[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleSubstrate specificity and action mechanism of the HerA-NurA nuclease from the hyperthermophilic archaeon .
Journal, issue, pagesmBio, Vol. 17, Issue 3, Page e0352325, Year 2026
Publish dateMar 11, 2026
AuthorsKeishiro Uda / Takeshi Yamagami / Sonoko Ishino / Christoph Gerle / Chai C Gopalasingam / Hideki Shigematsu / Tomoyuki Numata / Yoshizumi Ishino /
PubMed AbstractThe HerA-NurA complex reportedly functions in DNA end resection in archaea. End resection is important to start homologous recombination by forming a single-stranded DNA region with an overhanging 3'- ...The HerA-NurA complex reportedly functions in DNA end resection in archaea. End resection is important to start homologous recombination by forming a single-stranded DNA region with an overhanging 3'-end, which invades double-stranded DNA (dsDNA) with a homologous sequence to form a D-loop. Here, we studied the structure and functions of HerA-NurA from the hyperthermophilic archaeon, . Our analyses demonstrated that NurA is a non-directional and single-stranded specific nuclease, but the HerA-NurA complex cleaves both strands of dsDNA in an exonucleolytic manner, regardless of the structure of the DNA end. The 3D structures of HerA-NurA and its complex with dsDNA revealed the detailed molecular mechanisms of these nuclease reactions. These results suggest that HerA-NurA may not be involved in the end resection process but instead performs other functions, such as exerting an antiviral function by degrading the dsDNA of foreign viruses, similar to recent studies in bacteria.
IMPORTANCE: To understand the specific function of the HerA-NurA complex, which is believed to function in the end resection process to create a 3'-overhanging DNA for the following strand invasion in homologous recombination, we performed biochemical and structural analyses of this complex from a hyperthermophilic archaeon, , inhabiting a harsh environment where DNA is easily damaged. We found that the HerA-NurA complex cleaves both strands of double-stranded DNA in an exonucleolytic manner, regardless of the structure of the DNA end. Our structural analysis revealed the detailed characteristics of the nuclease activity exhibited by the HerA-NurA complex. Based on the presented information, it is unlikely that the HerA-NurA complex directly functions in end resection, but rather is involved in other functions, possibly in defense against viral infections.
External linksmBio / PubMed:41641993 / PubMed Central
MethodsEM (single particle)
Resolution2.3 - 3.1 Å
Structure data

66462

9x1l

EMDB-66462, PDB-9x1l:
The cryo-EM structure of HerA-NurA complex with AMPPNP from Thermococcus kodakarensis
Method: EM (single particle) / Resolution: 2.8 Å

66463

9x1m

EMDB-66463, PDB-9x1m:
The cryo-EM structure of HerA-NurA complex with AMPPNP and dsDNA from Thermococcus kodakarensis
Method: EM (single particle) / Resolution: 2.3 Å

66464

9x1n

EMDB-66464, PDB-9x1n:
The cryo-EM structure of HerA-NurA complex with ATPgammaS and dsDNA from Thermococcus kodakarensis (State 1)
Method: EM (single particle) / Resolution: 3.1 Å

66465

9x1o

EMDB-66465, PDB-9x1o:
The cryo-EM structure of HerA-NurA complex with ATPgammaS and dsDNA from Thermococcus kodakarensis (State 2)
Method: EM (single particle) / Resolution: 3.0 Å

66466

9x1p

EMDB-66466, PDB-9x1p:
The cryo-EM structure of HerA-NurA complex with ATPgammaS and dsDNA from Thermococcus kodakarensis (State 3)
Method: EM (single particle) / Resolution: 3.1 Å

Chemicals

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

ChemComp-MN:
Unknown entry

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

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

Source
  • thermococcus kodakarensis (archaea)
  • dna molecule (others)
KeywordsTRANSLOCASE / HerA / Helicase / NurA / Nuclease / DNA BINDING PROTEIN

+
About Yorodumi Papers

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more