Crystal structure of the flavin reductase of Acinetobacter baumannii p-hydroxyphenylacetate 3-hydroxylase (HPAH) and identification of amino acid residues underlying its regulation by aromatic ligands

2018 ◽  
Vol 653 ◽  
pp. 24-38 ◽  
Author(s):  
Anan Yuenyao ◽  
Nopphon Petchyam ◽  
Nuntaporn Kamonsutthipaijit ◽  
Pimchai Chaiyen ◽  
Danaya Pakotiprapha
Keyword(s):  
Crystal Structure ◽  
Amino Acid ◽  
Acinetobacter Baumannii ◽  
Amino Acid Residues ◽  
Flavin Reductase

scholarly journals Structure–function studies of human deoxyhypusine synthase: identification of amino acid residues critical for the binding of spermidine and NAD

2001 ◽  
Vol 355 (3) ◽  
pp. 841-849 ◽  
Author(s):  
Chang Hoon LEE ◽  
Patrick Y. UM ◽  
Myung Hee PARK
Keyword(s):  
Crystal Structure ◽  
Enzyme Activity ◽  
Amino Acid ◽  
Binding Sites ◽  
Binding Pocket ◽  
Complete Loss ◽  
Amino Acid Residues ◽  
Deoxyhypusine Synthase ◽  
Positive Identification ◽  
Insight Into

Deoxyhypusine synthase catalyses the first step in the biosynthesis of hypusine [Nε-(4-amino-2-hydroxybutyl)lysine]. The crystal structure of human deoxyhypusine synthase in complex with NAD revealed four NAD-binding sites per enzyme tetramer, and led to a prediction of the spermidine-binding pocket. We have replaced each of the seven amino acid residues at the predicted spermidine-binding site, and eleven residues that contact NAD, on an individual basis with alanine. Of the amino acid residues at the spermidine site, substitution of Asp-243, Trp-327, His-288, Asp-316 or Glu-323 with alanine caused an almost complete loss of spermidine binding and enzyme activity; only the mutation Tyr-305 → Ala showed partial binding and activity. His-288 → Ala was also deficient in terms of binding NAD. NAD binding was significantly reduced in all of the NAD-site mutant enzymes, except for Glu-137 → Ala, which showed a normal binding of NAD, but was totally lacking in spermidine binding. Of the NAD-site mutant enzymes, Asp-342 → Ala, Asp-313 → Ala and Asp-238 → Ala displayed the lowest binding of NAD. These enzymes and His-288Ala also showed a reduced binding of spermidine, presumably because spermidine binding is dependent on NAD. These findings permit the positive identification of amino acid residues critical for binding of spermidine and NAD, and provide a new insight into the complex molecular interactions involved in the deoxyhypusine synthase reaction.

scholarly journals Reconstruction of Mycobacterial Dehalogenase Rv2579 by Cumulative Mutagenesis of Haloalkane Dehalogenase LinB

2003 ◽  
Vol 69 (4) ◽  
pp. 2349-2355 ◽  
Author(s):  
Yuji Nagata ◽  
Zbyněk Prokop ◽  
Soňa Marvanová ◽  
Jana Sýkorová ◽  
Marta Monincová ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Mycobacterium Tuberculosis ◽  
Amino Acid ◽  
Active Site ◽  
Homology Model ◽  
Protein Family ◽  
Sphingomonas Paucimobilis ◽  
Amino Acid Residues ◽  
Haloalkane Dehalogenase

ABSTRACT The homology model of protein Rv2579 from Mycobacterium tuberculosis H37Rv was compared with the crystal structure of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26, and this analysis revealed that 6 of 19 amino acid residues which form an active site and entrance tunnel are different in LinB and Rv2579. To characterize the effect of replacement of these six amino acid residues, mutations were introduced cumulatively into the six amino acid residues of LinB. The sixfold mutant, which was supposed to have the active site of Rv2579, exhibited haloalkane dehalogenase activity with the haloalkanes tested, confirming that Rv2579 is a member of the haloalkane dehalogenase protein family.

scholarly journals Structure of human nucleosome containing the testis-specific histone variant TSH2B

2014 ◽  
Vol 70 (4) ◽  
pp. 444-449 ◽  
Author(s):  
Takashi Urahama ◽  
Naoki Horikoshi ◽  
Akihisa Osakabe ◽  
Hiroaki Tachiwana ◽  
Hitoshi Kurumizaka
Keyword(s):  
Crystal Structure ◽  
Amino Acid ◽  
Structural Changes ◽  
Structural Difference ◽  
Histone Variants ◽  
The Other ◽  
Human Testis ◽  
Amino Acid Residues ◽  
Histone H2b ◽  
Specific Amino Acid

The human histone H2B variant TSH2B is highly expressed in testis and may function in the chromatin transition during spermatogenesis. In the present study, the crystal structure of the human testis-specific nucleosome containing TSH2B was determined at 2.8 Å resolution. A local structural difference between TSH2B and canonical H2B in nucleosomes was detected around the TSH2B-specific amino-acid residue Ser85. The TSH2B Ser85 residue does not interact with H4 in the nucleosome, but in the canonical nucleosome the H2B Asn84 residue (corresponding to the TSH2B Ser85 residue) forms water-mediated hydrogen bonds with the H4 Arg78 residue. In contrast, the other TSH2B-specific amino-acid residues did not induce any significant local structural changes in the TSH2B nucleosome. These findings may provide important information for understanding how testis-specific histone variants form nucleosomes during spermatogenesis.

scholarly journals Molecular Dynamics Simulations of a Cytochrome P450 from Tepidiphilus thermophilus (P450-TT) Reveal How Its Substrate-Binding Channel Opens

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3614
Author(s):  
Abayomi S. Faponle ◽  
Anupom Roy ◽  
Ayodeji A. Adelegan ◽  
James W. Gauld
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Cytochrome P450 ◽  
Amino Acid ◽  
Molecular Dynamics Simulations ◽  
Organic Molecules ◽  
Side Chain ◽  
Relative Solvent Accessibility ◽  
Amino Acid Residues ◽  
Dynamics Simulations

Cytochrome P450s (P450) are important enzymes in biology with useful biochemical reactions in, for instance, drug and xenobiotics metabolisms, biotechnology, and health. Recently, the crystal structure of a new member of the CYP116B family has been resolved. This enzyme is a cytochrome P450 (CYP116B46) from Tepidiphilus thermophilus (P450-TT) and has potential for the oxy-functionalization of organic molecules such as fatty acids, terpenes, steroids, and statins. However, it was thought that the opening to its hitherto identified substrate channel was too small to allow organic molecules to enter. To investigate this, we performed molecular dynamics simulations on the enzyme. The results suggest that the crystal structure is not relaxed, possibly due to crystal packing effects, and that its tunnel structure is constrained. In addition, the simulations revealed two key amino acid residues at the mouth of the channel; a glutamyl and an arginyl. The glutamyl’s side chain tightens and relaxes the opening to the channel in conjunction with the arginyl’s, though the latter’s side chain is less dramatically changed after the initial relaxation of its conformations. Additionally, it was observed that the effect of increased temperature did not considerably affect the dynamics of the enzyme fold, including the relative solvent accessibility of the amino acid residues that make up the substrate channel wall even as compared to the changes that occurred at room temperature. Interestingly, the substrate channel became distinguishable as a prominent tunnel that is likely to accommodate small- to medium-sized organic molecules for bioconversions. That is, P450-TT has the ability to pass appropriate organic substrates to its active site through its elaborate substrate channel, and notably, is able to control or gate any molecules at the opening to this channel.

scholarly journals Distinct amino acid residues confer one of three UDP-sugar substrate specificities in Acinetobacter baumannii PglC phosphoglycosyltransferases

Glycobiology ◽  
2018 ◽  
Vol 28 (7) ◽  
pp. 522-533 ◽  
Author(s):  
Christian M Harding ◽  
M Florencia Haurat ◽  
Evgeny Vinogradov ◽  
Mario F Feldman
Keyword(s):  
Amino Acid ◽  
Acinetobacter Baumannii ◽  
Amino Acid Residues ◽  
Substrate Specificities

scholarly journals A Crystal Structure of the Dengue Virus Non-structural Protein 5 (NS5) Polymerase Delineates Interdomain Amino Acid Residues That Enhance Its Thermostability andde NovoInitiation Activities

2013 ◽  
Vol 288 (43) ◽  
pp. 31105-31114 ◽  
Author(s):  
Siew Pheng Lim ◽  
Jolene Hong Kiew Koh ◽  
Cheah Chen Seh ◽  
Chong Wai Liew ◽  
Andrew D. Davidson ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Amino Acid ◽  
Dengue Virus ◽  
Amino Acid Residues ◽  
Structural Protein

scholarly journals Identification of Channel-lining Amino Acid Residues in the Hydrophobic Segment of Colicin Ia

2008 ◽  
Vol 132 (6) ◽  
pp. 693-707 ◽  
Author(s):  
Paul K. Kienker ◽  
Karen S. Jakes ◽  
Alan Finkelstein
Keyword(s):  
Crystal Structure ◽  
Amino Acid ◽  
Lipid Bilayer ◽  
Open Channel ◽  
Structural Model ◽  
Water Soluble ◽  
Amino Acid Residues ◽  
Lipid Bilayer Membranes ◽  
Planar Bilayers ◽  
Colicin Ia

Colicin Ia is a bactericidal protein of 626 amino acid residues that kills its target cell by forming a channel in the inner membrane; it can also form voltage-dependent channels in planar lipid bilayer membranes. The channel-forming activity resides in the carboxy-terminal domain of ∼177 residues. In the crystal structure of the water-soluble conformation, this domain consists of a bundle of 10 α-helices, with eight mostly amphipathic helices surrounding a hydrophobic helical hairpin (helices H8-H9). We wish to know how this structure changes to form a channel in a lipid bilayer. Although there is evidence that the open channel has four transmembrane segments (H8, H9, and parts of H1 and H6-H7), their arrangement relative to the pore is largely unknown. Given the lack of a detailed structural model, it is imperative to better characterize the channel-lining protein segments. Here, we focus on a segment of 44 residues (573–616), which in the crystal structure comprises the H8-H9 hairpin and flanking regions. We mutated each of these residues to a unique cysteine, added the mutant colicins to the cis side of planar bilayers to form channels, and determined whether sulfhydryl-specific methanethiosulfonate reagents could alter the conduction of ions through the open channel. We found a pattern of reactivity consistent with parts of H8 and H9 lining the channel as α-helices, albeit rather short ones for spanning a lipid bilayer (12 residues). The effects of the reactions on channel conductance and selectivity tend to be greater for residues near the amino terminus of H8 and the carboxy terminus of H9, with particularly large effects for G577C, T581C, and G609C, suggesting that these residues may occupy a relatively constricted region near the cis end of the channel.

Crystal Structure of Dihydro-Heme d1 Dehydrogenase NirN from Pseudomonas aeruginosa Reveals Amino Acid Residues Essential for Catalysis

2019 ◽  
Vol 431 (17) ◽  
pp. 3246-3260 ◽  
Author(s):  
Thomas Klünemann ◽  
Arne Preuß ◽  
Julia Adamczack ◽  
Luis F.M. Rosa ◽  
Falk Harnisch ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Pseudomonas Aeruginosa ◽  
Amino Acid ◽  
Amino Acid Residues ◽  
Heme D1

scholarly journals Crystal structure of Boc-(S)-ABOC-(S)-Ala-(S)-ABOC-(S)-Phe-OBn chloroform monosolvate

2015 ◽  
Vol 71 (10) ◽  
pp. 1193-1195
Author(s):  
Emmanuel Wenger ◽  
Laure Moulat ◽  
Baptiste Legrand ◽  
Muriel Amblard ◽  
Monique Calmès ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Amino Acid ◽  
Carboxylic Acid ◽  
Hydrogen Bonds ◽  
Benzyl Ester ◽  
Protecting Groups ◽  
Amino Acid Residues ◽  
Hybrid Peptide ◽  
Proteinogenic Amino Acid ◽  
Solvent Molecules

In the title compound, phenyl (S)-2-[(S)-(1-{2-[(S)-(1-{[(tert-butoxy)carbonyl]amino}bicyclo[2.2.2]octan-2-yl)formamido]propanamido}bicyclo[2.2.2]octan-2-yl)formamido]-3-phenylpropanoate chloroform monosolvate, C42H56N4O7·CHCl3, the α,β-hybrid peptide contains two non-proteinogenic amino acid residues of (S)-1-aminobicyclo[2.2.2]octane-2-carboxylic acid [(S)-ABOC], two amino acid residues of (S)-2-aminopropanoic acid [(S)-Ala] and (S)-2-amino-3-phenylpropanoic acid [(S)-Phe], and protecting groups oftert-butoxycarbonyl (Boc) and benzyl ester (OBn). The tetramer folds into a right-handed mixed 11/9 helix stabilized by intramoleculari,i + 3 andi,i − 1 C=O...H—N hydrogen bonds. In the crystal, the oligomers are linked by N—H...O=C hydrogen bonds into chains along thea-axis direction. The chloroform solvent molecules are intercalated between the folded chainsviaC—H...O=C interactions.

Sign in / Sign up

Export Citation Format

Share Document