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	A unified view on enzyme catalysis by cryo-EM study of a DNA topoisomerase.
Journal, issue, pages	Commun Chem, Vol. 7, Issue 1, Page 45, Year 2024
Publish date	Feb 28, 2024
Authors	Chiung-Wen Mary Chang / Shun-Chang Wang / Chun-Hsiung Wang / Allan H Pang / Cheng-Han Yang / Yao-Kai Chang / Wen-Jin Wu / Ming-Daw Tsai /
PubMed Abstract	The theories for substrate recognition in enzyme catalysis have evolved from lock-key to induced fit, then conformational selection, and conformational selection followed by induced fit. However, the ...The theories for substrate recognition in enzyme catalysis have evolved from lock-key to induced fit, then conformational selection, and conformational selection followed by induced fit. However, the prevalence and consensus of these theories require further examination. Here we use cryogenic electron microscopy and African swine fever virus type 2 topoisomerase (AsfvTop2) to demonstrate substrate binding theories in a joint and ordered manner: catalytic selection by the enzyme, conformational selection by the substrates, then induced fit. The apo-AsfvTop2 pre-exists in six conformers that comply with the two-gate mechanism directing DNA passage and release in the Top2 catalytic cycle. The structures of AsfvTop2-DNA-inhibitor complexes show that substantial induced-fit changes occur locally from the closed apo-conformer that however is too far-fetched for the open apo-conformer. Furthermore, the ATPase domain of AsfvTop2 in the MgAMP-PNP-bound crystal structures coexist in reduced and oxidized forms involving a disulfide bond, which can regulate the AsfvTop2 function.
External links	Commun Chem / PubMed:38418525 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	1.14 - 3.68 Å
Structure data	36062 8j87 EMDB-36062, PDB-8j87: Asfv topoisomerase 2 - apo conformer Ia Method: EM (single particle) / Resolution: 3.42 Å 36063 8j88 EMDB-36063, PDB-8j88: Asfv topoisomerase 2 - apo conformer Ib Method: EM (single particle) / Resolution: 3.49 Å 36064 8j89 EMDB-36064, PDB-8j89: Cryo-EM structure of Asfv topoisomerase 2 - apo conformer IIa Method: EM (single particle) / Resolution: 2.31 Å 36065 8j8a EMDB-36065, PDB-8j8a: Cryo-EM structure of Asfv topoisomerase 2 - apo conformer IIb Method: EM (single particle) / Resolution: 2.51 Å 36066 8j8b EMDB-36066, PDB-8j8b: Cryo-EM structure of Asfv topoisomerase 2 - apo conformer IIIa Method: EM (single particle) / Resolution: 2.43 Å 36067 8j8c EMDB-36067, PDB-8j8c: Cryo-EM structure of Asfv topoisomerase 2 - apo conformer IIIb Method: EM (single particle) / Resolution: 2.69 Å 36116 8j9v EMDB-36116, PDB-8j9v: Cryo-EM structure of the African swine fever virus topoisomerase 2 complexed with Cut02aDNA and etoposide (EDI-1) Method: EM (single particle) / Resolution: 2.71 Å 36117 8j9w EMDB-36117, PDB-8j9w: Cryo-EM structure of the African swine fever virus topoisomerase 2 complexed with Cut02bDNA and etoposide (EDI-2) Method: EM (single particle) / Resolution: 2.76 Å 36118 8j9x EMDB-36118, PDB-8j9x: Cryo-EM structure of the African swine fever virus topoisomerase 2 complexed with Cut02aDNA and m-AMSA (EDI-3) Method: EM (single particle) / Resolution: 3.0 Å EMDB-36473: Cryo-EM structure of the full-length African swine fever virus topoisomerase 2 complexed with Cut02aDNA and etoposide Method: EM (single particle) / Resolution: 3.68 Å PDB-8ja1: ASFV Topoisomerase ATPase domain in complex with AMP-PNP and Mg2+ (oxidized form) Method: X-RAY DIFFRACTION / Resolution: 1.14 Å PDB-8ja2: ASFV Topoisomerase ATPase domain in complex with AMP-PNP and Mg2+ Method: X-RAY DIFFRACTION / Resolution: 1.73 Å
Chemicals	ChemComp-MG: Unknown entry ChemComp-EVP: (5S,5aR,8aR,9R)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol / medication, chemotherapyYM / Etoposide ChemComp-ASW: N-[4-(acridin-9-ylamino)-3-methoxyphenyl]methanesulfonamide / antineoplasticYM / Amsacrine ChemComp-ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogueYM ChemComp-HOH*: WATER / Water
Source	african swine fever virus homo sapiens (human)
Keywords	ISOMERASE / Topoisomerase / ASFV / VIRAL PROTEIN / ISOMERASE/DNA / inhibitor / ISOMERASE-DNA complex / GHKL NUCLEOTIDE-BINDING FOLD / AMP-PNP