Crystal structure of PA0833 periplasmic domain from Pseudomonas aeruginosa reveals an unexpected enlarged peptidoglycan binding pocket

2019 ◽  
Vol 511 (4) ◽  
pp. 875-881 ◽  
Author(s):  
Xi Lin ◽  
Fei Ye ◽  
Sheng Lin ◽  
Fanli Yang ◽  
Zimin Chen ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Pseudomonas Aeruginosa ◽  
Binding Pocket ◽  
Periplasmic Domain

scholarly journals Conformational differences between the Pfr and Pr states in Pseudomonas aeruginosa bacteriophytochrome

2009 ◽  
Vol 106 (37) ◽  
pp. 15639-15644 ◽  
Author(s):  
Xiaojing Yang ◽  
Jane Kuk ◽  
Keith Moffat
Keyword(s):  
Crystal Structure ◽  
Pseudomonas Aeruginosa ◽  
Crystal Packing ◽  
Red Light ◽  
Binding Pocket ◽  
Site Directed Mutagenesis ◽  
Light Responses ◽  
Propionate Group ◽  
Core Module ◽  
Absorbing States

Phytochromes are red-light photoreceptors that regulate light responses in plants, fungi, and bacteria by means of reversible photoconversion between red (Pr) and far-red (Pfr) light-absorbing states. Here, we report the crystal structure of the Q188L mutant of Pseudomonas aeruginosa bacteriophytochrome (PaBphP) photosensory core module, which exhibits altered photoconversion behavior and different crystal packing from wild type. We observe two distinct chromophore conformations in the Q188L crystal structure that we identify with the Pfr and Pr states. The Pr/Pfr compositions, varying from crystal to crystal, seem to correlate with light conditions under which the Q188L crystals are cryoprotected. We also compare all known Pr and Pfr structures. Using site-directed mutagenesis, we identify residues that are involved in stabilizing the 15Ea (Pfr) and 15Za (Pr) configurations of the biliverdin chromophore. Specifically, Ser-261 appears to be essential to form a stable Pr state in PaBphP, possibly by means of its interaction with the propionate group of ring C. We propose a “flip-and-rotate” model that summarizes the major conformational differences between the Pr and Pfr states of the chromophore and its binding pocket.

scholarly journals Crystal structure of steroid reductase SRD5A reveals conserved steroid reduction mechanism

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yufei Han ◽  
Qian Zhuang ◽  
Bo Sun ◽  
Wenping Lv ◽  
Sheng Wang ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Biochemical Characterization ◽  
Substrate Binding ◽  
Binding Pocket ◽  
Substrate Binding Pocket ◽  
Transmembrane Segments ◽  
Therapeutic Molecules ◽  
Binding Cavity ◽  
Immune System Regulation ◽  
Mediated Reduction

AbstractSteroid hormones are essential in stress response, immune system regulation, and reproduction in mammals. Steroids with 3-oxo-Δ4 structure, such as testosterone or progesterone, are catalyzed by steroid 5α-reductases (SRD5As) to generate their corresponding 3-oxo-5α steroids, which are essential for multiple physiological and pathological processes. SRD5A2 is already a target of clinically relevant drugs. However, the detailed mechanism of SRD5A-mediated reduction remains elusive. Here we report the crystal structure of PbSRD5A from Proteobacteria bacterium, a homolog of both SRD5A1 and SRD5A2, in complex with the cofactor NADPH at 2.0 Å resolution. PbSRD5A exists as a monomer comprised of seven transmembrane segments (TMs). The TM1-4 enclose a hydrophobic substrate binding cavity, whereas TM5-7 coordinate cofactor NADPH through extensive hydrogen bonds network. Homology-based structural models of HsSRD5A1 and -2, together with biochemical characterization, define the substrate binding pocket of SRD5As, explain the properties of disease-related mutants and provide an important framework for further understanding of the mechanism of NADPH mediated steroids 3-oxo-Δ4 reduction. Based on these analyses, the design of therapeutic molecules targeting SRD5As with improved specificity and therapeutic efficacy would be possible.

scholarly journals Insights into Class D β-Lactamases Are Revealed by the Crystal Structure of the OXA10 Enzyme from Pseudomonas aeruginosa

Structure ◽  
2000 ◽  
Vol 8 (12) ◽  
pp. 1289-1298 ◽  
Author(s):  
Laurent Maveyraud ◽  
Dasantila Golemi ◽  
Lakshmi P. Kotra ◽  
Samuel Tranier ◽  
Sergei Vakulenko ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Pseudomonas Aeruginosa ◽  
Class D

scholarly journals Characterization of the Acetate Binding Pocket in the Methanosarcina thermophila Acetate Kinase

2005 ◽  
Vol 187 (7) ◽  
pp. 2386-2394 ◽  
Author(s):  
Cheryl Ingram-Smith ◽  
Andrea Gorrell ◽  
Sarah H. Lawrence ◽  
Prabha Iyer ◽  
Kerry Smith ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Binding Site ◽  
Binding Pocket ◽  
Acetate Kinase ◽  
Phosphoryl Group ◽  
Acetyl Phosphate ◽  
Hydrophobic Pocket ◽  
Methanosarcina Thermophila ◽  
Methyl Group ◽  
Substrate Binding Sites

ABSTRACT Acetate kinase catalyzes the reversible magnesium-dependent synthesis of acetyl phosphate by transfer of the ATP γ-phosphoryl group to acetate. Inspection of the crystal structure of the Methanosarcina thermophila enzyme containing only ADP revealed a solvent-accessible hydrophobic pocket formed by residues Val93, Leu122, Phe179, and Pro232 in the active site cleft, which identified a potential acetate binding site. The hypothesis that this was a binding site was further supported by alignment of all acetate kinase sequences available from databases, which showed strict conservation of all four residues, and the recent crystal structure of the M. thermophila enzyme with acetate bound in this pocket. Replacement of each residue in the pocket produced variants with Km values for acetate that were 7- to 26-fold greater than that of the wild type, and perturbations of this binding pocket also altered the specificity for longer-chain carboxylic acids and acetyl phosphate. The kinetic analyses of variants combined with structural modeling indicated that the pocket has roles in binding the methyl group of acetate, influencing substrate specificity, and orienting the carboxyl group. The kinetic analyses also indicated that binding of acetyl phosphate is more dependent on interactions of the phosphate group with an unidentified residue than on interactions between the methyl group and the hydrophobic pocket. The analyses also indicated that Phe179 is essential for catalysis, possibly for domain closure. Alignments of acetate kinase, propionate kinase, and butyrate kinase sequences obtained from databases suggested that these enzymes have similar catalytic mechanisms and carboxylic acid substrate binding sites.

Structure and mechanism of the γ-glutamyl-γ-aminobutyrate hydrolase SpuA from Pseudomonas aeruginosa

2021 ◽  
Vol 77 (10) ◽  
pp. 1305-1316
Author(s):  
Yujing Chen ◽  
Haizhu Jia ◽  
Jianyu Zhang ◽  
Yakun Liang ◽  
Ruihua Liu ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Catalytic Mechanism ◽  
Substrate Binding ◽  
Binding Pocket ◽  
Class I ◽  
Polyamine Metabolism ◽  
Binding Assays ◽  
Starting Point ◽  
Family Activity ◽  
Living Organisms

Polyamines are important regulators in all living organisms and are implicated in essential biological processes including cell growth, differentiation and apoptosis. Pseudomonas aeruginosa possesses an spuABCDEFGHI gene cluster that is involved in the metabolism and uptake of two polyamines: spermidine and putrescine. In the proposed γ-glutamylation–putrescine metabolism pathway, SpuA hydrolyzes γ-glutamyl-γ-aminobutyrate (γ-Glu-GABA) to glutamate and γ-aminobutyric acid (GABA). In this study, crystal structures of P. aeruginosa SpuA are reported, confirming it to be a member of the class I glutamine amidotransferase (GAT) family. Activity and substrate-binding assays confirm that SpuA exhibits a preference for γ-Glu-GABA as a substrate. Structures of an inactive H221N mutant were determined with bound glutamate thioester intermediate or glutamate product, thus delineating the active site and substrate-binding pocket and elucidating the catalytic mechanism. The crystal structure of another bacterial member of the class I GAT family from Mycolicibacterium smegmatis (MsGATase) in complex with glutamine was determined for comparison and reveals a binding site for glutamine. Activity assays confirm that MsGATase has activity for glutamine as a substrate but not for γ-Glu-GABA. The work reported here provides a starting point for further investigation of polyamine metabolism in P. aeruginosa.

scholarly journals Crystal Structure of the Outer Membrane Protein OpdK from Pseudomonas aeruginosa

Structure ◽  
2008 ◽  
Vol 16 (7) ◽  
pp. 1027-1035 ◽  
Author(s):  
Shyamasri Biswas ◽  
Mohammad M. Mohammad ◽  
Liviu Movileanu ◽  
Bert van den Berg
Keyword(s):  
Crystal Structure ◽  
Pseudomonas Aeruginosa ◽  
Membrane Protein ◽  
Outer Membrane ◽  
Outer Membrane Protein

scholarly journals THE APPLICABILITY OF THE CRYSTAL STRUCTURE OF TERMOTOGA MARITIMA 4--GLUCANOTRANSFERASE AS THE TEMPLATE FOR SULOCHRIN AS -GLUCOSIDASE INHIBITORS

2010 ◽  
Vol 9 (3) ◽  
pp. 479-486
Author(s):  
Rizna Triana Dewi ◽  
Yulia Anita ◽  
Enade Perdana Istyastono ◽  
Akhmad Darmawan ◽  
Muhamad Hanafi
Keyword(s):  
Crystal Structure ◽  
Saccharomyces Cerevisiae ◽  
Thermotoga Maritima ◽  
Binding Pocket ◽  
Operating Environment ◽  
High Sequence Identity ◽  
Glucosidase Inhibitor ◽  
Glucosidase Inhibitors ◽  
Docking Method ◽  
Binding Residues

Interaction of sulochrin to active site of glucosidase enzyme of Termotoga maritime has been studied by employing docking method using Molecular Operating Environment (MOE), in comparison with those are reports of established inhibitor α-glucosidase such as acarbose, miglitol and voglibose, and salicinol, as reference compounds. The crystal structure T. maritima α-glucanotransferase (PDB code: 1LWJ) can be employed to serve as the template in the virtual screening of S. cerevisiae α-glucosidase. The comparison between the binding pocket residues of Thermotoga maritima α-glucanotransferase and Saccharomyces cerevisiae α-glucosidase show a high sequence identity and similarity. The result showed that sulochrin could be located in the binding pocket and formed some interactions with the binding residues. The ligands showed proper predicted binding energy (-6.74 - -4.13 kcal/mol) and predicted Ki values (0.011 - 0.939 mM). Sulochrin has a possibility to serve as a lead compound in the development of new α-glucosidase inhibitor.   Keywords: Docking, sulochrin, α-glucosidase Inhibitor, Thermotoga maritime α-glucotransferase, Saccharomyces cerevisiae α-glucosidase, MOE

scholarly journals A disulfide constrains the ToxR periplasmic domain structure, altering its interactions with ToxS and bile-salts

2020 ◽  
Author(s):  
Charles R Midgett ◽  
Rachel A Swindell ◽  
Maria Pellegrini ◽  
F Jon Kull
Keyword(s):  
Crystal Structure ◽  
Transcription Factor ◽  
Disulfide Bond ◽  
Bile Salts ◽  
Biochemical Analysis ◽  
Conformation Analysis ◽  
Binding Partner ◽  
Bile Resistance ◽  
Periplasmic Domain

AbstractToxR is a transmembrane transcription factor that, together with its integral membrane periplasmic binding partner ToxS, is conserved across the Vibrio family. In some pathogenic Vibrios, including V. parahaemolyticus and V. cholerae, ToxR is required for bile resistance and virulence, and ToxR is fully activated and protected from degradation by ToxS. ToxS achieves this in part by ensuring formation of an intra-chain disulfide bond in the C-terminal periplasmic domain of ToxR (dbToxRp). In this study, biochemical analysis showed dbToxRp to have a higher affinity for the ToxS periplasmic domain than the non-disulfide bonded conformation. Analysis of our dbToxRp crystal structure showed this is due to disulfide bond stabilization. Furthermore, dbToxRp is structurally homologous to the V. parahaemolyticus VtrA periplasmic domain. These results highlight the critical structural role of disulfide bond in ToxR and along with VtrA define a domain fold involved in environmental sensing conserved across the Vibrio family.

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