scholarly journals Structural basis for the substrate recognition mechanism of ATP-sulfurylase domain of human PAPS synthase 2

2021 ◽  
Author(s):  
Pan Zhang ◽  
Lin Zhang ◽  
Zhaoyuan Hou ◽  
Houwen Lin ◽  
Hai Gao ◽  
...  
Keyword(s):  
Substrate Recognition ◽  
Structural Basis ◽  
Atp Sulfurylase ◽  
Recognition Mechanism

scholarly journals Half Way to Hypusine—Structural Basis for Substrate Recognition by Human Deoxyhypusine Synthase

Biomolecules ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 522 ◽  
Author(s):  
Elżbieta Wątor ◽  
Piotr Wilk ◽  
Przemysław Grudnik
Keyword(s):  
Conformational Changes ◽  
Bound States ◽  
Substrate Recognition ◽  
Structural Basis ◽  
Dependent Manner ◽  
Post Translational Modification ◽  
Deoxyhypusine Synthase ◽  
Recognition Mechanism ◽  
Eukaryotic Translation ◽  
Potential Applications

Deoxyhypusine synthase (DHS) is a transferase enabling the formation of deoxyhypusine, which is the first, rate-limiting step of a unique post-translational modification: hypusination. DHS catalyses the transfer of a 4-aminobutyl moiety of polyamine spermidine to a specific lysine of eukaryotic translation factor 5A (eIF5A) precursor in a nicotinamide adenine dinucleotide (NAD)-dependent manner. This modification occurs exclusively on one protein, eIF5A, and it is essential for cell proliferation. Malfunctions of the hypusination pathway, including those caused by mutations within the DHS encoding gene, are associated with conditions such as cancer or neurodegeneration. Here, we present a series of high-resolution crystal structures of human DHS. Structures were determined as the apoprotein, as well as ligand-bound states at high-resolutions ranging from 1.41 to 1.69 Å. By solving DHS in complex with its natural substrate spermidine (SPD), we identified the mode of substrate recognition. We also observed that other polyamines, namely spermine (SPM) and putrescine, bind DHS in a similar manner as SPD. Moreover, we performed activity assays showing that SPM could to some extent serve as an alternative DHS substrate. In contrast to previous studies, we demonstrate that no conformational changes occur in the DHS structure upon spermidine-binding. By combining mutagenesis and a light-scattering approach, we show that a conserved “ball-and-chain” motif is indispensable to assembling a functional DHS tetramer. Our study substantially advances our knowledge of the substrate recognition mechanism by DHS and may aid the design of pharmacological compounds for potential applications in cancer therapy.

scholarly journals Structural basis for the substrate recognition of aminoglycoside 7′′-phosphotransferase-Ia from Streptomyces hygroscopicus

2019 ◽  
Vol 75 (9) ◽  
pp. 599-607
Author(s):  
Mihoko Takenoya ◽  
Tatsuro Shimamura ◽  
Ryuji Yamanaka ◽  
Yuya Adachi ◽  
Shinsaku Ito ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Substrate Recognition ◽  
Streptomyces Hygroscopicus ◽  
Structural Basis ◽  
Hydroxyl Groups ◽  
Recognition Mechanism ◽  
Conserved Residues ◽  
Helical Domain ◽  
Structural Differences ◽  
Aminoglycoside Phosphotransferases

Hygromycin B (HygB) is one of the aminoglycoside antibiotics, and it is widely used as a reagent in molecular-biology experiments. Two kinases are known to inactivate HygB through phosphorylation: aminoglycoside 7′′-phosphotransferase-Ia [APH(7′′)-Ia] from Streptomyces hygroscopicus and aminoglycoside 4-phosphotransferase-Ia [APH(4)-Ia] from Escherichia coli. They phosphorylate the hydroxyl groups at positions 7′′ and 4 of the HygB molecule, respectively. Previously, the crystal structure of APH(4)-Ia was reported as a ternary complex with HygB and 5′-adenylyl-β,γ-imidodiphosphate (AMP-PNP). To investigate the differences in the substrate-recognition mechanism between APH(7′′)-Ia and APH(4)-Ia, the crystal structure of APH(7′′)-Ia complexed with HygB is reported. The overall structure of APH(7′′)-Ia is similar to those of other aminoglycoside phosphotransferases, including APH(4)-Ia, and consists of an N-terminal lobe (N-lobe) and a C-terminal lobe (C-lobe). The latter also comprises a core and a helical domain. Accordingly, the APH(7′′)-Ia and APH(4)-Ia structures fit globally when the structures are superposed at three catalytically important conserved residues, His, Asp and Asn, in the Brenner motif, which is conserved in aminoglycoside phosphotransferases as well as in eukaryotic protein kinases. On the other hand, the phosphorylated hydroxyl groups of HygB in both structures come close to the Asp residue, and the HygB molecules in each structure lie in opposite directions. These molecules were held by the helical domain in the C-lobe, which exhibited structural differences between the two kinases. Furthermore, based on the crystal structures of APH(7′′)-Ia and APH(4)-Ia, some mutated residues in their thermostable mutants reported previously were located at the same positions in the two enzymes.

scholarly journals Structural Basis and Sequence Rules for Substrate Recognition by Tankyrase Explain the Basis for Cherubism Disease

Cell ◽  
2012 ◽  
Vol 148 (1-2) ◽  
pp. 376
Author(s):  
Sebastian Guettler ◽  
Jose LaRose ◽  
Evangelia Petsalaki ◽  
Gerald Gish ◽  
Andy Scotter ◽  
...  
Keyword(s):  
Substrate Recognition ◽  
Structural Basis ◽  
Sequence Rules

scholarly journals Structural basis of HMCES interactions with DNA reveals multivalent substrate recognition

2019 ◽  
Author(s):  
Levon Halabelian ◽  
Mani Ravichandran ◽  
Yanjun Li ◽  
Hong Zheng ◽  
L. Aravind ◽  
...  
Keyword(s):  
Dna Damage ◽  
Crystal Structures ◽  
Genome Instability ◽  
Substrate Recognition ◽  
Catalytic Triad ◽  
Structural Basis ◽  
Replication Forks ◽  
Abasic Sites ◽  
Stalled Replication Forks ◽  
Gapped Dna

ABSTRACTHMCES can covalently crosslink to abasic sites in single-stranded DNA at stalled replication forks to prevent genome instability. Here, we report crystal structures of the HMCES SRAP domain in complex with DNA-damage substrates, revealing interactions with both single-stranded and duplex segments of 3’ overhang DNA. HMCES may also bind gapped DNA and 5’ overhang structures to align single stranded abasic sites for crosslinking to the conserved Cys2 of its catalytic triad.

scholarly journals Structural basis of substrate recognition and translocation by human ABCD1

2021 ◽  
Author(s):  
Zhipeng Chen ◽  
Da Xu ◽  
Liang Wang ◽  
Cong-Zhao Zhou ◽  
Wen-Tao Hou ◽  
...  
Keyword(s):  
Genetic Disorder ◽  
Substrate Recognition ◽  
Acyl Chain ◽  
Chain Fatty Acid ◽  
Structural Basis ◽  
Long Chain Fatty Acid ◽  
Lateral Entry ◽  
Binding Domains ◽  
Acyl Chains ◽  
Functional States

Human ATP-binding cassette (ABC) subfamily D transporter ABCD1 can transport CoA esters of saturated/monounsaturated long/very long chain fatty acid into the peroxisome for β-oxidation. Dysfunction of human ABCD1 causes X-linked adrenoleukodystrophy, which is a severe progressive genetic disorder affecting the nervous system. Nevertheless, the mechanistic details of substrate recognition and translocation by ABCD1 remains obscure. Here, we present three cryo-EM structures of human ABCD1 in distinct functional states. In the apo-form structure of 3.53 Å resolution, ABCD1 exhibits an inward-facing conformation, allowing the lateral entry of substrate from the lipid bilayer. In the 3.59 Å structure of substrate-bound ABCD1, two molecules of C22:0-CoA, the physiological substrate of ABCD1, is symmetrically bound in two transmembrane domains (TMDs). Each C22:0-CoA adopts a L-shape, with its CoA portion and acyl chain components bound to two TMDs respectively, resembling a pair of strings that pull the TMDs closer, resultantly generating a narrower outward-facing conformation. In the 2.79 Å ATP-bound ABCD1 structure, the two nucleotide-binding domains dimerize, leading to an outward-facing conformation, which opens the translocation cavity exit towards the peroxisome matrix side and releases the substrates. Our study provides a molecular basis to understand the mechanism of ABCD1-mediated substrate recognition and translocation, and suggests a unique binding pattern for amphipathic molecules with long acyl chains.

Structural basis of substrate recognition and translocation by human ABCA4

2021 ◽  
Author(s):  
Tian Xie ◽  
Zike Zhang ◽  
Bowen Du ◽  
Qi Fang ◽  
Xin Gong
Keyword(s):  
Substrate Recognition ◽  
Bound State ◽  
Lipid Transport ◽  
Structural Basis ◽  
Lateral Entry ◽  
Closed Conformation ◽  
Hereditary Disorders ◽  
Extrusion Mechanism ◽  
Functional States ◽  
Lipid Compounds

AbstractHuman ATP-binding cassette (ABC) subfamily A (ABCA) transporters mediate the transport of various lipid compounds across the membrane. Mutations in human ABCA transporters have been described to cause severe hereditary disorders associated with impaired lipid transport. However, little is known about the mechanistic details of substrate recognition and translocation by ABCA transporters. Here, we present three cryo-EM structures of human ABCA4, a retinal-specific ABCA transporter, in distinct functional states at resolutions of 3.3-3.4 Å. In the nucleotide-free state, the two transmembrane domains (TMDs) exhibited a lateral-opening conformation, allowing the lateral entry of substrate from the lipid bilayer. N-retinylidene-phosphatidylethanolamine (NRPE), the physiological lipid substrate of ABCA4, is sandwiched between the two TMDs in the luminal leaflet and is further stabilized by an extended loop from extracellular domain 1. In the ATP-bound state, the two TMDs displayed an unprecedented closed conformation, which precludes the substrate binding. Our study provides a molecular basis to understand the mechanism of ABCA4-mediated NRPE recognition and translocation, and suggests a common ‘lateral access and extrusion’ mechanism for ABCA-mediated lipid transport.

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