4P4P

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 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 10.1016/j.dnarep.2014.03.001
  • Primary Citation of 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 ...

    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. Electronic address: miguel.garcia-diaz@stonybrook.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase betaA378Leishmania 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
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*CP*AP*GP*TP*AP*CP*T)-3')B [auth C]7synthetic construct
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*GP*CP*CP*G)-3')C [auth D]4synthetic construct
Protein Feature View
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*CP*GP*GP*CP*AP*GP*TP*AP*CP*TP*G)-3')D [auth B]11synthetic construct
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download Ideal Coordinates CCD File 
E [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.195 
  • 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