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Structure paper

TitleStructural insight into the assembly and working mechanism of helicase-primase D5 from Mpox virus.
Journal, issue, pagesNat Struct Mol Biol, Vol. 31, Issue 1, Page 68-81, Year 2024
Publish dateJan 4, 2024
AuthorsYaning Li / Jing Zhu / Yingying Guo / Renhong Yan /
PubMed AbstractThe Mpox pandemic, caused by the Mpox virus (or monkeypox virus, MPXV), has gained global attention. The D5 protein, a putative helicase-primase found in MPXV, plays a vital role in viral replication ...The Mpox pandemic, caused by the Mpox virus (or monkeypox virus, MPXV), has gained global attention. The D5 protein, a putative helicase-primase found in MPXV, plays a vital role in viral replication and genome uncoating. Here we determined multiple cryo-EM structures of full-length hexameric D5 in diverse states. These states were captured during ATP hydrolysis while moving along the single-stranded DNA (ssDNA) track. Through comprehensive structural analysis combined with the helicase activity system, we revealed that when the primase domain is truncated or the interaction between the primase and helicase domains is disrupted, the double-stranded DNA (dsDNA) unwinds into ssDNA, suggesting a critical regulatory role of the primase domain. Two transition states bound with ssDNA substrate during unwinding reveals that two ATP molecules were consumed to drive DNA moving forward two nucleotides. Collectively, our findings shed light on the molecular mechanism that links ATP hydrolysis to the DNA unwinding in poxviruses.
External linksNat Struct Mol Biol / PubMed:38177671
MethodsEM (single particle)
Resolution3.0 - 3.9 Å
Structure data

35051

8hwa

EMDB-35051, PDB-8hwa:
D5 ATP-ADP-Apo-ssDNA IS1
Method: EM (single particle) / Resolution: 3.7 Å

35052

8hwb

EMDB-35052, PDB-8hwb:
D5 ATP-ADP-Apo-ssDNA IS2
Method: EM (single particle) / Resolution: 3.9 Å

35053

8hwc

EMDB-35053, PDB-8hwc:
Cryo-EM Structure of D5 Apo
Method: EM (single particle) / Resolution: 3.3 Å

35054

8hwd

EMDB-35054, PDB-8hwd:
Cryo-EM Structure of D5 ADP form
Method: EM (single particle) / Resolution: 3.3 Å

35055

8hwe

EMDB-35055, PDB-8hwe:
Cryo-EM Structure of D5 ATP-ADP form
Method: EM (single particle) / Resolution: 3.3 Å

35056

8hwf

EMDB-35056, PDB-8hwf:
Cryo-EM Structure of D5 ADP-ssDNA form
Method: EM (single particle) / Resolution: 3.3 Å

35057

8hwg

EMDB-35057, PDB-8hwg:
D5 ATPrS-ADP-ssDNA form
Method: EM (single particle) / Resolution: 3.0 Å

35058

8hwh

EMDB-35058, PDB-8hwh:
Cryo-EM Structure of D5 Apo-ssDNA form
Method: EM (single particle) / Resolution: 3.6 Å

Chemicals

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

ChemComp-MG:
Unknown entry

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

Source
  • monkeypox virus
  • homo sapiens (human)
KeywordsVIRAL PROTEIN / MPVX

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