2KXE | pdb_00002kxe

N-terminal domain of the DP1 subunit of an archaeal D-family DNA polymerase

• PDB DOI: https://doi.org/10.2210/pdb2KXE/pdb
• BMRB: 16986

• Classification: TRANSFERASE
• Organism(s): Pyrococcus horikoshii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-04-30 Released: 2010-08-18 
• Deposition Author(s): Yamasaki, K., Matsui, I.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Solution structure of the N-terminal domain of the archaeal D-family DNA polymerase small subunit reveals evolutionary relationship to eukaryotic B-family polymerases

Yamasaki, K., Urushibata, Y., Yamasaki, T., Arisaka, F., Matsui, I.

(2010) FEBS Lett 584: 3370-3375

• PubMed: 20598295 
• DOI: https://doi.org/10.1016/j.febslet.2010.06.026
• Primary Citation Related Structures: 
  2KXE


• PubMed Abstract: 
  

  Archaea-specific D-family DNA polymerase forms a heterotetramer consisting of two large polymerase subunits and two small exonuclease subunits. We analyzed the structure of the N-terminal 200 amino-acid regulatory region of the small subunit by NMR and revealed that the N-terminal approximately 70 amino-acid region is folded. The structure consists of a four-alpha-helix bundle including a short parallel beta-sheet, which is similar to the N-terminal regions of the B subunits of human DNA polymerases alpha and epsilon, establishing evolutionary relationships among these archaeal and eukaryotic polymerases. We observed monomer-dimer equilibrium of this domain, which may be related to holoenzyme architecture and/or functional regulation.

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Organizational Affiliation: 
• Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8566, Japan. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 8.53 kDa 
• Atom Count: 582 
• Modeled Residue Count: 72 
• Deposited Residue Count: 75 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase II small subunit	A	75	Pyrococcus horikoshii	Mutation(s): 0  EC: 2.7.7.7 (PDB Primary Data), 3.1.11.1 (UniProt)
UniProt
Find proteins for O57863 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O57863  Go to UniProtKB:  O57863

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-18 
Deposition Author(s): Yamasaki, K., Matsui, I.

Revision History  

• Version 1.0: 2010-08-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-02-26
  Changes: Database references, Derived calculations, Other
• Version 1.3: 2023-06-14
  Changes: Database references, Other
• Version 1.4: 2024-05-15
  Changes: Data collection, Database references