The crystal structure of an essential high-temperature requirement protein HtrA1 (Rv1223) from Mycobacterium tuberculosis reveals its unique features

2018 ◽  
Vol 74 (9) ◽  
pp. 906-921 ◽  
Author(s):  
Khundrakpam Herojit Singh ◽  
Savita Yadav ◽  
Deepak Kumar ◽  
Bichitra Kumar Biswal
Keyword(s):  
Crystal Structure ◽  
Amino Acids ◽  
Mycobacterium Tuberculosis ◽  
High Temperature ◽  
Protein Quality ◽  
Pdz Domain ◽  
Survival Strategies ◽  
Dimensional Structure ◽  
Protease Domain ◽  
Temperature Requirement

High-temperature requirement A (HtrA) proteins, which are members of the heat-shock-induced serine protease family, are involved in extracytoplasmic protein quality control and bacterial survival strategies under stress conditions, and are associated with the virulence of several pathogens; they are therefore major drug targets. Mycobacterium tuberculosis possesses three putative HtrAs: HtrA1 (Rv1223), HtrA2 (Rv0983) and HtrA3 (Rv0125). Each has a cytoplasmic region, a transmembrane helix and a periplasmic region. Here, the crystal structure of the periplasmic region consisting of a protease domain (PD) and a PDZ domain from an M. tuberculosis HtrA1 mutant (mHtrA1S387A) is reported at 2.7 Å resolution. Although the mHtrA1S387A PD shows structural features similar to those of other HtrAs, its loops, particularly L3 and LA, display different conformations. Loop L3 communicates between the PDs of the trimer and the PDZ domains and undergoes a transition from an active to an inactive conformation, as reported for an equivalent HtrA (DegS). Loop LA, which is responsible for higher oligomer formation owing to its length (50 amino acids) in DegP, is very short in mHtrA1S387A (five amino acids), as in mHtrA2 (also five amino acids), and therefore lacks essential interactions for the formation of higher oligomers. Notably, a well ordered loop known as the insertion clamp in the PDZ domain interacts with the protease domain of the adjacent molecule, which possibly aids in the stabilization of a trimeric functional unit of this enzyme. The three-dimensional structure of mHtrA1S387A presented here will be useful in the design of enzyme-specific antituberculosis inhibitors.

scholarly journals The crystal structure of Mycobacterium tuberculosis high-temperature requirement A protein reveals an autoregulatory mechanism

2018 ◽  
Vol 74 (12) ◽  
pp. 803-809
Author(s):  
Arvind Kumar Gupta ◽  
Debashree Behera ◽  
Balasubramanian Gopal
Keyword(s):  
Crystal Structure ◽  
Mycobacterium Tuberculosis ◽  
High Temperature ◽  
Catalytic Domain ◽  
Pdz Domain ◽  
Regulatory Pathways ◽  
Inactive Conformation ◽  
Temperature Requirement ◽  
Autoregulatory Mechanism

The crystal structure of Mycobacterium tuberculosis high-temperature requirement A (HtrA) protein was determined at 1.83 Å resolution. This membrane-associated protease is essential for the survival of M. tuberculosis. The crystal structure reveals that interactions between the PDZ domain and the catalytic domain in HtrA lead to an inactive conformation. This finding is consistent with its proposed role as a regulatory protease that is conditionally activated upon appropriate environmental triggers. The structure provides a basis for directed studies to evaluate the role of this essential protein and the regulatory pathways that are influenced by this protease.

scholarly journals Identification and cloning of two isoforms of human high-temperature requirement factor A3 (HtrA3), characterization of its genomic structure and comparison of its tissue distribution with HtrA1 and HtrA2

2003 ◽  
Vol 371 (1) ◽  
pp. 39-48 ◽  
Author(s):  
Gui-Ying NIE ◽  
Anne HAMPTON ◽  
Ying LI ◽  
Jock K. FINDLAY ◽  
Lois A. SALAMONSEN
Keyword(s):  
Alternative Splicing ◽  
High Temperature ◽  
Short Form ◽  
Genomic Structure ◽  
Expression Patterns ◽  
Pdz Domain ◽  
Northern Blotting ◽  
Specific Function ◽  
Temperature Requirement ◽  
Long Form

In the present study, we identified an additional member of the human high-temperature requirement factor A (HtrA) protein family, called pregnancy-related serine protease or HtrA3, which was most highly expressed in the heart and placenta. We cloned the full-length sequences of two forms (long and short) of human HtrA3 mRNA, located the gene on chromosome 4p16.1, determined its genomic structure and revealed how the two mRNA variants are produced through alternative splicing. The alternative splicing was also verified by Northern blotting. Four distinct domains were found for the long form HtrA3 protein: (i) an insulin/insulin-like growth factor binding domain, (ii) a Kazal-type S protease-inhibitor domain, (iii) a trypsin protease domain and (iv) a PDZ domain. The short form is identical to the long form except it lacks the PDZ domain. Comparison of all members of human HtrA proteins, including their isoforms, suggests that both isoforms of HtrA3 represent active serine proteases, that they may have different substrate specificities and that HtrA3 may have similar functions to HtrA1. All three HtrA family members showed very different mRNA-expression patterns in 76 human tissues, indicating a specific function for each. Interestingly, both HtrA1 and HtrA3 are highly expressed in the placenta. Identification of the tissue-specific function of each HtrA family member is clearly of importance.

scholarly journals Crystal structure of the solid solution Ba8.35Pb0.65(B3O6)6

2017 ◽  
Vol 73 (3) ◽  
pp. 349-353 ◽  
Author(s):  
Wenwu Zhao
Keyword(s):  
Crystal Structure ◽  
Solid Solution ◽  
High Temperature ◽  
Single Crystals ◽  
Solid Solutions ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Barium Borate ◽  
Three Dimensional Structure ◽  
Spontaneous Nucleation

Single crystals of lead barium borate, Ba8.35Pb0.65(B3O6)6, octabarium lead(II) hexakis(triborate), have been obtained by spontaneous nucleation from a high-temperature melt. Its three-dimensional structure is constructed on the basis of a BaO9polyhedron, a (Pb/Ba)O6octahedron (occupancy ratio Pb:Ba = 0.216:0.784) and a condensed B3O6ring anion. In the crystal, the planar B3O6anions are stacked in an alternating fashion with Ba and (Pb/Ba) atoms along [001]. A comparison is made with the structures of related solid solutions in the system Ba/Pb/B/O.

scholarly journals Crystal structure and magnetic properties of bis[butyltris(1H-pyrazol-1-yl)borato]iron(II)

2019 ◽  
Vol 75 (9) ◽  
pp. 1327-1330
Author(s):  
Maksym Seredyuk ◽  
Kateryna Znovjyak ◽  
Igor O. Fritsky ◽  
Tatiana Y. Sliva ◽  
Mykola S. Slobodyanik
Keyword(s):  
Crystal Structure ◽  
Magnetic Properties ◽  
Magnetic Susceptibility ◽  
High Temperature ◽  
Three Dimensional ◽  
Bond Distance ◽  
Dimensional Structure ◽  
Inversion Center ◽  
Asymmetric Unit ◽  
Complex Molecules

The asymmetric unit of the title compound, [Fe(C13H18BN6)2], contains two half independent complex molecules. In each complex, the FeII atom is located on an inversion center and is surrounded by two scorpionate ligand butyltris(1H-pyrazol-1-yl)borate molecules that coordinate to the iron(II) ion through the N atoms of the pyrazole groups. The two independent complex molecules differ essentially in the conformation of the butyl substituents. In the crystal, the complex molecules are linked by a series of C—H...π interactions, which generate a supramolecular three-dimensional structure. At 120 K, the average Fe—N bond distance is 1.969 Å, indicating the low-spin state of the iron(II) atom, which does not change upon heating, as demonstrated by high-temperature magnetic susceptibility measurements.

scholarly journals Dissecting the role of interprotomer cooperativity in the activation of oligomeric high-temperature requirement A2 protein

2021 ◽  
Vol 118 (35) ◽  
pp. e2111257118
Author(s):  
Yuki Toyama ◽  
Robert W. Harkness ◽  
Lewis E. Kay
Keyword(s):  
High Temperature ◽  
Ligand Binding ◽  
Pdz Domain ◽  
Nmr Studies ◽  
Transverse Relaxation ◽  
Temperature Requirement ◽  
Biochemical Assays ◽  
Substrate Concentrations ◽  
Binding Substrate

The human high-temperature requirement A2 (HtrA2) mitochondrial protease is critical for cellular proteostasis, with mutations in this enzyme closely associated with the onset of neurodegenerative disorders. HtrA2 forms a homotrimeric structure, with each subunit composed of protease and PDZ (PSD-95, DLG, ZO-1) domains. Although we had previously shown that successive ligand binding occurs with increasing affinity, and it has been suggested that allostery plays a role in regulating catalysis, the molecular details of how this occurs have not been established. Here, we use cysteine-based chemistry to generate subunits in different conformational states along with a protomer mixing strategy, biochemical assays, and methyl-transverse relaxation optimized spectroscopy–based NMR studies to understand the role of interprotomer allostery in regulating HtrA2 function. We show that substrate binding to a PDZ domain of one protomer increases millisecond-to-microsecond timescale dynamics in neighboring subunits that prime them for binding substrate molecules. Only when all three PDZ-binding sites are substrate bound can the enzyme transition into an active conformation that involves significant structural rearrangements of the protease domains. Our results thus explain why when one (or more) of the protomers is fixed in a ligand-binding–incompetent conformation or contains the inactivating S276C mutation that is causative for a neurodegenerative phenotype in mouse models of Parkinson’s disease, transition to an active state cannot be formed. In this manner, wild-type HtrA2 is only active when substrate concentrations are high and therefore toxic and unregulated proteolysis of nonsubstrate proteins can be suppressed.

Molecular Docking Analysis of Flavonoid Compounds with Matrix Metalloproteinase-8 for the Identification of Potential Effective Inhibitors

2020 ◽  
Vol 17 ◽  
Author(s):  
Amir Taherkhani ◽  
Athena Orangi ◽  
Shirin Moradkhani ◽  
Zahra Khamverdi
Keyword(s):  
Amino Acids ◽  
Molecular Docking ◽  
Amino Acid ◽  
Matrix Metalloproteinase ◽  
Ligand Binding ◽  
Chronic Inflammation ◽  
Cancer Progression ◽  
Dimensional Structure ◽  
Control Test ◽  
Therapeutic Procedures

Background: Matrix metalloproteinase-8 (MMP-8) participates in degradation of different types of collagens in the extracellular matrix and basement membrane. Up-regulation of the MMP-8 has been demonstrated in many of disorders including cancer development, tooth caries, periodontal/peri-implant soft and hard tissue degeneration, and acute/chronic inflammation. Therefore, MMP-8 has become an encouraging target for therapeutic procedures for scientists. We carried out molecular docking approach to study the binding affinity of 29 flavonoids, as drug candidates, with the MMP-8. Pharmacokinetic and toxicological properties of the compounds were also studied. Moreover, it was attempted to identify the most important amino acids participating in ligand binding based on degree of each of the amino acids in the ligand-amino acid interaction network for MMP-8. Methods: Three-dimensional structure of the protein was gained from the RCSB database (PDB ID: 4QKZ). AutoDock version 4.0 and Cytoscape 3.7.2 were used for molecular docking and network analysis, respectively. Notably, the inhibitor of the protein in the crystalline structure of the 4QKZ was considered as a control test. Pharmacokinetic and toxicological features of compounds were predicted using bioinformatic web tools. Post-docking analyses were performed using BIOVIA Discovery Studio Visualizer version 19.1.0.18287. Results and Discussions: According to results, 24 of the studied compounds considered to be top potential inhibitors for MMP-8 based on their salient estimated free energy of binding and inhibition constant as compared with the control test: Apigenin-7-glucoside, nicotiflorin, luteolin, glabridin, taxifolin, apigenin, licochalcone A, quercetin, isorhamnetin, myricetin, herbacetin, kaemferol, epicatechin, chrysin, amentoflavone, rutin, orientin, epiafzelechin, quercetin-3-rhamnoside, formononetin, isoliquiritigenin, vitexin, catechine, isoquercitrin. Moreover, His-197 was found to be the most important amino acid involved in the ligand binding for the enzyme. Conclusion: The results of the current study could be used in the prevention and therapeutic procedures of a number of disorders such as cancer progression and invasion, oral diseases, and acute/chronic inflammation. Although, in vitro and in vivo tests are inevitable in the future.

scholarly journals High-pressure synthesis and crystal structure of the mixed-cation borate Ga4In4B15O33(OH)3

2019 ◽  
Vol 74 (4) ◽  
pp. 357-363
Author(s):  
Daniela Vitzthum ◽  
Hubert Huppertz
Keyword(s):  
Crystal Structure ◽  
High Pressure ◽  
High Temperature ◽  
Diffraction Data ◽  
X Ray Diffraction ◽  
Synthesis And Crystal Structure ◽  
X Ray ◽  
Mixed Cation ◽  
High Pressure High Temperature ◽  
Pressure Synthesis

AbstractThe mixed cation triel borate Ga4In4B15O33(OH)3 was synthesized in a Walker-type multianvil apparatus at high-pressure/high-temperature conditions of 12.5 GPa and 1300°C. Although the product could not be reproduced in further experiments, its crystal structure could be reliably determined via single-crystal X-ray diffraction data. Ga4In4B15O33(OH)3 crystallizes in the tetragonal space group I41/a (origin choice 2) with the lattice parameters a = 11.382(2), c = 15.244(2) Å, and V = 1974.9(4) Å3. The structure of the quaternary triel borate consists of a complex network of BO4 tetrahedra, edge-sharing InO6 octahedra in dinuclear units, and very dense edge-sharing GaO6 octahedra in tetranuclear units.

scholarly journals Are Dietary Amino Acids or Protein Quality Associated with Infant Length Gain from 6 to 12 Months in Rural Malawi? (P10-010-19)

2019 ◽  
Vol 3 (Supplement_1) ◽  
Author(s):  
Andrew Matchado ◽  
Kathryn Dewey ◽  
Christine Stewart ◽  
Per Ashorn ◽  
Ulla Ashorn ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Breast Milk ◽  
Protein Quality ◽  
Complementary Food ◽  
Complementary Foods ◽  
Acid Intake ◽  
Dietary Amino Acid ◽  
Amino Acid Intake ◽  
Length Gain

Abstract Objectives 1) to estimate the probability of inadequate amino acid intake among infants 9–10 months of age in rural Malawi 2) to evaluate whether dietary amino acid intake or protein quality are associated with length gain from 6 to 12 months of age Methods We assessed total amino acid intake from breast milk and complementary foods in 285 infants. Breast milk intake and complementary foods were estimated using dose-to-mother deuterium oxide dilution method and repeat 4-pass interactive 24-hour recall interviews, respectively. Amino acid composition values were taken from FAO human milk profile, Tanzania Food Composition table and International Minilist. Protein quality was estimated using Digestible Indispensable Amino Acid Score (DIAAS). Probability of intake below Estimated Average Requirement (EAR) for each amino acid was estimated using National Cancer Institute (NCI) method. We estimated protein quality of complementary food using median DIAAS. We assumed a DIAAS of ≥0.75 to represent a diet or food with good protein quality. Relationships between amino acid intake or protein quality with length gain were assessed using regression models. Length was measured at 6 and 12 months of age and length for age z-score (LAZ) velocity was calculated (ΔLAZ/months). Results The probability of inadequate amino acid intake from breast milk and complementary food that included a lipid-based nutrient supplement (LNS) was 3% for lysine, 0% for tryptophan, threonine, valine, histidine, isoleucine, leucine, sulfur containing amino acids (SAA), and aromatic amino acids (AAA). Without LNS, the probability was 7% for lysine and 0–2% for the other amino acids. The median (interquartile range) DIAAS for complementary food with and without LNS was 0.70 (0.28) and 0.64 (0.32), respectively. Dietary amino acid intake and protein quality were not significantly associated with length gain velocity from 6 to 12 months even after adjusting for confounding factors. Conclusions The prevalence of inadequate amino acid intake in 9–10 months old infants in rural Malawi is very low. However, in conditions of frequent clinical or sub-clinical infections this situation may be different. Linear growth at 6–12 months does not appear to be limited by dietary amino acid intake or protein quality in this setting. Funding Sources The Bill & Melinda Gates Foundation.

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