ResiduesEnzymeProteinSubstrateHistidine and aspartateAmino acidsSerineMutationEnzymesProteinsIons bindReceptorDehydrogenaseMechanismAcidicCleftEscherichiaHydrolase activityReactionInterproscanSynapticDomainCharacterizationActivitySodiumSiteInteractionPeptideCatalyzeMotifDirectlySitesPocketSwitchTransport
Residues7
- Aspartate-97, aspartate-188, and glutamate-326 make up the active site, which is a triad of acidic residues. (wikipedia.org)
- The computational results are validated by experimental mutation studies, which demonstrate the importance of the Mg2+-binding residues for the catalytic activity. (jefferson.edu)
- Quantum mechanical calculations show that the methyl transfer is energetically feasible only when Mg2+ is bound in the position revealed by the MD simulations, demonstrating that its function is to align the active site residues within the topological knot-fold in a geometry optimal for catalysis. (jefferson.edu)
- The structure bound to the substrate analogue along with mutagenesis of predicted critical amino acid residues led us to suggest a reaction mechanism distinct from all known NADases. (nature.com)
- In the ACE2 receptor, the largest number of amino acids playing a crucial role in the mechanism of interaction and recognition with the S protein is located in the C-terminal part, which represents the main binding region between ACE2 and S. This fragment is abundant in coordination residues such as aspartates, glutamates, and histidine that could be targeted by metal ions. (bvsalud.org)
- Although conserved residues in the nucleotide-binding domains of various dehydrogenases have been linked to cofactor preferences, the structural basis for specificity in the GDH family remains poorly understood. (anl.gov)
- Conserved residues therein, D203 (IIIa), Y229 (IV) and N373, G377, S382 and R389 (VIII), provide Na + binding sites and the translocation pathway. (tcdb.org)
Enzyme10
- Using molecular dynamics (MD) simulations, we identify a plausible Mg2+ binding pocket within the active site of the enzyme, wherein the ion is coordinated by two aspartates and a glutamate. (jefferson.edu)
- A histidine in the N-terminal section of the enzyme has been shown [ 4 ] to be involved in the catalytic mechanism of the enzyme. (expasy.org)
- The structure of the dimeric A. fumigatus enzyme revealed the presence of a Ca 2+ binding site whose occupancy partially regulates enzymatic activity. (nature.com)
- We also solved the structure of the enzyme bound to the reaction products, nicotinamide and ADP ribose, and the non-hydrolysable substrate analogue benzamide adenine dinucleotide (BAD). (nature.com)
- SARS-CoV-2 infects cells via its spike (S) protein binding to its surface receptor angiotensin-converting enzyme 2 (ACE2) and results in the production of multiple proinflammatory cytokines, especially in the lungs, leading to what is known as COVID-19. (bvsalud.org)
- The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection relies on its spike protein binding to angiotensin-converting enzyme 2 (ACE2) on host cells to initiate cellular entry. (bvsalud.org)
- The spike protein (S) of SARS-CoV-2 is able to bind to the human angiotensin-converting enzyme 2 (ACE2) receptor with a much higher affinity compared to other coronaviruses. (bvsalud.org)
- We found that they do not generally enhance either OP or pyrethroid hydrolysis in these esterases but the Aspartate mutation did increase OP hydrolysis in one enzyme by about 14 fold and the Leucine mutation caused a 4-6 fold increase in activity (more in one case) of another three against some of the most insecticidal isomers of fenvalerate and cypermethrin. (inra.fr)
- The Aspartate enzyme and one of the Leucine enzymes occur in regions of the H. armigera esterase isozyme profile that have been previously implicated in OP and pyrethroid resistance, respectively. (inra.fr)
- Serum elevations of ALT activity are rarely observed, except in parenchymal liver disease, since ALT is a more liver-specific enzyme than aspartate aminotransferase (AST). (cdc.gov)
Protein22
- Mg2+ is required for the catalytic activity of TrmD, a bacteria-specific methyltransferase that is made up of a protein topological knot-fold, to synthesize methylated m1G37-tRNA to support life. (jefferson.edu)
- The 1.6 Å X-ray structure of the homodimeric A. fumigatus protein reveals unique properties including N-linked glycosylation and a Ca 2+ -binding site whose occupancy regulates activity. (nature.com)
- In this study, we used human cultured mast cells that are plentiful in the lungs and showed that recombinant SARS-CoV-2 full-length S protein (1-10 ng/mL), but not its receptor-binding domain (RBD), stimulates the secretion of the proinflammatory cytokine interleukin-1ß (IL-1ß) as well as the proteolytic enzymes chymase and tryptase. (bvsalud.org)
- The binding interface between the ACE2 receptor and the spike protein plays a critical role in the entry mechanism of the SARS-CoV-2 virus. (bvsalud.org)
- Zn2+ ions bind to the ACE2 receptor in its catalytic site and modulate its activity, but it could also contribute to the structural stability of the entire protein. (bvsalud.org)
- The ability of the human ACE2 receptor to coordinate metal ions, such as Zn2+, in the same region where it binds to the S protein could have a crucial impact on the mechanism of recognition and interaction of ACE2-S, with consequences on their binding affinity that deserve to be investigated. (bvsalud.org)
- A Rab protein is always bound to another molecule, which determines whether it is inactive or active. (elifesciences.org)
- Binding to a molecule called GDP makes the Rab protein inactive, while binding to GTP makes it active. (elifesciences.org)
- Proteins called guanine nucleotide exchange factors, or GEFs for short, activate the Rab protein by promoting the release of GDP and the binding of GTP. (elifesciences.org)
- For example, the amino acid glutamine is involved when the Listeria GEF and one of the human GEFs activate the protein, whereas a different amino acid-aspartate-is involved when one of the other human GEFs is responsible for the activation. (elifesciences.org)
- Allosterically regulated enzymes additionally rely on the free energy of ligand binding to stabilize the protein in a catalytically competent state. (ward-lab.ch)
- We demonstrate the interplay of protein folding energetics and functional group tuning to convert calmodulin (CaM), a regulatory binding protein, into AlleyCat, an allosterically controlled eliminase. (ward-lab.ch)
- It is a membrane-bound protein that acts as a dimer of two identical subunits. (rcsb.org)
- 47904) TATA-box binding family protein CP001857 CDS Arcpr_0059 47991. (go.jp)
- This diploma thesis revolves around the preparation of biocompatible polymeric conjugates called "iBodies" that will be used to induce targeted lysosomal degradation of two model enzymes - Fibroblast activation protein α, and Glutamate carboxypeptidase II. (nusl.cz)
- Rb is also controlled by phosphorylation: by adding phosphate groups to the protein, it can't bind to E2F and the genes that control cell division are expressed. (rcsb.org)
- Notice that the leucine and cysteine are buried in the protein, so some rearrangement will probably be necessary when the RBBP9 binds to Rb. (rcsb.org)
- Surprisingly, the LxCxE motif is bound inside the protein in this crystallographic structure, so the protein must either rearrange a bit to interact with Rb, or interact through a previously unseen mechanism. (rcsb.org)
- protein_coding" "AGT23894","N559_2182","Klebsiella pneumoniae","putative ABC-type taurine transport system periplasmic binding component [Ensembl]. (ntu.edu.sg)
- protein_coding" "AGT24100","N559_2404","Klebsiella pneumoniae","putative ABC transporter substrate binding protein [Ensembl]. (ntu.edu.sg)
- A protein bound on the interior of a cell membrane that generates a second messenger. (flashcardmachine.com)
- Lead also binds to metallothionein, a sulfhydryl-rich protein, but does not appear to displace cadmium or zinc. (cdc.gov)
Substrate7
- The structure in complex with a substrate analogue suggests a catalytic mechanism that is distinct from those of known NADases, ADP-ribosyl cyclases and transferases. (nature.com)
- Subunits of homo-hexameric bacterial enzymes comprise a substrate-binding domain I followed by a nucleotide-binding domain II. (anl.gov)
- GH43 are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. (unl.edu)
- A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. (unl.edu)
- These are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. (unl.edu)
- The dehydration of the carboxylate, although intrinsically thermodynamically unfavorable, is achieved by harnessing the free energy of folding and substrate binding to reach the required basicity. (ward-lab.ch)
- During movement of the transport domain, the substrate-binding site is occluded from the solvent and shielded by the tips of two pseudo-symmetrical helical hairpins (HP1 and HP2). (nature.com)
Histidine and aspartate2
- A serine performs the cleavage reaction, which is made more chemically active by nearby histidine and aspartate amino acids. (rcsb.org)
- The catalytic triad in the active site, composed of a serine, histidine and aspartate, are also shown in atomic colors. (rcsb.org)
Amino acids2
- By using sequence alignment of herpesviruses homologs, we identified conserved amino acids in the putative pUL105 ATP binding site and in the putative pUL70 zinc finger pattern. (frontiersin.org)
- The cleavage reaction is performed by a catalytic triad of amino acids very similar to serine proteases such as trypsin and elastase . (rcsb.org)
Serine3
- The amino acid located between the regulatory threonine and the catalytic histidine is highly conserved being serine in PPDK and cysteine in PEPS. (scirp.org)
- In addition, a serine that follows the P7 aspartate is presumed to form a hydrogen bond with the 2'-phosphate. (anl.gov)
- RBBP9 binds to Rb and also has a serine protease active site. (rcsb.org)
Mutation3
- Through this mutation, the study of Tn5 becomes possible, but some steps in the catalytic process are lost as a result. (wikipedia.org)
- Remarkably, a single mutation of an apolar residue at the bottom of an otherwise hydrophobic cavity confers catalytic activity on calmodulin. (ward-lab.ch)
- One mutation converts a Glycine to an Aspartate, and the other converts a Tryptophan to a Leucine in the enzymes' active site. (inra.fr)
Enzymes4
- A transposase is any of a class of enzymes capable of binding to the end of a transposon and catalysing its movement to another part of a genome, typically by a cut-and-paste mechanism or a replicative mechanism, in a process known as transposition. (wikipedia.org)
- Upon binding to genomic lesions, these enzymes utilise NAD+ to modify a plethora of proteins with mono- and poly(ADP-ribose) signals that are important for subsequent chromatin decompaction and repair factor recruitment3,4. (diamond.ac.uk)
- A comparison of known PPDK and PEPS sequences revealed a high level of conservation of the amino acid sequence surrounding the catalytic histidine located within a central domain of the enzymes that was composed of GGXTS/CHAAI/VI/VA/SR with the regulatory threonine and catalytic histidine (shown in bold) conserved in all species. (scirp.org)
- A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. (unl.edu)
Proteins4
- It should be pointed out that although the two proteins (PPDK and PEPS) share some homology, especially around a central catalytic site, they can be identified using the signature sequences identified by Tjaden and colleagues [10]. (scirp.org)
- The Rab subfamily of proteins is part of the large Ras superfamily, and all members of this superfamily are activated and inactivated in a similar way, with the binding and unbinding of GDP and GTP taking place at a structure called the G-domain. (elifesciences.org)
- Each contains two domains: the domains at the top of each subunit are involved in interacting with other extracellular proteins, and the domains at the bottom carry the catalytic triad. (rcsb.org)
- In the interaction with proteins, lead binds with virtually every available functional group, including sulfhydryl, amine, phosphate, and carboxyl groups, with sulfhydryl having the highest affinity. (cdc.gov)
Ions bind2
- Here, we systematically measured aspartate uptake rates in proteoliposomes containing purified Glt Tk , and derived the rate equation for a mechanism in which two sodium ions bind before and another after aspartate. (nature.com)
- These experiments have indicated that most likely two sodium ions bind first, then aspartate, and finally the third sodium ion. (nature.com)
Receptor1
- We report here on peptide amphiphile supramolecular nanofibers that display a sequence from ACE2 in order to promote interactions with the SARS-CoV-2 spike receptor binding domain. (bvsalud.org)
Dehydrogenase2
- Structure of NADP(+)-dependent glutamate dehydrogenase from Escherichia coli--reflections on the basis of coenzyme specificity in the family of glutamate dehydrogenases. (anl.gov)
- Glucose-6-phosphate dehydrogenase, NAD-binding [Interproscan]. (ntu.edu.sg)
Mechanism3
- However, neither the location of Mg2+ in the structure of TrmD nor its role in the catalytic mechanism is known. (jefferson.edu)
- It is well-established that the secondary active transporters Glt Tk and Glt Ph catalyze coupled uptake of aspartate and three sodium ions, but insight in the kinetic mechanism of transport is fragmentary. (nature.com)
- Combined with previous pre-equilibrium binding studies, a full kinetic mechanism of structurally characterized aspartate transporters of the SLC1A family is now emerging. (nature.com)
Acidic1
- Two acidic glutamates assist with the reaction by holding tightly to the free amino end of the hormone, locking it into position. (rcsb.org)
Cleft2
Escherichia1
- Using antibodies, we demonstrated that the regulation of both Listeria monocytogenes PPDK and Escherichia coli PEP synthetase involves the phosphorylation of a threonine residue located close to the catalytic histidine residue. (scirp.org)
Hydrolase activity1
- Changing G137 to glutamate or histidine was less effective than aspartate in improving OP hydrolase activity and like G137D, it diminished MCE activity, primarily through increases in Km. (inra.fr)
Reaction1
- The DDE motif is said to coordinate divalent metal ions, most often magnesium and manganese, which are important in the catalytic reaction. (wikipedia.org)
Interproscan4
- Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding [Interproscan]. (ntu.edu.sg)
- NAD(P)-binding domain [InterProScan]. (ntu.edu.sg)
- NAD binding domain [InterProScan]. (ntu.edu.sg)
- 2Fe-2S iron-sulfur cluster binding domain, 2Fe-2S ferredoxin-type iron-sulfur binding domain [InterProScan]. (ntu.edu.sg)
Synaptic3
- There are several steps which catalyze the movement of the transposon, including Tnp binding, synapsis (the creation of a synaptic complex), cleavage, target capture, and strand transfer. (wikipedia.org)
- Once the transposase binds to the transposon, it produces a synaptic complex in which two transposases are bound in a cis/trans relationship with the transposon. (wikipedia.org)
- Excitatory amino acid transporters (EAATs) of the solute carrier family 1A (SLC1A) take up the neurotransmitter L-glutamate from the synaptic environment, which is necessary to keep the extracellular concentration low and prevent neurotoxicity 1 , 2 . (nature.com)
Domain4
- The N-terminal domain binds the glutaconyl-CoA, and the C-terminal domain binds the biotinyl lysine moiety. (tcdb.org)
- The central domain of Rb is included in this structure, shown here in blue, with a short peptide bound in this pocket, with the backbone in green and the leucine-cysteine-glutamate in atomic colors. (rcsb.org)
- The C-terminal domain binds to the transcription factor E2F, removing it from the genes involved in cell division. (rcsb.org)
- Therefore, to evade problems with the missing backbone in the course of this task, the structure was truncated to contain only the C-terminal, catalytic domain, Glyco_hydro_20. (tu-muenchen.de)
Characterization1
- Characterization of DNA binding, transcriptional activation, and regulated nuclear association of recombinant human NFATp. (colorado.edu)
Activity2
- The presence of Mg2+ in the binding pocket induces SAM to adopt a unique bent shape required for the methyl transfer activity and causes a structural reorganization of the active site. (jefferson.edu)
- In its binding with sulfhydryl groups, lead may interfere with the activity of zinc metalloenzymes, as zinc binds to a sulfhydryl group at the active site. (cdc.gov)
Sodium1
- 2005). Sodium ion pumps and hydrogen production in glutamate fermenting anaerobic bacteria. (tcdb.org)
Site4
- Transposase then binds to the DNA strand and creates a clamp over the transposon end of the DNA and inserts into the active site. (wikipedia.org)
- Determining the exact binding site and its structural assessment would help to better understand the interaction between the parasite and the host, which is necessary for the disease progression and thus for the development of a potential therapy. (nusl.cz)
- D203 is absolutely essential for function and may provide the primary intramembranous Na + -binding site. (tcdb.org)
- Modulators likely bind at a site other than the active site. (flashcardmachine.com)
Interaction1
- It binds to the motif LxCxE, shown here in green, which is found in many of its interaction partners. (rcsb.org)
Peptide1
- To test this possibility, this study aims to characterize the coordination ability of Zn2+, and also Cu2+ for comparison, with selected peptide models of the ACE2 binding interface using spectroscopic and potentiometric techniques. (bvsalud.org)
Catalyze1
- Transport assays in proteoliposomes have revealed that both Glt Ph and Glt Tk catalyze electrogenic transport with a strict stoichiometry of three co-transported Na + ions per aspartate 14 , 32 . (nature.com)
Motif2
Directly1
- They also appear to bind nicotinic, cardiac muscarinic, and glutamate N -methyl-d-aspartate (NMDA) receptors directly, suggesting that they may have additional mechanisms of action yet to be defined. (medscape.com)
Sites2
- For example, the carboxylates of glutamate and aspartate are weakly basic in water but become strongly basic when dehydrated in enzymatic sites. (ward-lab.ch)
- D203 and S382 may provide two binding sites for the two Na + ions. (tcdb.org)
Pocket2
- Upon binding Ca(II), native CaM opens a hydrophobic pocket on each of its domains. (ward-lab.ch)
- Two mutations occur naturally, G137D in the oxyanion hole of the esterase, and W251L in the acyl binding pocket. (inra.fr)
Switch1
- By contrast, in Rab5 the switch II aspartate is required for Rabex mediated GDP-release. (elifesciences.org)
Transport1
- Our work underlines the value of bona fide transport experiments to reveal mechanistic features of Na + -aspartate symport that cannot be observed in detergent solution. (nature.com)