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TitleA unified view on enzyme catalysis by cryo-EM study of a DNA topoisomerase.
Journal, issue, pagesCommun Chem, Vol. 7, Issue 1, Page 45, Year 2024
Publish dateFeb 28, 2024
AuthorsChiung-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 AbstractThe 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 linksCommun Chem / PubMed:38418525 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution1.14 - 3.68 Å
Structure data

EMDB-36062, PDB-8j87:
Asfv topoisomerase 2 - apo conformer Ia
Method: EM (single particle) / Resolution: 3.42 Å

EMDB-36063, PDB-8j88:
Asfv topoisomerase 2 - apo conformer Ib
Method: EM (single particle) / Resolution: 3.49 Å

EMDB-36064, PDB-8j89:
Cryo-EM structure of Asfv topoisomerase 2 - apo conformer IIa
Method: EM (single particle) / Resolution: 2.31 Å

EMDB-36065, PDB-8j8a:
Cryo-EM structure of Asfv topoisomerase 2 - apo conformer IIb
Method: EM (single particle) / Resolution: 2.51 Å

EMDB-36066, PDB-8j8b:
Cryo-EM structure of Asfv topoisomerase 2 - apo conformer IIIa
Method: EM (single particle) / Resolution: 2.43 Å

EMDB-36067, PDB-8j8c:
Cryo-EM structure of Asfv topoisomerase 2 - apo conformer IIIb
Method: EM (single particle) / Resolution: 2.69 Å

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

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

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, chemotherapy*YM

ChemComp-ASW:
N-[4-(acridin-9-ylamino)-3-methoxyphenyl]methanesulfonamide / antineoplastic*YM

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

ChemComp-HOH:
WATER

Source
  • african swine fever virus
  • homo sapiens (human)
KeywordsISOMERASE / Topoisomerase / ASFV / VIRAL PROTEIN / ISOMERASE/DNA / inhibitor / ISOMERASE-DNA complex / GHKL NUCLEOTIDE-BINDING FOLD / AMP-PNP

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