4P4P | pdb_00004p4p

Crystal structure of Leishmania infantum polymerase beta: Nick complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.234 (Depositor), 0.223 (DCC) 
  • R-Value Work: 
    0.191 (Depositor) 
  • R-Value Observed: 
    0.195 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Structures of the Leishmania infantum polymerase beta.

Mejia, E.Burak, M.Alonso, A.Larraga, V.Kunkel, T.A.Bebenek, K.Garcia-Diaz, M.

(2014) DNA Repair (Amst) 18: 1-9

  • DOI: https://doi.org/10.1016/j.dnarep.2014.03.001
  • Primary Citation Related Structures: 
    4P4M, 4P4O, 4P4P

  • PubMed Abstract: 

    Protozoans of the genus Leishmania, the pathogenic agent causing leishmaniasis, encode the family X DNA polymerase Li Pol β. Here, we report the first crystal structures of Li Pol β. Our pre- and post-catalytic structures show that the polymerase adopts the common family X DNA polymerase fold. However, in contrast to other family X DNA polymerases, the dNTP-induced conformational changes in Li Pol β are much more subtle. Moreover, pre- and post-catalytic structures reveal that Li Pol β interacts with the template strand through a nonconserved, variable region known as loop3. Li Pol β Δloop3 mutants display a higher catalytic rate, catalytic efficiency and overall error rates with respect to WT Li Pol β. These results further demonstrate the subtle structural variability that exists within this family of enzymes and provides insight into how this variability underlies the substantial functional differences among their members.


  • Organizational Affiliation
    • Department of Pharmacological Sciences, Stony Brook University, BST 7-169, Stony Brook, NY 11794-8651, USA.

Macromolecule Content 

  • Total Structure Weight: 49.65 kDa 
  • Atom Count: 2,867 
  • Modeled Residue Count: 301 
  • Deposited Residue Count: 400 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 3

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA polymerase beta378Leishmania infantumMutation(s): 0 
EC: 2.7.7.7
UniProt
Find proteins for Q9U6N3 (Leishmania infantum)
Explore Q9U6N3 
Go to UniProtKB:  Q9U6N3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9U6N3
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*AP*GP*TP*AP*CP*T)-3')B [auth C]7synthetic construct
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*CP*CP*G)-3')C [auth D]4synthetic construct
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*GP*GP*CP*AP*GP*TP*AP*CP*TP*G)-3')D [auth B]11synthetic construct
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NA

Query on NA



Download:Ideal Coordinates CCD File
E [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.234 (Depositor), 0.223 (DCC) 
  • R-Value Work:  0.191 (Depositor) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.497α = 90
b = 106.497β = 90
c = 159.609γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM100021-02

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-06
    Type: Initial release
  • Version 1.1: 2017-09-06
    Changes: Author supporting evidence, Derived calculations, Other, Source and taxonomy
  • Version 1.2: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description