5KT7

Teranry complex of human DNA polymerase iota(1-445) inserting dCMPNPP opposite template G in the presence of Mn2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.151 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Kinetic and Structural Impact of Metal Ions and Genetic Variations on Human DNA Polymerase iota.

Choi, J.Y.Patra, A.Yeom, M.Lee, Y.S.Zhang, Q.Egli, M.Guengerich, F.P.

(2016) J.Biol.Chem. 291: 21063-21073

  • DOI: 10.1074/jbc.M116.748285
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • DNA polymerase (pol) ι is a Y-family polymerase involved in translesion synthesis, exhibiting higher catalytic activity with Mn <sup>2+ </sup> than Mg <sup>2+ </sup> The human germline R96G variant impairs both Mn <sup>2+ </sup>-dependent and Mg <sup ...

    DNA polymerase (pol) ι is a Y-family polymerase involved in translesion synthesis, exhibiting higher catalytic activity with Mn 2+ than Mg 2+ The human germline R96G variant impairs both Mn 2+ -dependent and Mg 2+ -dependent activities of pol ι, whereas the Δ1-25 variant selectively enhances its Mg 2+ -dependent activity. We analyzed pre-steady-state kinetic and structural effects of these two metal ions and genetic variations on pol ι using pol ι core (residues 1-445) proteins. The presence of Mn 2+ (0.15 mm) instead of Mg 2+ (2 mm) caused a 770-fold increase in efficiency (k pol /K d ,dCTP ) of pol ι for dCTP insertion opposite G, mainly due to a 450-fold decrease in K d ,dCTP The R96G and Δ1-25 variants displayed a 53-fold decrease and a 3-fold increase, respectively, in k pol /K d ,dCTP for dCTP insertion opposite G with Mg 2+ when compared with wild type, substantially attenuated by substitution with Mn 2+ Crystal structures of pol ι ternary complexes, including the primer terminus 3'-OH and a non-hydrolyzable dCTP analogue opposite G with the active-site Mg 2+ or Mn 2+ , revealed that Mn 2+ achieves more optimal octahedral coordination geometry than Mg 2+ , with lower values in average coordination distance geometry in the catalytic metal A-site. Crystal structures of R96G revealed the loss of three H-bonds of residues Gly-96 and Tyr-93 with an incoming dNTP, due to the lack of an arginine, as well as a destabilized Tyr-93 side chain secondary to the loss of a cation-π interaction between both side chains. These results provide a mechanistic basis for alteration in pol ι catalytic function with coordinating metals and genetic variation.


    Organizational Affiliation

    the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, and f.guengerich@vanderbilt.edu.,From the Division of Pharmacology, Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Gyeonggi-do 16419, Republic of Korea.,the Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu 42988, Republic of Korea.,the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, and.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase iota
A
445Homo sapiensMutation(s): 0 
Gene Names: POLI (RAD30B)
EC: 2.7.7.7
Find proteins for Q9UNA4 (Homo sapiens)
Go to Gene View: POLI
Go to UniProtKB:  Q9UNA4
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(P*TP*GP*GP*GP*GP*TP*CP*CP*T)-3')T10synthetic construct
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*AP*GP*GP*AP*CP*CP*C)-3')P7synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, P
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
0KX
Query on 0KX

Download SDF File 
Download CCD File 
A
2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine
C9 H17 N4 O12 P3
STYMTWKSQLVXJN-SHYZEUOFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.151 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.202 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 97.740α = 90.00
b = 97.740β = 90.00
c = 202.013γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health SciencesUnited StatesR01 ES010375
National Institutes of Health/National Institute of Environmental Health SciencesUnited StatesR01 ES010546

Revision History 

  • Version 1.0: 2016-08-31
    Type: Initial release
  • Version 1.1: 2016-09-07
    Type: Database references
  • Version 1.2: 2016-10-19
    Type: Database references
  • Version 1.3: 2017-09-13
    Type: Author supporting evidence, Database references, Derived calculations