Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Coupling enzymatic activity and gating in an ancient TRPM chanzyme and its molecular evolution.
Journal, issue, pages	Nat Struct Mol Biol, Vol. 31, Issue 10, Page 1509-1521, Year 2024
Publish date	May 21, 2024
Authors	Yihe Huang / Sushant Kumar / Junuk Lee / Wei Lü / Juan Du /
PubMed Abstract	Channel enzymes represent a class of ion channels with enzymatic activity directly or indirectly linked to their channel function. We investigated a TRPM2 chanzyme from choanoflagellates that ...Channel enzymes represent a class of ion channels with enzymatic activity directly or indirectly linked to their channel function. We investigated a TRPM2 chanzyme from choanoflagellates that integrates two seemingly incompatible functions into a single peptide: a channel module activated by ADP-ribose with high open probability and an enzyme module (NUDT9-H domain) consuming ADP-ribose at a remarkably slow rate. Using time-resolved cryogenic-electron microscopy, we captured a complete series of structural snapshots of gating and catalytic cycles, revealing the coupling mechanism between channel gating and enzymatic activity. The slow kinetics of the NUDT9-H enzyme module confers a self-regulatory mechanism: ADPR binding triggers NUDT9-H tetramerization, promoting channel opening, while subsequent hydrolysis reduces local ADPR, inducing channel closure. We further demonstrated how the NUDT9-H domain has evolved from a structurally semi-independent ADP-ribose hydrolase module in early species to a fully integrated component of a gating ring essential for channel activation in advanced species.
External links	Nat Struct Mol Biol / PubMed:38773335 / PubMed Central
Methods	EM (single particle)
Resolution	1.97 - 4.14 Å
Structure data	40721 8sr7 EMDB-40721, PDB-8sr7: Cryo-EM structure of TRPM2 chanzyme in the presence of Magnesium, Adenosine monophosphate, and Ribose-5-phosphate Method: EM (single particle) / Resolution: 1.97 Å 40722 8sr8 EMDB-40722, PDB-8sr8: Cryo-EM structure of TRPM2 chanzyme in the presence of EDTA (apo state) Method: EM (single particle) / Resolution: 2.77 Å 40723 8sr9 EMDB-40723, PDB-8sr9: Cryo-EM structure of TRPM2 chanzyme in the presence of Magnesium Method: EM (single particle) / Resolution: 3.05 Å 40724 8sra EMDB-40724, PDB-8sra: Cryo-EM structure of TRPM2 chanzyme in the presence of Calcium Method: EM (single particle) / Resolution: 2.93 Å 40725 8srb EMDB-40725, PDB-8srb: Cryo-EM structure of TRPM2 chanzyme in the presence of EDTA and ADP-ribose Method: EM (single particle) / Resolution: 2.82 Å 40726 8src EMDB-40726, PDB-8src: Cryo-EM structure of TRPM2 chanzyme in the presence of Calcium and ADP-ribose Method: EM (single particle) / Resolution: 2.92 Å 40727 8srd EMDB-40727, PDB-8srd: Cryo-EM structure of TRPM2 chanzyme in the presence of Magnesium and ADP-ribose, open state Method: EM (single particle) / Resolution: 2.91 Å 40728 8sre EMDB-40728, PDB-8sre: Cryo-EM structure of TRPM2 chanzyme in the presence of Magnesium and ADP-ribose, closed state Method: EM (single particle) / Resolution: 2.52 Å 40729 8srf EMDB-40729, PDB-8srf: Cryo-EM structure of TRPM2 chanzyme in the presence of Magnesium, ADP-ribose, Adenosine monophosphate, and Ribose-5-phosphate, closed state Method: EM (single particle) / Resolution: 2.52 Å 40730 8srg EMDB-40730, PDB-8srg: Cryo-EM structure of TRPM2 chanzyme in the presence of Magnesium, Adenosine monophosphate, and Ribose-5-phosphate Method: EM (single particle) / Resolution: 3.03 Å 40731 8srh EMDB-40731, PDB-8srh: Cryo-EM structure of TRPM2 chanzyme (E1114A) in the presence of Magnesium and ADP-ribose, open state Method: EM (single particle) / Resolution: 3.79 Å 40732 8sri EMDB-40732, PDB-8sri: Cryo-EM structure of TRPM2 chanzyme (E1114A) in the presence of Magnesium and ADP-ribose, closed state Method: EM (single particle) / Resolution: 2.73 Å 40733 8srj EMDB-40733, PDB-8srj: Cryo-EM structure of TRPM2 chanzyme (without NUDT9-H domain) in the presence of EDTA, apo state Method: EM (single particle) / Resolution: 3.74 Å 40734 8srk EMDB-40734, PDB-8srk: Cryo-EM structure of TRPM2 chanzyme (without NUDT9-H domain) in the presence of Ca and ADP-ribose Method: EM (single particle) / Resolution: 4.14 Å EMDB-40865: NUDT9-H domain focused cryo-EM map of TRPM2 chanzyme in the presence of Calcium and ADP-ribose Method: EM (single particle) / Resolution: 3.69 Å EMDB-40866: NUDT9-H domain focused cryo-EM map of TRPM2 chanzyme in the presence of Magnesium, Adenosine monophosphate, and Ribose-5-phosphate Method: EM (single particle) / Resolution: 2.8 Å EMDB-40867: NUDT9-H domain focused cryo-EM map of TRPM2 chanzyme in the presence of Magnesium, Adenosine monophosphate, and Ribose-5-phosphate Method: EM (single particle) / Resolution: 3.83 Å EMDB-40868: NUDT9-H domain focused cryo-EM map of TRPM2 chanzyme in the presence of Magnesium and ADP-ribose, open state Method: EM (single particle) / Resolution: 3.13 Å EMDB-40869: NUDT9-H domain focused cryo-EM map of TRPM2 chanzyme in the presence of Magnesium and ADP-ribose, closed state Method: EM (single particle) / Resolution: 2.8 Å EMDB-40870: NUDT9-H domain focused cryo-EM map of TRPM2 chanzyme in the presence of Magnesium, ADP-ribose, Adenosine monophosphate, and Ribose-5-phosphate, closed state Method: EM (single particle) / Resolution: 2.8 Å EMDB-40871: NUDT9-H domain focused cryo-EM map of TRPM2 chanzyme (E1114A) in the presence of Magnesium and ADP-ribose, open state Method: EM (single particle) / Resolution: 4.08 Å EMDB-40872: NUDT9-H domain focused cryo-EM map of TRPM2 chanzyme (E1114A) in the presence of Magnesium and ADP-ribose, closed state Method: EM (single particle) / Resolution: 3.27 Å EMDB-40875: Raw consensus map of TRPM2 chanzyme in the presence of Magnesium, Adenosine monophosphate, and Ribose-5-phosphate Method: EM (single particle) / Resolution: 1.97 Å EMDB-40876: Raw consensus map of TRPM2 chanzyme in the presence of Magnesium Method: EM (single particle) / Resolution: 3.16 Å EMDB-40877: Raw consensus map of TRPM2 chanzyme in the presence of Calcium Method: EM (single particle) / Resolution: 3.03 Å EMDB-40878: Raw consensus map of TRPM2 chanzyme in the presence of EDTA and ADP-ribose Method: EM (single particle) / Resolution: 3.3 Å EMDB-40879: Raw consensus map of TRPM2 chanzyme in the presence of Magnesium and ADP-ribose, open state Method: EM (single particle) / Resolution: 2.93 Å EMDB-40880: Raw consensus map of TRPM2 chanzyme in the presence of Magnesium and ADP-ribose, closed state Method: EM (single particle) / Resolution: 3.87 Å EMDB-40881: Raw consensus map of TRPM2 chanzyme in the presence of Magnesium, ADP-ribose, Adenosine monophosphate, and Ribose-5-phosphate, closed state Method: EM (single particle) / Resolution: 3.71 Å EMDB-40883: Raw consensus map of TRPM2 chanzyme in the presence of Magnesium, Adenosine monophosphate, and Ribose-5-phosphate Method: EM (single particle) / Resolution: 2.8 Å EMDB-40887: Raw consensus map of TRPM2 chanzyme (E1114A) in the presence of Magnesium and ADP-ribose, open state Method: EM (single particle) / Resolution: 3.87 Å EMDB-40888: Raw consensus map of TRPM2 chanzyme (E1114A) in the presence of Magnesium and ADP-ribose, closed state Method: EM (single particle) / Resolution: 2.82 Å EMDB-40893: Raw consensus map of TRPM2 chanzyme in the presence of Calcium and ADP-ribose. Method: EM (single particle) / Resolution: 2.99 Å EMDB-40895: Raw consensus map of TRPM2 chanzyme in the presence of EDTA (apo state) Method: EM (single particle) / Resolution: 3.02 Å
Chemicals	ChemComp-RP5: 5-O-phosphono-beta-D-ribofuranose ChemComp-AMP: ADENOSINE MONOPHOSPHATE / AMPYM ChemComp-MG: Unknown entry ChemComp-CLR: CHOLESTEROL ChemComp-HOH: WATER ChemComp-CA: Unknown entry ChemComp-APR*: ADENOSINE-5-DIPHOSPHORIBOSE
Source	salpingoeca rosetta (eukaryote)
Keywords	TRANSPORT PROTEIN / TRPM2 Chanzyme / Channel-enzyme / MEMBRANE PROTEIN