Structural Basis of Salicylic Acid Decarboxylase Reveals a Unique Substrate Recognition Mode and Access Channel

2021 ◽  
Author(s):  
Xin Gao ◽  
Mian Wu ◽  
Wei Zhang ◽  
Chao Li ◽  
Rey-Ting Guo ◽  
...  
Keyword(s):  
Salicylic Acid ◽  
Substrate Recognition ◽  
Structural Basis ◽  
Acid Decarboxylase ◽  
Access Channel

scholarly journals Structural Basis for Substrate Recognition in the Salicylic Acid Carboxyl Methyltransferase Family

2003 ◽  
Vol 15 (8) ◽  
pp. 1704-1716 ◽  
Author(s):  
Chloe Zubieta ◽  
Jeannine R. Ross ◽  
Paul Koscheski ◽  
Yue Yang ◽  
Eran Pichersky ◽  
...  
Keyword(s):  
Salicylic Acid ◽  
Substrate Recognition ◽  
Structural Basis ◽  
Carboxyl Methyltransferase

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.

scholarly journals Structural basis for divergent and convergent evolution of catalytic machineries in plant aromatic amino acid decarboxylase proteins

2020 ◽  
Vol 117 (20) ◽  
pp. 10806-10817 ◽  
Author(s):  
Michael P. Torrens-Spence ◽  
Ying-Chih Chiang ◽  
Tyler Smith ◽  
Maria A. Vicent ◽  
Yi Wang ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Convergent Evolution ◽  
Structural Features ◽  
Divergent Evolution ◽  
Structural Basis ◽  
Acid Decarboxylase ◽  
Substrate Selectivity ◽  
Amino Acid Decarboxylase ◽  
Catalytic Mechanisms

Radiation of the plant pyridoxal 5′-phosphate (PLP)-dependent aromatic l-amino acid decarboxylase (AAAD) family has yielded an array of paralogous enzymes exhibiting divergent substrate preferences and catalytic mechanisms. Plant AAADs catalyze either the decarboxylation or decarboxylation-dependent oxidative deamination of aromatic l-amino acids to produce aromatic monoamines or aromatic acetaldehydes, respectively. These compounds serve as key precursors for the biosynthesis of several important classes of plant natural products, including indole alkaloids, benzylisoquinoline alkaloids, hydroxycinnamic acid amides, phenylacetaldehyde-derived floral volatiles, and tyrosol derivatives. Here, we present the crystal structures of four functionally distinct plant AAAD paralogs. Through structural and functional analyses, we identify variable structural features of the substrate-binding pocket that underlie the divergent evolution of substrate selectivity toward indole, phenyl, or hydroxyphenyl amino acids in plant AAADs. Moreover, we describe two mechanistic classes of independently arising mutations in AAAD paralogs leading to the convergent evolution of the derived aldehyde synthase activity. Applying knowledge learned from this study, we successfully engineered a shortened benzylisoquinoline alkaloid pathway to produce (S)-norcoclaurine in yeast. This work highlights the pliability of the AAAD fold that allows change of substrate selectivity and access to alternative catalytic mechanisms with only a few mutations.

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