author(s):  
Marios Zouridakis ◽  
Petros Giastas ◽  
Eleftherios Zarkadas ◽  
Dafni Chroni-Tzartou ◽  
Piotr Bregestovski ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Nicotinic Receptor ◽  
Bound States ◽  
Extracellular Domain

scholarly journals Dynamic Structural Changes Accompany the Production of 2-Dihydroxypropanesulfonate by Sulfolactaldehyde Reductase

2019 ◽  
Author(s):  
Mahima Sharma ◽  
Palika Abayakoon ◽  
James P. Lingford ◽  
Yi Jin ◽  
Ruwan Epa ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Bound States ◽  
Ternary Complex ◽  
Structural Changes ◽  
Reductase Activity ◽  
Complex Structure ◽  
Peptide Sequence ◽  
Sequence Motifs ◽  
Conserved Sequence ◽  
K 12

2,3-Dihydroxypropanesulfonate (DHPS) is a major sulfur species in the biosphere. One important route for the production of DHPS includes sulfoglycolytic catabolism of sulfoquinovose (SQ) through the Embden-Meyerhof-Parnas (sulfo-EMP) pathway. SQ is a sulfonated carbohydrate present in plant and cyanobacterial sulfolipids (sulfoquinovosyl diacylglyceride and its metabolites) and is biosynthesised globally at a rate of around 10 billion tonnes per annum. The final step in the bacterial sulfo-EMP pathway involves reduction of sulfolactaldehyde (SLA) to DHPS, catalysed by an NADH-dependent SLA reductase. On the basis of conserved sequence motifs, we assign SLA reductase to the β-hydroxyacid dehydrogenase (β-HAD) family, making it the first example of a β-HAD enzyme that acts on a sulfonic acid, rather than a carboxylic acid substrate. We report crystal structures of the SLA reductase YihU from E. coli K-12 in its apo and cofactor-bound states, as well as the ternary complex YihU•NADH•DHPS with the cofactor and product bound in the active site. Conformational flexibility observed in these structures, combined with kinetic studies, confirm a sequential mechanism and provide evidence for dynamic domain movements that occur during catalysis. The ternary complex structure reveals a conserved sulfonate pocket in SLA reductase that recognises the sulfonate oxygens through hydrogen bonding to Asn174, Ser178, and the backbone amide of Arg123, along with an ordered water molecule. This triad of residues distinguishes these enzymes from classical β-HADs that act on carboxylate substrates. A comparison of YihU crystal structures with close structural homologues within the β-HAD family highlights key differences in the overall domain organization and identifies a unique peptide sequence that is predictive of SLA reductase activity.<br>

scholarly journals Dynamic Structural Changes Accompany the Production of 2-Dihydroxypropanesulfonate by Sulfolactaldehyde Reductase

2019 ◽  
Author(s):  
Mahima Sharma ◽  
Palika Abayakoon ◽  
James P. Lingford ◽  
Yi Jin ◽  
Ruwan Epa ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Bound States ◽  
Ternary Complex ◽  
Structural Changes ◽  
Reductase Activity ◽  
Complex Structure ◽  
Peptide Sequence ◽  
Sequence Motifs ◽  
Conserved Sequence ◽  
K 12

2,3-Dihydroxypropanesulfonate (DHPS) is a major sulfur species in the biosphere. One important route for the production of DHPS includes sulfoglycolytic catabolism of sulfoquinovose (SQ) through the Embden-Meyerhof-Parnas (sulfo-EMP) pathway. SQ is a sulfonated carbohydrate present in plant and cyanobacterial sulfolipids (sulfoquinovosyl diacylglyceride and its metabolites) and is biosynthesised globally at a rate of around 10 billion tonnes per annum. The final step in the bacterial sulfo-EMP pathway involves reduction of sulfolactaldehyde (SLA) to DHPS, catalysed by an NADH-dependent SLA reductase. On the basis of conserved sequence motifs, we assign SLA reductase to the β-hydroxyacid dehydrogenase (β-HAD) family, making it the first example of a β-HAD enzyme that acts on a sulfonic acid, rather than a carboxylic acid substrate. We report crystal structures of the SLA reductase YihU from E. coli K-12 in its apo and cofactor-bound states, as well as the ternary complex YihU•NADH•DHPS with the cofactor and product bound in the active site. Conformational flexibility observed in these structures, combined with kinetic studies, confirm a sequential mechanism and provide evidence for dynamic domain movements that occur during catalysis. The ternary complex structure reveals a conserved sulfonate pocket in SLA reductase that recognises the sulfonate oxygens through hydrogen bonding to Asn174, Ser178, and the backbone amide of Arg123, along with an ordered water molecule. This triad of residues distinguishes these enzymes from classical β-HADs that act on carboxylate substrates. A comparison of YihU crystal structures with close structural homologues within the β-HAD family highlights key differences in the overall domain organization and identifies a unique peptide sequence that is predictive of SLA reductase activity.<br>

scholarly journals Dynamic Structural Changes Accompany the Production of 2-Dihydroxypropanesulfonate by Sulfolactaldehyde Reductase

2019 ◽  
Author(s):  
Mahima Sharma ◽  
Palika Abayakoon ◽  
James P. Lingford ◽  
Yi Jin ◽  
Ruwan Epa ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Bound States ◽  
Ternary Complex ◽  
Structural Changes ◽  
Reductase Activity ◽  
Complex Structure ◽  
Peptide Sequence ◽  
Sequence Motifs ◽  
Conserved Sequence ◽  
K 12

2,3-Dihydroxypropanesulfonate (DHPS) is a major sulfur species in the biosphere. One important route for the production of DHPS includes sulfoglycolytic catabolism of sulfoquinovose (SQ) through the Embden-Meyerhof-Parnas (sulfo-EMP) pathway. SQ is a sulfonated carbohydrate present in plant and cyanobacterial sulfolipids (sulfoquinovosyl diacylglyceride and its metabolites) and is biosynthesised globally at a rate of around 10 billion tonnes per annum. The final step in the bacterial sulfo-EMP pathway involves reduction of sulfolactaldehyde (SLA) to DHPS, catalysed by an NADH-dependent SLA reductase. On the basis of conserved sequence motifs, we assign SLA reductase to the β-hydroxyacid dehydrogenase (β-HAD) family, making it the first example of a β-HAD enzyme that acts on a sulfonic acid, rather than a carboxylic acid substrate. We report crystal structures of the SLA reductase YihU from E. coli K-12 in its apo and cofactor-bound states, as well as the ternary complex YihU•NADH•DHPS with the cofactor and product bound in the active site. Conformational flexibility observed in these structures, combined with kinetic studies, confirm a sequential mechanism and provide evidence for dynamic domain movements that occur during catalysis. The ternary complex structure reveals a conserved sulfonate pocket in SLA reductase that recognises the sulfonate oxygens through hydrogen bonding to Asn174, Ser178, and the backbone amide of Arg123, along with an ordered water molecule. This triad of residues distinguishes these enzymes from classical β-HADs that act on carboxylate substrates. A comparison of YihU crystal structures with close structural homologues within the β-HAD family highlights key differences in the overall domain organization and identifies a unique peptide sequence that is predictive of SLA reductase activity.<br>

Crystal structures of the methyltransferase and helicase from the ZIKA 1947 MR766 Uganda strain

2017 ◽  
Vol 73 (9) ◽  
pp. 767-774 ◽  
Author(s):  
Malgorzata Bukrejewska ◽  
Urszula Derewenda ◽  
Malwina Radwanska ◽  
Daniel A. Engel ◽  
Zygmunt S. Derewenda
Keyword(s):  
Crystal Structures ◽  
Zika Virus ◽  
Bound States ◽  
Nonstructural Proteins ◽  
Induced Fit ◽  
Conformational Selection

Two nonstructural proteins encoded byZika virusstrain MR766 RNA, a methyltransferase and a helicase, were crystallized and their structures were solved and refined at 2.10 and 2.01 Å resolution, respectively. The NS5 methyltransferase contains a boundS-adenosyl-L-methionine (SAM) co-substrate. The NS3 helicase is in the apo form. Comparison with published crystal structures of the helicase in the apo, nucleotide-bound and single-stranded RNA (ssRNA)-bound states suggests that binding of ssRNA to the helicase may occur through conformational selection rather than induced fit.

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