Structure of the PSD-95/MAP1A complex reveals a unique target recognition mode of the MAGUK GK domain

2017 ◽  
Vol 474 (16) ◽  
pp. 2817-2828 ◽  
Author(s):  
Yitian Xia ◽  
Yuan Shang ◽  
Rongguang Zhang ◽  
Jinwei Zhu
Keyword(s):  
Conformational Transition ◽  
Target Recognition ◽  
Complex Structure ◽  
Scaffold Proteins ◽  
Peptide Sequence ◽  
Structural Comparison ◽  
Dynamic Regulation ◽  
Hydrophobic Residues ◽  
Recognition Specificity ◽  
Hydrophobic Site

The PSD-95 family of membrane-associated guanylate kinases (MAGUKs) are major synaptic scaffold proteins and play crucial roles in the dynamic regulation of dendritic remodelling, which is understood to be the foundation of synaptogenesis and synaptic plasticity. The guanylate kinase (GK) domain of MAGUK family proteins functions as a phosphor-peptide binding module. However, the GK domain of PSD-95 has been found to directly bind to a peptide sequence within the C-terminal region of neuronal-specific microtubule-associated protein 1A (MAP1A), although the detailed molecular mechanism governing this phosphorylation-independent interaction at the atomic level is missing. In the present study, we determine the crystal structure of PSD-95 GK in complex with the MAP1A peptide at 2.6-Å resolution. The complex structure reveals that, unlike a linear and elongated conformation in the phosphor-peptide/GK complexes, the MAP1A peptide adopts a unique conformation with a stretch of hydrophobic residues far from each other in the primary sequence clustering and interacting with the ‘hydrophobic site’ of PSD-95 GK and a highly conserved aspartic acid of MAP1A (D2117) mimicking the phosphor-serine/threonine in binding to the ‘phosphor-site’ of PSD-95 GK. We demonstrate that the MAP1A peptide may undergo a conformational transition upon binding to PSD-95 GK. Further structural comparison of known DLG GK-mediated complexes reveals the target recognition specificity and versatility of DLG GKs.

scholarly journals Mapping the substrate specificity of the Plasmodium M1 and M17 aminopeptidases.

2021 ◽  
Author(s):  
Tess R Malcolm ◽  
Karolina W. Swiderska ◽  
Brooke K Hayes ◽  
Chaille T Webb ◽  
Marcin Drag ◽  
...  
Keyword(s):  
Substrate Specificity ◽  
Drug Targets ◽  
Protein Production ◽  
Turnover Rate ◽  
Plasmodium Species ◽  
Peptide Sequence ◽  
Sequence Specificity ◽  
Model Species ◽  
Hydrophobic Residues ◽  
Digestion Process

During malarial infection, Plasmodium parasites digest human hemoglobin to obtain free amino acids for protein production and maintenance of osmotic pressure. The Plasmodium M1 and M17 aminopeptidases are both postulated to have an essential role in the terminal stages of the hemoglobin digestion process and are validated drug targets for the design of new dual-target anti-malarial compounds. In this study, we profiled the substrate specificity fingerprints and kinetic behaviors of M1 and M17 aminopeptidases from Plasmodium falciparum and Plasmodium vivax, and the mouse model species, Plasmodium berghei. We found that although the Plasmodium M1 aminopeptidases share a largely similar, broad specificity at the P1 position, the P. falciparum M1 displays the greatest diversity in specificity and P. berghei M1 showing a preference for charged P1 residues. In contrast, the Plasmodium M17 aminopeptidases share a highly conserved preference for hydrophobic residues at the P1 position. The aminopeptidases also demonstrated intra-peptide sequence specificity, particularly the M1 aminopeptidases, which showed a definitive preference for peptides with fewer negatively charged intrapeptide residues. Overall, the P. vivax and P. berghei enzymes had a faster substrate turnover rate than the P. falciparum enzymes, which we postulate is due to subtle differences in structural dynamicity. Together, these results build a kinetic profile that allows us to better understand the catalytic nuances of the M1 and M17 aminopeptidases from different Plasmodium species.

scholarly journals Mapping the substrate sequence and length of the Plasmodium M1 and M17 aminopeptidases

2020 ◽  
Author(s):  
Tess R Malcolm ◽  
Karolina W. Swiderska ◽  
Brooke K Hayes ◽  
Marcin Drag ◽  
Nyssa Drinkwater ◽  
...  
Keyword(s):  
Drug Targets ◽  
Protein Production ◽  
Behavioral Responses ◽  
Peptide Sequence ◽  
Sequence Specificity ◽  
Model Species ◽  
Hydrophobic Residues ◽  
Digestion Process ◽  
Malarial Infection ◽  
Peptide Length

AbstractDuring malarial infection, Plasmodium parasites digest human hemoglobin to obtain free amino acids for protein production and maintenance of osmotic pressure. The Plasmodium M1 and M17 aminopeptidases are both postulated to have an essential role in the terminal stages of the hemoglobin digestion process and are validated drug targets for the design of new dualtarget anti-malarial compounds. In this study, we profiled the substrate specificity fingerprints and kinetic behaviors of M1 and M17 aminopeptidases from Plasmodium falciparum and Plasmodium vivax, and the mouse model species, Plasmodium berghei. We found that although the Plasmodium M1 aminopeptidases share a largely similar, broad specificity at the P1 position, the P. falciparum M1 displays the greatest diversity in specificity and P. berghei M1 showing a preference for charged P1 residues. In contrast, the Plasmodium M17 aminopeptidases share a highly conserved preference for hydrophobic residues at the P1 position. The aminopeptidases also demonstrated intra-peptide sequence specificity, particularly the M1 aminopeptidases, which showed a definitive preference for peptides with fewer negatively charged intrapeptide residues. When tested with a panel of peptides of increasing length, each aminopeptidase exhibited unique catalytic behavioral responses to the increase in peptide length, although all six aminopeptidases exhibited an increase in cooperativity as peptide length increased. Overall the P. vivax and P. berghei enzymes were generally faster than the P. falciparum enzymes, which we postulate is due to subtle differences in structural dynamicity. Together, these results build a kinetic profile that allows us to better understand the catalytic nuances of the M1 and M17 aminopeptidases from different Plasmodium species.

scholarly journals Crystal structure of the toxin Msmeg_6760, the structural homolog ofMycobacterium tuberculosisRv2035, a novel type II toxin involved in the hypoxic response

2016 ◽  
Vol 72 (12) ◽  
pp. 863-869 ◽  
Author(s):  
R. Alexandra Bajaj ◽  
Mark A. Arbing ◽  
Annie Shin ◽  
Duilio Cascio ◽  
Linda Miallau
Keyword(s):  
Crystal Structure ◽  
Mycobacterium Tuberculosis ◽  
Structural Features ◽  
Bacterial Toxins ◽  
Type Ii ◽  
Structural Comparison ◽  
Macrophage Infection ◽  
Bioinformatics Analyses ◽  
Hydrophobic Residues ◽  
Hydrophobic Ligand

The structure of Msmeg_6760, a protein of unknown function, has been determined. Biochemical and bioinformatics analyses determined that Msmeg_6760 interacts with a protein encoded in the same operon, Msmeg_6762, and predicted that the operon is a toxin–antitoxin (TA) system. Structural comparison of Msmeg_6760 with proteins of known function suggests that Msmeg_6760 binds a hydrophobic ligand in a buried cavity lined by large hydrophobic residues. Access to this cavity could be controlled by a gate–latch mechanism. The function of the Msmeg_6760 toxin is unknown, but structure-based predictions revealed that Msmeg_6760 and Msmeg_6762 are homologous to Rv2034 and Rv2035, a predicted novel TA system involved inMycobacterium tuberculosislatency during macrophage infection. The Msmeg_6760 toxin fold has not been previously described for bacterial toxins and its unique structural features suggest that toxin activation is likely to be mediated by a novel mechanism.

scholarly journals Crystal Structure of Uroporphyrinogen Decarboxylase from Bacillus subtilis

2006 ◽  
Vol 189 (9) ◽  
pp. 3573-3580 ◽  
Author(s):  
Jun Fan ◽  
Qun Liu ◽  
Quan Hao ◽  
Maikun Teng ◽  
Liwen Niu
Keyword(s):  
Crystal Structure ◽  
Bacillus Subtilis ◽  
Light Scattering ◽  
Chlorophyll Biosynthesis ◽  
Asymmetric Unit ◽  
Structural Comparison ◽  
Uroporphyrinogen Decarboxylase ◽  
Biological Unit ◽  
Hydrophobic Residues ◽  
Scattering Measurements

ABSTRACT Uroporphyrinogen decarboxylase (UROD) is a branch point enzyme in the biosynthesis of the tetrapyrroles. It catalyzes the decarboxylation of four acetate groups of uroporphyrinogen III to yield coproporphyrinogen III, leading to heme and chlorophyll biosynthesis. UROD is a special type of nonoxidative decarboxylase, since no cofactor is essential for catalysis. In this work, the first crystal structure of a bacterial UROD, Bacillus subtilis UROD (URODBs), has been determined at a 2.3 Å resolution. The biological unit of URODBs was determined by dynamic light scattering measurements to be a homodimer in solution. There are four molecules in the crystallographic asymmetric unit, corresponding to two homodimers. Structural comparison of URODBs with eukaryotic URODs reveals a variation of two loops, which possibly affect the binding of substrates and release of products. Structural comparison with the human UROD-coproporphyrinogen III complex discloses a similar active cleft, with five invariant polar residues (Arg29, Arg33, Asp78, Tyr154, and His322) and three invariant hydrophobic residues (Ile79, Phe144, and Phe207), in URODBs. Among them, Asp78 may interact with the pyrrole NH groups of the substrate, and Arg29 is a candidate for positioning the acetate groups of the substrate. Both residues may also play catalytic roles.

Histone H1 and the dynamic regulation of chromatin function

2003 ◽  
Vol 81 (3) ◽  
pp. 221-227 ◽  
Author(s):  
David T Brown
Keyword(s):  
Chromatin Structure ◽  
Transcriptional Activation ◽  
Dynamic Properties ◽  
Dominant Role ◽  
Complex Structure ◽  
Strong Support ◽  
Histone H1 ◽  
Covalent Modification ◽  
Dynamic Regulation ◽  
Reversible Covalent

Eukaryotic DNA is organized in a complex structure called chromatin. Although a primary function of chromatin is compaction of DNA, this must done such that the underlying DNA is potentially accessible to factor-mediated regulatory responses. Chromatin structure clearly plays a dominant role in regulating much of eukaryotic transcription. The demonstration that reversible covalent modification of the core histones contribute to transcriptional activation and repression by altering chromatin structure and the identification of numerous ATP-dependent chromatin remodeling enzymes provide strong support for this view. Chromatin is much more dynamic than was previously thought and regulation of the dynamic properties of chromatin is a key aspect of gene regulation. This review will focus on recent attempts to elucidate the specific contribution of histone H1 to chromatin-mediated regulation of gene expression.Key words: histone H1, chromatin, gene expression.

scholarly journals Dynamic Structural Changes Accompany the Production of 2-Dihydroxypropanesulfonate by Sulfolactaldehyde Reductase

2019 ◽  
Author(s):  
Mahima Sharma ◽  
Palika Abayakoon ◽  
James P. Lingford ◽  
Yi Jin ◽  
Ruwan Epa ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Bound States ◽  
Ternary Complex ◽  
Structural Changes ◽  
Reductase Activity ◽  
Complex Structure ◽  
Peptide Sequence ◽  
Sequence Motifs ◽  
Conserved Sequence ◽  
K 12

2,3-Dihydroxypropanesulfonate (DHPS) is a major sulfur species in the biosphere. One important route for the production of DHPS includes sulfoglycolytic catabolism of sulfoquinovose (SQ) through the Embden-Meyerhof-Parnas (sulfo-EMP) pathway. SQ is a sulfonated carbohydrate present in plant and cyanobacterial sulfolipids (sulfoquinovosyl diacylglyceride and its metabolites) and is biosynthesised globally at a rate of around 10 billion tonnes per annum. The final step in the bacterial sulfo-EMP pathway involves reduction of sulfolactaldehyde (SLA) to DHPS, catalysed by an NADH-dependent SLA reductase. On the basis of conserved sequence motifs, we assign SLA reductase to the β-hydroxyacid dehydrogenase (β-HAD) family, making it the first example of a β-HAD enzyme that acts on a sulfonic acid, rather than a carboxylic acid substrate. We report crystal structures of the SLA reductase YihU from E. coli K-12 in its apo and cofactor-bound states, as well as the ternary complex YihU•NADH•DHPS with the cofactor and product bound in the active site. Conformational flexibility observed in these structures, combined with kinetic studies, confirm a sequential mechanism and provide evidence for dynamic domain movements that occur during catalysis. The ternary complex structure reveals a conserved sulfonate pocket in SLA reductase that recognises the sulfonate oxygens through hydrogen bonding to Asn174, Ser178, and the backbone amide of Arg123, along with an ordered water molecule. This triad of residues distinguishes these enzymes from classical β-HADs that act on carboxylate substrates. A comparison of YihU crystal structures with close structural homologues within the β-HAD family highlights key differences in the overall domain organization and identifies a unique peptide sequence that is predictive of SLA reductase activity.<br>

scholarly journals Dynamic Structural Changes Accompany the Production of 2-Dihydroxypropanesulfonate by Sulfolactaldehyde Reductase

2019 ◽  
Author(s):  
Mahima Sharma ◽  
Palika Abayakoon ◽  
James P. Lingford ◽  
Yi Jin ◽  
Ruwan Epa ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Bound States ◽  
Ternary Complex ◽  
Structural Changes ◽  
Reductase Activity ◽  
Complex Structure ◽  
Peptide Sequence ◽  
Sequence Motifs ◽  
Conserved Sequence ◽  
K 12

2,3-Dihydroxypropanesulfonate (DHPS) is a major sulfur species in the biosphere. One important route for the production of DHPS includes sulfoglycolytic catabolism of sulfoquinovose (SQ) through the Embden-Meyerhof-Parnas (sulfo-EMP) pathway. SQ is a sulfonated carbohydrate present in plant and cyanobacterial sulfolipids (sulfoquinovosyl diacylglyceride and its metabolites) and is biosynthesised globally at a rate of around 10 billion tonnes per annum. The final step in the bacterial sulfo-EMP pathway involves reduction of sulfolactaldehyde (SLA) to DHPS, catalysed by an NADH-dependent SLA reductase. On the basis of conserved sequence motifs, we assign SLA reductase to the β-hydroxyacid dehydrogenase (β-HAD) family, making it the first example of a β-HAD enzyme that acts on a sulfonic acid, rather than a carboxylic acid substrate. We report crystal structures of the SLA reductase YihU from E. coli K-12 in its apo and cofactor-bound states, as well as the ternary complex YihU•NADH•DHPS with the cofactor and product bound in the active site. Conformational flexibility observed in these structures, combined with kinetic studies, confirm a sequential mechanism and provide evidence for dynamic domain movements that occur during catalysis. The ternary complex structure reveals a conserved sulfonate pocket in SLA reductase that recognises the sulfonate oxygens through hydrogen bonding to Asn174, Ser178, and the backbone amide of Arg123, along with an ordered water molecule. This triad of residues distinguishes these enzymes from classical β-HADs that act on carboxylate substrates. A comparison of YihU crystal structures with close structural homologues within the β-HAD family highlights key differences in the overall domain organization and identifies a unique peptide sequence that is predictive of SLA reductase activity.<br>

scholarly journals Dynamic Structural Changes Accompany the Production of 2-Dihydroxypropanesulfonate by Sulfolactaldehyde Reductase

2019 ◽  
Author(s):  
Mahima Sharma ◽  
Palika Abayakoon ◽  
James P. Lingford ◽  
Yi Jin ◽  
Ruwan Epa ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Bound States ◽  
Ternary Complex ◽  
Structural Changes ◽  
Reductase Activity ◽  
Complex Structure ◽  
Peptide Sequence ◽  
Sequence Motifs ◽  
Conserved Sequence ◽  
K 12

2,3-Dihydroxypropanesulfonate (DHPS) is a major sulfur species in the biosphere. One important route for the production of DHPS includes sulfoglycolytic catabolism of sulfoquinovose (SQ) through the Embden-Meyerhof-Parnas (sulfo-EMP) pathway. SQ is a sulfonated carbohydrate present in plant and cyanobacterial sulfolipids (sulfoquinovosyl diacylglyceride and its metabolites) and is biosynthesised globally at a rate of around 10 billion tonnes per annum. The final step in the bacterial sulfo-EMP pathway involves reduction of sulfolactaldehyde (SLA) to DHPS, catalysed by an NADH-dependent SLA reductase. On the basis of conserved sequence motifs, we assign SLA reductase to the β-hydroxyacid dehydrogenase (β-HAD) family, making it the first example of a β-HAD enzyme that acts on a sulfonic acid, rather than a carboxylic acid substrate. We report crystal structures of the SLA reductase YihU from E. coli K-12 in its apo and cofactor-bound states, as well as the ternary complex YihU•NADH•DHPS with the cofactor and product bound in the active site. Conformational flexibility observed in these structures, combined with kinetic studies, confirm a sequential mechanism and provide evidence for dynamic domain movements that occur during catalysis. The ternary complex structure reveals a conserved sulfonate pocket in SLA reductase that recognises the sulfonate oxygens through hydrogen bonding to Asn174, Ser178, and the backbone amide of Arg123, along with an ordered water molecule. This triad of residues distinguishes these enzymes from classical β-HADs that act on carboxylate substrates. A comparison of YihU crystal structures with close structural homologues within the β-HAD family highlights key differences in the overall domain organization and identifies a unique peptide sequence that is predictive of SLA reductase activity.<br>

scholarly journals Structural basis underlying complex assembly and conformational transition of the type I R-M system

2017 ◽  
Vol 114 (42) ◽  
pp. 11151-11156 ◽  
Author(s):  
Yan-Ping Liu ◽  
Qun Tang ◽  
Jie-Zhong Zhang ◽  
Li-Fei Tian ◽  
Pu Gao ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Molecular Mechanisms ◽  
Conformational Transition ◽  
Structural Information ◽  
Structural Basis ◽  
Type I ◽  
Structural Comparison ◽  
Complex Assembly ◽  
Adenosyl Methionine ◽  
Restriction Modification

Type I restriction-modification (R-M) systems are multisubunit enzymes with separate DNA-recognition (S), methylation (M), and restriction (R) subunits. Despite extensive studies spanning five decades, the detailed molecular mechanisms underlying subunit assembly and conformational transition are still unclear due to the lack of high-resolution structural information. Here, we report the atomic structure of a type I MTase complex (2M+1S) bound to DNA and cofactor S-adenosyl methionine in the “open” form. The intermolecular interactions between M and S subunits are mediated by a four-helix bundle motif, which also determines the specificity of the interaction. Structural comparison between open and previously reported low-resolution “closed” structures identifies the huge conformational changes within the MTase complex. Furthermore, biochemical results show that R subunits prefer to load onto the closed form MTase. Based on our results, we proposed an updated model for the complex assembly. The work reported here provides guidelines for future applications in molecular biology.

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