6CTV

Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CF2, beta, gamma dCTP analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.183 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs.

Batra, V.K.Oertell, K.Beard, W.A.Kashemirov, B.A.McKenna, C.E.Goodman, M.F.Wilson, S.H.

(2018) Biochemistry 57: 3934-3944

  • DOI: https://doi.org/10.1021/acs.biochem.8b00418
  • Primary Citation of Related Structures:  
    6BEL, 6BEM, 6CR3, 6CR4, 6CR5, 6CR6, 6CR7, 6CR8, 6CR9, 6CRB, 6CRC, 6CTI, 6CTJ, 6CTK, 6CTL, 6CTM, 6CTN, 6CTO, 6CTP, 6CTQ, 6CTR, 6CTT, 6CTU, 6CTV, 6CTW, 6CTX, 6G2Q

  • PubMed Abstract: 

    We report high-resolution crystal structures of DNA polymerase (pol) β in ternary complex with a panel of incoming dNTPs carrying acidity-modified 5'-triphosphate groups. These novel dNTP analogues have a variety of halomethylene substitutions replacing the bridging oxygen between Pβ and Pγ of the incoming dNTP, whereas other analogues have alkaline substitutions at the bridging oxygen. Use of these analogues allows the first systematic comparison of effects of 5'-triphosphate acidity modification on active site structures and the rate constant of DNA synthesis. These ternary complex structures with incoming dATP, dTTP, and dCTP analogues reveal the enzyme's active site is not grossly altered by the acidity modifications of the triphosphate group, yet with analogues of all three incoming dNTP bases, subtle structural differences are apparent in interactions around the nascent base pair and at the guanidinium groups of active site arginine residues. These results are important for understanding how acidity modification of the incoming dNTP's 5'-triphosphate can influence DNA polymerase activity and the significance of interactions at arginines 183 and 149 in the active site.


  • Organizational Affiliation

    Genome Integrity and Structural Biology Laboratory , National Institute of Environmental Health Sciences, National Institutes of Health , 111 T. W. Alexander Drive , Research Triangle Park , North Carolina 27709 , United States.


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase betaD [auth A]335Homo sapiensMutation(s): 0 
Gene Names: POLB
EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (PDB Primary Data), 4.2.99.18 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P06746 (Homo sapiens)
Explore P06746 
Go to UniProtKB:  P06746
PHAROS:  P06746
GTEx:  ENSG00000070501 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06746
Sequence Annotations
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*CP*GP*AP*CP*GP*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')A [auth T]16Homo sapiens
Sequence Annotations
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(2DA))-3')B [auth P]10Homo sapiens
Sequence Annotations
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*TP*CP*GP*G)-3')C [auth D]5Homo sapiens
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FFJ (Subject of Investigation/LOI)
Query on FFJ

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K [auth A]2'-deoxy-5'-O-[(R)-{[(R)-[difluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine
C10 H16 F2 N3 O12 P3
FBLKJJQPZBDPCI-SHYZEUOFSA-N
DC
Query on DC

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L [auth A]2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
C9 H14 N3 O7 P
NCMVOABPESMRCP-SHYZEUOFSA-N
CL
Query on CL

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J [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

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E [auth T],
G [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

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F [auth A],
H [auth A],
I [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.666α = 90
b = 79.251β = 107.75
c = 55.337γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2018-07-11
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description