scholarly journals Crystal structure of phosphoribulokinase from Synechococcus sp. strain PCC 6301

2019 ◽  
Vol 75 (4) ◽  
pp. 278-289 ◽  
Author(s):  
Robert H. Wilson ◽  
Manajit Hayer-Hartl ◽  
Andreas Bracher
Keyword(s):  
Crystal Structure ◽  
Disulfide Bond ◽  
Carbon Fixation ◽  
Adaptor Protein ◽  
Structural Basis ◽  
Dimer Interface ◽  
Synechococcus Sp ◽  
Β Sheet ◽  
Loop Residue

Phosphoribulokinase (PRK) catalyses the ATP-dependent phosphorylation of ribulose 5-phosphate to give ribulose 1,5-bisphosphate. Regulation of this reaction in response to light controls carbon fixation during photosynthesis. Here, the crystal structure of PRK from the cyanobacterium Synechococcus sp. strain PCC 6301 is presented. The enzyme is dimeric and has an α/β-fold with an 18-stranded β-sheet at its core. Interestingly, a disulfide bond is found between Cys40 and the P-loop residue Cys18, revealing the structural basis for the redox inactivation of PRK activity. A second disulfide bond appears to rigidify the dimer interface and may thereby contribute to regulation by the adaptor protein CP12 and glyceraldehyde-3-phosphate dehydrogenase.

scholarly journals Crystal structure of enolase fromDrosophila melanogaster

2017 ◽  
Vol 73 (4) ◽  
pp. 228-234 ◽  
Author(s):  
Congcong Sun ◽  
Baokui Xu ◽  
Xueyan Liu ◽  
Zhen Zhang ◽  
Zhongliang Su
Keyword(s):  
Crystal Structure ◽  
Catalytic Activity ◽  
Structural Basis ◽  
Molecular Replacement ◽  
Biological Processes ◽  
Conserved Residues ◽  
Dimer Interface ◽  
Open Conformation ◽  
Evolutionary Studies ◽  
Important Enzyme

Enolase is an important enzyme in glycolysis and various biological processes. Its dysfunction is closely associated with diseases. Here, the enolase fromDrosophila melanogaster(DmENO) was purified and crystallized. A crystal of DmENO diffracted to 2.0 Å resolution and belonged to space groupR32. The structure was solved by molecular replacement. Like most enolases, DmENO forms a homodimer with conserved residues in the dimer interface. DmENO possesses an open conformation in this structure and contains conserved elements for catalytic activity. This work provides a structural basis for further functional and evolutionary studies of enolase.

Crystal structures of a β-trefoil lectin from Entamoeba histolytica in monomeric and a novel disulfide bond-mediated dimeric forms

Glycobiology ◽  
2020 ◽  
Vol 30 (7) ◽  
pp. 474-488 ◽  
Author(s):  
Farha Khan ◽  
Devanshu Kurre ◽  
K Suguna
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Entamoeba Histolytica ◽  
Disulfide Bond ◽  
Structural Basis ◽  
Free Form ◽  
Biophysical Characterization ◽  
Biophysical Studies ◽  
First Time

Abstract β-Trefoil lectins are galactose/N-acetyl galactosamine specific lectins, which are widely distributed across all kingdoms of life and are known to perform several important functions. However, there is no report available on the characterization of these lectins from protozoans. We have performed structural and biophysical studies on a β-trefoil lectin from Entamoeba histolytica (EntTref), which exists as a mixture of monomers and dimers in solution. Further, we have determined the affinities of EntTref for rhamnose, galactose and different galactose-linked sugars. We obtained the crystal structure of EntTref in a sugar-free form (EntTref_apo) and a rhamnose-bound form (EntTref_rham). A novel Cys residue-mediated dimerization was revealed in the crystal structure of EntTref_apo while the structure of EntTref_rham provided the structural basis for the recognition of rhamnose by a β-trefoil lectin for the first time. To the best of our knowledge, this is the only report of the structural, functional and biophysical characterization of a β-trefoil lectin from a protozoan source and the first report of Cys-mediated dimerization in this class of lectins.

scholarly journals Biochemical and Structural Characterisation of a Novel D-Lyxose Isomerase From the Hyperthermophilic Archaeon Thermofilum sp.

2021 ◽  
Vol 9 ◽  
Author(s):  
Simone Antonio De Rose ◽  
Tom Kuprat ◽  
Michail N. Isupov ◽  
Andreas Reinhardt ◽  
Peter Schönheit ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Escherichia Coli ◽  
Disulfide Bond ◽  
Industrial Applications ◽  
Free Form ◽  
Solvent Tolerance ◽  
Dimer Interface ◽  
Hyperthermophilic Archaeon ◽  
Structural Characterisation ◽  
Ligand Free

A novel D-lyxose isomerase has been identified within the genome of a hyperthermophilic archaeon belonging to the Thermofilum species. The enzyme has been cloned and over-expressed in Escherichia coli and biochemically characterised. This enzyme differs from other enzymes of this class in that it is highly specific for the substrate D-lyxose, showing less than 2% activity towards mannose and other substrates reported for lyxose isomerases. This is the most thermoactive and thermostable lyxose isomerase reported to date, showing activity above 95°C and retaining 60% of its activity after 60 min incubation at 80°C. This lyxose isomerase is stable in the presence of 50% (v/v) of solvents ethanol, methanol, acetonitrile and DMSO. The crystal structure of the enzyme has been resolved to 1.4–1.7 A. resolution in the ligand-free form and in complexes with both of the slowly reacting sugar substrates mannose and fructose. This thermophilic lyxose isomerase is stabilised by a disulfide bond between the two monomers of the dimeric enzyme and increased hydrophobicity at the dimer interface. These overall properties of high substrate specificity, thermostability and solvent tolerance make this lyxose isomerase enzyme a good candidate for potential industrial applications.

scholarly journals The crystal structure of mouse LC3B in complex with the FYCO1 LIR reveals the importance of the flanking region of the LIR motif

2017 ◽  
Vol 73 (3) ◽  
pp. 130-137 ◽  
Author(s):  
Shunya Sakurai ◽  
Taisuke Tomita ◽  
Toshiyuki Shimizu ◽  
Umeharu Ohto
Keyword(s):  
Crystal Structure ◽  
Coiled Coil ◽  
Adaptor Protein ◽  
Structural Basis ◽  
Core Sequence ◽  
Coiled Coil Domain ◽  
Flanking Sequences ◽  
Flanking Region ◽  
Membrane Components ◽  
Lir Motif

FYVE and coiled-coil domain-containing protein 1 (FYCO1), a multidomain autophagy adaptor protein, mediates microtubule plus-end-directed autophagosome transport by interacting with kinesin motor proteins and with the autophagosomal membrane components microtubule-associated protein 1 light chain 3 (LC3), Rab7 and phosphatidylinositol 3-phosphate (PI3P). To establish the structural basis for the recognition of FYCO1 by LC3, the crystal structure of mouse LC3B in complex with the FYCO1 LC3-interacting region (LIR) motif peptide was determined. Structural analysis showed that the flanking sequences N-terminal and C-terminal to the LIR core sequence of FYCO1, as well as the tetrapeptide core sequence, were specifically recognized by LC3B and contributed to the binding. Moreover, comparisons of related structures revealed a conserved mechanism of FYCO1 recognition by different LC3 isoforms among different species.

scholarly journals Structural basis for the recognition of the scaffold protein Frmpd4/Preso1 by the TPR domain of the adaptor protein LGN

2015 ◽  
Vol 71 (2) ◽  
pp. 175-183 ◽  
Author(s):  
Hiroki Takayanagi ◽  
Satoru Yuzawa ◽  
Hideki Sumimoto
Keyword(s):  
Crystal Structure ◽  
Consensus Sequence ◽  
Adaptor Protein ◽  
Structural Basis ◽  
Tetratricopeptide Repeat ◽  
Amino Acid Residues ◽  
Binding Region ◽  
Α Helix ◽  
Tpr Domain ◽  
Partner Proteins

The adaptor protein LGN interactsviathe N-terminal domain comprising eight tetratricopeptide-repeat (TPR) motifs with its partner proteins mInsc, NuMA, Frmpd1 and Frmpd4 in a mutually exclusive manner. Here, the crystal structure of the LGN TPR domain in complex with human Frmpd4 is described at 1.5 Å resolution. In the complex, the LGN-binding region of Frmpd4 (amino-acid residues 990–1011) adopts an extended structure that runs antiparallel to LGN along the concave surface of the superhelix formed by the TPR motifs. Comparison with the previously determined structures of the LGN–Frmpd1, LGN–mInsc and LGN–NuMA complexes reveals that these partner proteins interact with LGN TPR1–6viaa common core binding region with consensus sequence (E/Q)XEX4–5(E/D/Q)X1–2(K/R)X0–1(V/I). In contrast to Frmpd1, Frmpd4 makes additional contacts with LGNviaregions N- and C-terminal to the core sequence. The N-terminal extension is replaced by a specific α-helix in mInsc, which drastically increases the direct contacts with LGN TPR7/8, consistent with the higher affinity of mInsc for LGN. A crystal structure of Frmpd4-bound LGN in an oxidized form is also reported, although oxidation does not appear to strongly affect the interaction with Frmpd4.

scholarly journals Structural basis of Naa20 activity towards a canonical NatB substrate

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Dominik Layer ◽  
Jürgen Kopp ◽  
Miriam Fontanillo ◽  
Maja Köhn ◽  
Karine Lapouge ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Drug Development ◽  
Catalytic Mechanism ◽  
Peptide Binding ◽  
Competitive Inhibitor ◽  
Structural Basis ◽  
Substrate Affinity ◽  
Protein Homeostasis ◽  
Auxiliary Subunit

AbstractN-terminal acetylation is one of the most common protein modifications in eukaryotes and is carried out by N-terminal acetyltransferases (NATs). It plays important roles in protein homeostasis, localization, and interactions and is linked to various human diseases. NatB, one of the major co-translationally active NATs, is composed of the catalytic subunit Naa20 and the auxiliary subunit Naa25, and acetylates about 20% of the proteome. Here we show that NatB substrate specificity and catalytic mechanism are conserved among eukaryotes, and that Naa20 alone is able to acetylate NatB substrates in vitro. We show that Naa25 increases the Naa20 substrate affinity, and identify residues important for peptide binding and acetylation activity. We present the first Naa20 crystal structure in complex with the competitive inhibitor CoA-Ac-MDEL. Our findings demonstrate how Naa20 binds its substrates in the absence of Naa25 and support prospective endeavors to derive specific NAT inhibitors for drug development.

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