Functional insight into Maelstrom in the germline piRNA pathway: a unique domain homologous to the DnaQ-H 3'–5' exonuclease, its lineage-specific expansion/loss and evolutionarily active site switch

Crystal structures of human mitochondrial 3-ketoacyl-CoA thiolase (hT1) in the apo form and in complex with CoA have been determined at 2.0 Å resolution. The structures confirm the tetrameric quaternary structure of this degradative thiolase. The active site is surprisingly similar to the active site of theZoogloea ramigerabiosynthetic tetrameric thiolase (PDB entries 1dm3 and 1m1o) and different from the active site of the peroxisomal dimeric degradative thiolase (PDB entries 1afw and 2iik). A cavity analysis suggests a mode of binding for the fatty-acyl tail in a tunnel lined by the Nβ2–Nα2 loop of the adjacent subunit and the Lα1 helix of the loop domain. Soaking of the apo hT1 crystals with octanoyl-CoA resulted in a crystal structure in complex with CoA owing to the intrinsic acyl-CoA thioesterase activity of hT1. Solution studies confirm that hT1 has low acyl-CoA thioesterase activity for fatty acyl-CoA substrates. The fastest rate is observed for the hydrolysis of butyryl-CoA. It is also shown that T1 has significant biosynthetic thiolase activity, which is predicted to be of physiological importance.

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Class III nucleotide cyclases in bacteria and archaebacteria: lineage-specific expansion of adenylyl cyclases and a dearth of guanylyl cyclases

FEBS Letters ◽

10.1016/s0014-5793(04)00128-0 ◽

2004 ◽

Vol 561 (1-3) ◽

pp. 11-21 ◽

Cited By ~ 34

Author(s):

Avinash R. Shenoy ◽

Sandhya S. Visweswariah

Keyword(s):

Adenylyl Cyclases ◽

Class Iii ◽

Guanylyl Cyclases ◽

Lineage Specific Expansion ◽

Specific Expansion

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Automated docking of phospholipids to the phospholipase D active site: insight into the catalytic mechanism

10.31274/rtd-20200803-109 ◽

2003 ◽

Author(s):

Christopher Lynn Aikens

Keyword(s):

Phospholipase D ◽

Active Site ◽

Catalytic Mechanism ◽

Automated Docking ◽

Insight Into

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Mitochondrial ClpX activates an essential biosynthetic enzyme through partial unfolding

eLife ◽

10.7554/elife.54387 ◽

2020 ◽

Vol 9 ◽

Cited By ~ 3

Author(s):

Julia R Kardon ◽

Jamie A Moroco ◽

John R Engen ◽

Tania A Baker

Keyword(s):

Active Site ◽

Autonomous System ◽

Aminolevulinic Acid ◽

Structural Features ◽

Biosynthetic Enzyme ◽

Cofactor Binding ◽

Partial Unfolding ◽

Chaperone Interactions ◽

Aaa Protein ◽

Insight Into

Mitochondria control the activity, quality, and lifetime of their proteins with an autonomous system of chaperones, but the signals that direct substrate-chaperone interactions and outcomes are poorly understood. We previously discovered that the mitochondrial AAA+ protein unfoldase ClpX (mtClpX) activates the initiating enzyme for heme biosynthesis, 5-aminolevulinic acid synthase (ALAS), by promoting cofactor incorporation. Here, we ask how mtClpX accomplishes this activation. Using S. cerevisiae proteins, we identified sequence and structural features within ALAS that position mtClpX and provide it with a grip for acting on ALAS. Observation of ALAS undergoing remodeling by mtClpX revealed that unfolding is limited to a region extending from the mtClpX-binding site to the active site. Unfolding along this path is required for mtClpX to gate cofactor binding to ALAS. This targeted unfolding contrasts with the global unfolding canonically executed by ClpX homologs and provides insight into how substrate-chaperone interactions direct the outcome of remodeling.

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