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	Conformational flexibility associated with remote residues regulates the kinetic properties of glutamate dehydrogenase.
Journal, issue, pages	Protein Sci, Vol. 34, Issue 3, Page e70038, Year 2025
Publish date	Feb 21, 2025
Authors	Barsa Kanchan Jyotshna Godsora / Parijat Das / Prasoon Kumar Mishra / Anjali Sairaman / Sandip Kaledhonkar / Narayan S Punekar / Prasenjit Bhaumik /
PubMed Abstract	Glutamate dehydrogenase (GDH) is a pivotal metabolic enzyme in all living organisms, and some of the GDHs exhibit substrate-dependent homotropic cooperativity. However, the mode of allosteric ...Glutamate dehydrogenase (GDH) is a pivotal metabolic enzyme in all living organisms, and some of the GDHs exhibit substrate-dependent homotropic cooperativity. However, the mode of allosteric communication during the homotropic effect in GDHs remains poorly understood. In this study, we examined two homologous GDHs, Aspergillus niger GDH (AnGDH) and Aspergillus terreus GDH (AtGDH), with differing substrate utilization kinetics to uncover the factors driving their distinct behavior. We report the crystal structures and first-ever cryo-EM structures of apo- AtGDH and AnGDH that captured arrays of conformational ensembles. A wider mouth opening (~ 21 Å) is observed for the cooperative AnGDH as compared to the non-cooperative AtGDH (~17 Å) in their apo states. A network of interactions related to the substitutions in Domain II influence structural flexibility in these GDHs. Remarkably, we have identified a distant substitution (R246 to S) in Domain II, as a part of this network, which can impact the mouth opening and converts non-cooperative AtGDH into a cooperative enzyme. Our study demonstrates that remote residues can influence structural and kinetic properties in homologous GDHs.
External links	Protein Sci / PubMed:39981924 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	2.05 - 3.65 Å
Structure data	39722 8z1c EMDB-39722, PDB-8z1c: Cryo-EM structure of apo Aspergillus terreus glutamate dehydrogenase (AtGDH) in the closed conformation (form 1) Method: EM (single particle) / Resolution: 3.15 Å 39730 8z1m EMDB-39730, PDB-8z1m: Cryo-EM structure of apo Aspergillus terreus glutamate dehydrogenase (AtGDH) in the partially closed conformation (form 2) Method: EM (single particle) / Resolution: 3.25 Å 39731 8z1n EMDB-39731, PDB-8z1n: Cryo-EM structure of apo Aspergillus terreus glutamate dehydrogenase (AtGDH) in the closed conformation (form 2) Method: EM (single particle) / Resolution: 3.18 Å 39732 8z1o EMDB-39732, PDB-8z1o: Cryo-EM structure of apo Aspergillus niger glutamate dehydrogenase (AnGDH) in the closed conformation Method: EM (single particle) / Resolution: 3.6 Å 39744 8z2f EMDB-39744, PDB-8z2f: Cryo-EM structure of apo Aspergillus terreus glutamate dehydrogenase (AtGDH) in the partially closed conformation (form 1) Method: EM (single particle) / Resolution: 3.65 Å PDB-8z29: Crystal structure of apo Aspergillus terreus glutamate dehydrogenase (AtGDH) deletion mutant (T262-A263) Method: X-RAY DIFFRACTION / Resolution: 2.85 Å PDB-8z2a: Crystal structure of Aspergillus terreus glutamate dehydrogenase (AtGDH) with sequential mutations Method: X-RAY DIFFRACTION / Resolution: 3.1 Å PDB-8z2b: Crystal structure of apo Aspergillus terreus glutamate dehydrogenase (AtGDH) in the partially closed conformation (form II) Method: X-RAY DIFFRACTION / Resolution: 2.85 Å PDB-8z2c: Crystal structure of apo Aspergillus terreus glutamate dehydrogenase (AtGDH) with open and partially closed conformations (form I) Method: X-RAY DIFFRACTION / Resolution: 2.05 Å
Chemicals	ChemComp-CL: Unknown entry ChemComp-HOH: WATER ChemComp-ACT: ACETATE ION
Source	aspergillus terreus (mold) aspergillus niger (mold)
Keywords	OXIDOREDUCTASE / glutamate dehydrogenase / allostery / cooperativity / Aspergillus / cryo-EM / domain dynamics