Structural basis of [NiFe] hydrogenase maturation by Hyp proteins

2012 ◽  
Vol 393 (10) ◽  
pp. 1089-1100 ◽  
Author(s):  
Satoshi Watanabe ◽  
Daisuke Sasaki ◽  
Taiga Tominaga ◽  
Kunio Miki
Keyword(s):  
Hydrogen Production ◽  
Dynamic Process ◽  
Active Site ◽  
The Other ◽  
Structural Basis ◽  
Structural Studies ◽  
Hydrogenase Maturation ◽  
Recent Advances

Abstract [NiFe] hydrogenases catalyze reversible hydrogen production/consumption. The active site of [NiFe] hydrogenases contains a complex NiFe(CN)2CO center, and the biosynthesis/maturation of these enzymes is a complex and dynamic process, primarily involving six Hyp proteins (HypABCDEF). HypA and HypB are involved in the Ni insertion, whereas the other four Hyp proteins (HypCDEF) are required for the biosynthesis, assembly and insertion of the Fe(CN)2CO group. Over the last decades, a large number of functional and structural studies on maturation proteins have been performed, revealing detailed functions of each Hyp protein and the framework of the maturation pathway. This article will focus on recent advances in structural studies of the Hyp proteins and on mechanistic insights into the [NiFe] hydrogenase maturation.

scholarly journals Structural Basis of Specific Glucoimidazole and Mannoimidazole Binding by Os3BGlu7

Biomolecules ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 907
Author(s):  
Bodee Nutho ◽  
Salila Pengthaisong ◽  
Anupong Tankrathok ◽  
Vannajan Sanghiran Lee ◽  
James R. Ketudat Cairns ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Binding Energy ◽  
Active Site ◽  
The Other ◽  
Strong Preference ◽  
Structural Basis ◽  
Active Site Residue ◽  
Weakly Bound ◽  
Sugar Moiety ◽  
Dynamics Simulations

β-Glucosidases and β-mannosidases hydrolyze substrates that differ only in the epimer of the nonreducing terminal sugar moiety, but most such enzymes show a strong preference for one activity or the other. Rice Os3BGlu7 and Os7BGlu26 β-glycosidases show a less strong preference, but Os3BGlu7 and Os7BGlu26 prefer glucosides and mannosides, respectively. Previous studies of crystal structures with glucoimidazole (GIm) and mannoimidazole (MIm) complexes and metadynamic simulations suggested that Os7BGlu26 hydrolyzes mannosides via the B2,5 transition state (TS) conformation preferred for mannosides and glucosides via their preferred 4H3/4E TS conformation. However, MIm is weakly bound by both enzymes. In the present study, we found that MIm was not bound in the active site of crystallized Os3BGlu7, but GIm was tightly bound in the −1 subsite in a 4H3/4E conformation via hydrogen bonds with the surrounding residues. One-microsecond molecular dynamics simulations showed that GIm was stably bound in the Os3BGlu7 active site and the glycone-binding site with little distortion. In contrast, MIm initialized in the B2,5 conformation rapidly relaxed to a E3/4H3 conformation and moved out into a position in the entrance of the active site, where it bound more stably despite making fewer interactions. The lack of MIm binding in the glycone site in protein crystals and simulations implies that the energy required to distort MIm to the B2,5 conformation for optimal active site residue interactions is sufficient to offset the energy of those interactions in Os3BGlu7. This balance between distortion and binding energy may also provide a rationale for glucosidase versus mannosidase specificity in plant β-glycosidases.

An unusual diphosphatase from the PhnP family cleaves reactive FAD photoproducts

2018 ◽  
Vol 475 (1) ◽  
pp. 261-272 ◽  
Author(s):  
Guillaume A.W. Beaudoin ◽  
Qiang Li ◽  
Steven D. Bruner ◽  
Andrew D. Hanson
Keyword(s):  
Active Site ◽  
Damage Control ◽  
The Other ◽  
Cellular Damage ◽  
Structural Basis ◽  
Breakdown Product ◽  
Phosphodiesterase Activity ◽  
Bacterial Genomes ◽  
Toxic Compounds ◽  
Cyclic Phosphate

Flavins are notoriously photolabile, but while the photoproducts derived from the iso-alloxazine ring are well known the other photoproducts are not. In the case of FAD, typically the main cellular flavin, the other photoproducts are predicted to include four- and five-carbon sugars linked to ADP. These FAD photoproducts were shown to be potent glycating agents, more so than ADP-ribose. Such toxic compounds would require disposal via an ADP-sugar diphosphatase or other route. Comparative analysis of bacterial genomes uncovered a candidate disposal gene that is chromosomally clustered with genes for FAD synthesis or transport and is predicted to encode a protein of the PhnP cyclic phosphodiesterase family. The representative PhnP family enzyme from Koribacter versatilis (here named Fpd, FAD photoproduct diphosphatase) was found to have high, Mn2+-dependent diphosphatase activity against FAD photoproducts, FAD, and ADP-ribose, but almost no phosphodiesterase activity against riboflavin 4′,5′-cyclic phosphate, a chemical breakdown product of FAD. To provide a structural basis of the unique Fpd activity, the crystal structure of K. versatilis Fpd was determined. The results place Fpd in the broad metallo-β-lactamase-like family of hydrolases, a diverse family commonly using two metals for hydrolytic catalysis. The active site of Fpd contains two Mn2+ ions and a bound phosphate, consistent with a diphosphatase mechanism. Our results characterize the first PhnP family member that is a diphosphatase rather than a cyclic phosphodiesterase and suggest its involvement in a cellular damage-control system that efficiently hydrolyzes the reactive, ADP-ribose-like products of FAD photodegradation.

scholarly journals Structural basis for the biosynthesis of the CN ligand of [NiFe] hydrogenase

2014 ◽  
Vol 70 (a1) ◽  
pp. C484-C484
Author(s):  
Satoshi Watanabe ◽  
Taiga Tominaga ◽  
Rie Matsumi ◽  
Haruyuki Atomi ◽  
Tadayuki Imanaka ◽  
...  
Keyword(s):  
Active Site ◽  
Transfer Reaction ◽  
Catalytic Mechanism ◽  
Close Contact ◽  
Cysteine Residue ◽  
The Other ◽  
Proton Acceptor ◽  
Structural Basis ◽  
Proton Abstraction ◽  
Cyanide Ligands

[NiFe] hydrogenases carry a NiFe(CN)2CO center at the active site, catalyzing the reversible H2oxidation. The complex NiFe center is biosynthesized and inserted into the enzyme by six specific maturation proteins: Hyp proteins (HypABCDEF). HypE and HypF are involved in biosynthesis of cyanide ligands, which are attached to the Fe atom in the NiFe center. First, HypF catalyzes a transfer reaction of the carbamoyl moiety of carbamoylphosphate to the C-terminal cysteine residue of HypE. Then, HypE catalyzes an ATP-dependent dehydration of the carbamoylated C-terminal cysteine of HypE to thiocyanate. Although structures of HypE proteins have been determined, there has been no structural evidence to explain how HypE dehydrates thiocarboxamide into thiocyanate. In order to elucidate the catalytic mechanism of HypE, we have determined the crystal structures of the carbamoylated and cyanated states of HypE from Thermococcus kodakarensis in complex with nucleotides at 1.53 Å and 1.64 Å resolution, respectively [1]. Carbamoylation of the C-terminal cysteine (Cys338) of HypE by chemical modification is clearly observed in the present structures. A conserved glutamate residue (Glu272) is close to the thiocarboxamide nitrogen atom of Cys338. However, the configuration of Glu272 is less favorable for proton abstraction. On the other hand, the thiocarboxamide oxygen atom of Cys338 interacts with a conserved lysine residue (Lys134) through a water molecule. Interestingly, a conserved arginine residue makes close contact with Lys134 and lowers the pKa of Lys134, suggesting that Lys134 functions as a proton acceptor. These observations suggest that the dehydration of thiocarboxamide into thiocyanate is catalyzed by a two-step deprotonation process, in which Lys134 and Glu272 function as the first and second bases, respectively.

An ultrastructural study on the shark liver

1990 ◽  
Vol 48 (3) ◽  
pp. 512-513
Author(s):  
Masako Yamada ◽  
Yutaka Tanuma
Keyword(s):  
Portal Vein ◽  
Kupffer Cells ◽  
Ultrastructural Study ◽  
Lipid Droplets ◽  
Microscopic Level ◽  
The Other ◽  
Fish Stock ◽  
Structural Studies ◽  
Light Microscopic Level ◽  
Perfusion Fixation

Although many fine structural studies on the vertebrate liver have been reported on mammals, avians, reptiles, amphibians, teleosts and cyclostomes, there are no studies on elasmobranchii liver except one by T. Ito etal. (1962) who studied it on light microscopic level. The purpose of the present study was to as certain the ultrastructural details and cytochemical characteristics of normal elasmobranchii liver and was to compare with the other higher vertebrate ones.Seventeen Scyliorhinus torazame, one kind of elasmobranchii, were obtained from the fish stock of the Ueno Zoo aquarium, Ueno, Tokyo. The sharks weighing about 300-600g were anesthetized with MS-222 (Sigma), and the livers were fixed by perfusion fixation via the portal vein according to the procedure of Y. Saito et al. (1980) for 10 min. Then the liver tissues were immersed in the same fixative for 2 hours and postfixed with 1% OsO4-solution in 0.1 Mc acodylate buffer for one hour. In order to make sure a phagocytic activity of Kupffer cells, latex particles (0.8 μm in diameter, 0.05mg/100 g b.w.) were injected through the portal vein for one min before fixation. For preservation of lipid droplets in the cytoplasm, a series of these procedure were performed under ice cold temperature until the end of dehydration.

Structures of c-di-GMP/cGAMP degrading phosphodiesterase VcEAL: identification of a novel conformational switch and its implication

2019 ◽  
Vol 476 (21) ◽  
pp. 3333-3353 ◽  
Author(s):  
Malti Yadav ◽  
Kamalendu Pal ◽  
Udayaditya Sen
Keyword(s):  
Active Site ◽  
Metal Binding ◽  
Metal Ion ◽  
Triosephosphate Isomerase ◽  
Catalytic Mechanism ◽  
Degradation Mechanism ◽  
Structural Basis ◽  
Conserved Residues ◽  
Phosphodiester Bond ◽  
Cyclic Dinucleotides

Cyclic dinucleotides (CDNs) have emerged as the central molecules that aid bacteria to adapt and thrive in changing environmental conditions. Therefore, tight regulation of intracellular CDN concentration by counteracting the action of dinucleotide cyclases and phosphodiesterases (PDEs) is critical. Here, we demonstrate that a putative stand-alone EAL domain PDE from Vibrio cholerae (VcEAL) is capable to degrade both the second messenger c-di-GMP and hybrid 3′3′-cyclic GMP–AMP (cGAMP). To unveil their degradation mechanism, we have determined high-resolution crystal structures of VcEAL with Ca2+, c-di-GMP-Ca2+, 5′-pGpG-Ca2+ and cGAMP-Ca2+, the latter provides the first structural basis of cGAMP hydrolysis. Structural studies reveal a typical triosephosphate isomerase barrel-fold with substrate c-di-GMP/cGAMP bound in an extended conformation. Highly conserved residues specifically bind the guanine base of c-di-GMP/cGAMP in the G2 site while the semi-conserved nature of residues at the G1 site could act as a specificity determinant. Two metal ions, co-ordinated with six stubbornly conserved residues and two non-bridging scissile phosphate oxygens of c-di-GMP/cGAMP, activate a water molecule for an in-line attack on the phosphodiester bond, supporting two-metal ion-based catalytic mechanism. PDE activity and biofilm assays of several prudently designed mutants collectively demonstrate that VcEAL active site is charge and size optimized. Intriguingly, in VcEAL-5′-pGpG-Ca2+ structure, β5–α5 loop adopts a novel conformation that along with conserved E131 creates a new metal-binding site. This novel conformation along with several subtle changes in the active site designate VcEAL-5′-pGpG-Ca2+ structure quite different from other 5′-pGpG bound structures reported earlier.

scholarly journals Flower-Shaped C-Dots/Co3O4{111} Constructed with Dual-Reaction Centers for Enhancement of Fenton-Like Reaction Activity and Peroxymonosulfate Conversion to Sulfate Radical

Catalysts ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 135
Author(s):  
Zhibin Wen ◽  
Qianqian Zhu ◽  
Jiali Zhou ◽  
Shudi Zhao ◽  
Jinnan Wang ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Active Site ◽  
High Surface ◽  
High Surface Area ◽  
Reaction Centers ◽  
Organic Radicals ◽  
The Other ◽  
High Catalytic Activity ◽  
High Adsorption ◽  
High Turnover

Novel flower-shaped C-dots/Co3O4{111} with dual-reaction centers were constructed to improve the Fenton-like reaction activity and peroxymonosulfate (PMS) conversion to sulfate radicals. Due to the exposure of a high surface area and Co3O4{111} facets, flower-shaped C-dots/Co3O4{111} could provide more Co(II) for PMS activation than traditional spherical Co3O4{110}. Meanwhile, PMS was preferred for adsorption on Co3O4{111} facets because of a high adsorption energy and thereby facilitated the electron transfer from Co(II) to PMS. More importantly, the Co–O–C linkage between C-dots and Co3O4{111} induced the formation of the dual-reaction center, which promoted the production of reactive organic radicals (R•). PMS could be directly reduced to SO4−• by R• over C-dots. On the other hand, electron transferred from R• to Co via Co–O–C linkage could accelerate the redox of Co(II)/(III), avoiding the invalid decomposition of PMS. Thus, C-dots doped on Co3O4{111} improved the PMS conversion rate to SO4−• over the single active site, resulting in high turnover numbers (TONs). In addition, TPR analysis indicated that the optimal content of C-dots doped on Co3O4{111} is 2.5%. More than 99% of antibiotics and dyes were degraded over C-dots/Co3O4{111} within 10 min. Even after six cycles, C-dots/Co3O4{111} still remained a high catalytic activity.

scholarly journals Catalytic Conversion of n-C7 Asphaltenes and Resins II into Hydrogen Using CeO2-Based Nanocatalysts

Nanomaterials ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1301
Author(s):  
Oscar E. Medina ◽  
Jaime Gallego ◽  
Sócrates Acevedo ◽  
Masoud Riazi ◽  
Raúl Ocampo-Pérez ◽  
...  
Keyword(s):  
Hydrogen Production ◽  
Low Temperatures ◽  
Gaseous Mixture ◽  
H2 Production ◽  
The Other ◽  
Hydrogen Release ◽  
Catalytic Gasification ◽  
Three Samples ◽  
Main Decomposition ◽  
Catalytic Capacity

This study focuses on evaluating the volumetric hydrogen content in the gaseous mixture released from the steam catalytic gasification of n-C7 asphaltenes and resins II at low temperatures (<230 °C). For this purpose, four nanocatalysts were selected: CeO2, CeO2 functionalized with Ni-Pd, Fe-Pd, and Co-Pd. The catalytic capacity was measured by non-isothermal (from 100 to 600 °C) and isothermal (220 °C) thermogravimetric analyses. The samples show the main decomposition peak between 200 and 230 °C for bi-elemental nanocatalysts and 300 °C for the CeO2 support, leading to reductions up to 50% in comparison with the samples in the absence of nanoparticles. At 220 °C, the conversion of both fractions increases in the order CeO2 < Fe-Pd < Co-Pd < Ni-Pd. Hydrogen release was quantified for the isothermal tests. The hydrogen production agrees with each material’s catalytic activity for decomposing both fractions at the evaluated conditions. CeNi1Pd1 showed the highest performance among the other three samples and led to the highest hydrogen production in the effluent gas with values of ~44 vol%. When the samples were heated at higher temperatures (i.e., 230 °C), H2 production increased up to 55 vol% during catalyzed n-C7 asphaltene and resin conversion, indicating an increase of up to 70% in comparison with the non-catalyzed systems at the same temperature conditions.

Discovery of natural product ovalicin sensitive type 1 methionine aminopeptidases: molecular and structural basis

2019 ◽  
Vol 476 (6) ◽  
pp. 991-1003 ◽  
Author(s):  
Vijaykumar Pillalamarri ◽  
Tarun Arya ◽  
Neshatul Haque ◽  
Sandeep Chowdary Bala ◽  
Anil Kumar Marapaka ◽  
...  
Keyword(s):  
Natural Product ◽  
Active Site ◽  
Covalent Modification ◽  
Structural Basis ◽  
Wild Type ◽  
Methionine Aminopeptidases ◽  
Synthetic Derivative ◽  
Dynamics Simulations

Abstract Natural product ovalicin and its synthetic derivative TNP-470 have been extensively studied for their antiangiogenic property, and the later reached phase 3 clinical trials. They covalently modify the conserved histidine in Type 2 methionine aminopeptidases (MetAPs) at nanomolar concentrations. Even though a similar mechanism is possible in Type 1 human MetAP, it is inhibited only at millimolar concentration. In this study, we have discovered two Type 1 wild-type MetAPs (Streptococcus pneumoniae and Enterococcus faecalis) that are inhibited at low micromolar to nanomolar concentrations and established the molecular mechanism. F309 in the active site of Type 1 human MetAP (HsMetAP1b) seems to be the key to the resistance, while newly identified ovalicin sensitive Type 1 MetAPs have a methionine or isoleucine at this position. Type 2 human MetAP (HsMetAP2) also has isoleucine (I338) in the analogous position. Ovalicin inhibited F309M and F309I mutants of human MetAP1b at low micromolar concentration. Molecular dynamics simulations suggest that ovalicin is not stably placed in the active site of wild-type MetAP1b before the covalent modification. In the case of F309M mutant and human Type 2 MetAP, molecule spends more time in the active site providing time for covalent modification.

scholarly journals Structural basis for an atypical active site of anl-aspartate/glutamate-specific racemase fromEscherichia coli

FEBS Letters ◽  
2015 ◽  
Vol 589 (24PartB) ◽  
pp. 3842-3847 ◽  
Author(s):  
Jae-Woo Ahn ◽  
Jeong Ho Chang ◽  
Kyung-Jin Kim
Keyword(s):  
Active Site ◽  
Structural Basis ◽  
Fromescherichia Coli

Structural Studies on N-(2,4,6-Trimethylphenyl)-methyl/ chloro-acetamides, 2,4,6-(CH3)3C6H2NH-CO-CH3–yXy (X = CH3 or Cl and y = 0, 1, 2)

2006 ◽  
Vol 61 (10-11) ◽  
pp. 588-594 ◽  
Author(s):  
Basavalinganadoddy Thimme Gowda ◽  
Jozef Kožíšek ◽  
Hartmut Fuess
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Structural Data ◽  
The Other ◽  
Side Chain ◽  
Structural Studies ◽  
Asymmetric Unit ◽  
Lattice Constants ◽  
Peptide Linkage ◽  
The Mean

TMPAThe effect of substitutions in the ring and in the side chain on the crystal structure of N- (2,4,6-trimethylphenyl)-methyl/chloro-acetamides of the configuration 2,4,6-(CH3)3C6H2NH-COCH3− yXy (X = CH3 or Cl and y = 0,1, 2) has been studied by determining the crystal structures of N-(2,4,6-trimethylphenyl)-acetamide, 2,4,6-(CH3)3C6H2NH-CO-CH3 (); N-(2,4,6- trimethylphenyl)-2-methylacetamide, 2,4,6-(CH3)3C6H2NH-CO-CH2-CH3 (TMPMA); N-(2,4,6- trimethylphenyl)-2,2-dimethylacetamide, 2,4,6-(CH3)3C6H2NH-CO-CH(CH3)2 (TMPDMA) and N-(2,4,6-trimethylphenyl)-2,2-dichloroacetamide, 2,4,6-(CH3)3C6H2NH-CO-CHCl2 (TMPDCA). The crystallographic system, space group, formula units and lattice constants in Å are: TMPA: monoclinic, Pn, Z = 2, a = 8.142(3), b = 8.469(3), c = 8.223(3), β = 113.61(2)◦; TMPMA: monoclinic, P21/n, Z = 8, a = 9.103(1), b = 15.812(2), c = 16.4787(19), α = 89.974(10)◦, β = 96.951(10)◦, γ =89.967(10)◦; TMPDMA: monoclinic, P21/c, Z = 4, a =4.757(1), b= 24.644(4), c =10.785(2), β = 99.647(17)◦; TMPDCA: triclinic, P¯1, Z = 2, a = 4.652(1), b = 11.006(1), c = 12.369(1), α = 82.521(7)◦, β = 83.09(1)◦, γ = 79.84(1)◦. The results are analyzed along with the structural data of N-phenylacetamide, C6H5NH-CO-CH3; N-(2,4,6-trimethylphenyl)-2-chloroacetamide, 2,4,6-(CH3)3C6H2NH-CO-CH2Cl; N-(2,4,6-trichlorophenyl)-acetamide, 2,4,6-Cl3C6H2NH-COCH3; N-(2,4,6-trichlorophenyl)-2-chloroacetamide, 2,4,6-Cl3C6H2NH-CO-CH2Cl; N-(2,4,6-trichlorophenyl)- 2,2-dichloroacetamide, 2,4,6-Cl3C6H2NH-CO-CHCl2 and N-(2,4,6-trichlorophenyl)- 2,2,2-trichloroacetamide, 2,4,6-Cl3C6H2NH-CO-CCl3. TMPA, TMPMA and TMPDCA have one molecule each in their asymmetric units, while TMPDMA has two molecules in its asymmetric unit. Changes in the mean ring distances are smaller on substitution as the effect has to be transmitted through the peptide linkage. The comparison of the other bond parameters reveal that there are significant changes in them on substitution.

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