5WM1 | pdb_00005wm1

Structure of the 10S (+)-trans-BP-dG modified Rev1 ternary complex

• PDB DOI: https://doi.org/10.2210/pdb5WM1/pdb
• NAKB: 5WM1

• Classification: TRANSFERASE/DNA
• Organism(s): synthetic construct, Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-07-28 Released: 2017-10-25 
• Deposition Author(s): Rechkoblit, O., Kolbanovsky, A., Landes, H., Geacintov, N.E., Aggarwal, A.K.
• Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.206 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

Mechanism of error-free replication across benzo[a]pyrene stereoisomers by Rev1 DNA polymerase.

Rechkoblit, O., Kolbanovskiy, A., Landes, H., Geacintov, N.E., Aggarwal, A.K.

(2017) Nat Commun 8: 965-965

• PubMed: 29042535 
• DOI: https://doi.org/10.1038/s41467-017-01013-5
• Primary Citation Related Structures: 
  5WM1, 5WM8, 5WMB


• PubMed Abstract: 
  

  Benzo[a]pyrene (BP) is a carcinogen in cigarette smoke which, after metabolic activation, can react with the exocyclic N ² amino group of guanine to generate four stereoisomeric BP-N ² -dG adducts. Rev1 is unique among translesion synthesis DNA polymerases in employing a protein-template-directed mechanism of DNA synthesis opposite undamaged and damaged guanine. Here we report high-resolution structures of yeast Rev1 with three BP-N ² -dG adducts, namely the 10S (+)-trans-BP-N ² -dG, 10R (+)-cis-BP-N ² -dG, and 10S ( - )-cis-BP-N ² -dG. Surprisingly, in all three structures, the bulky and hydrophobic BP pyrenyl residue is entirely solvent-exposed in the major groove of the DNA. This is very different from the adduct alignments hitherto observed in free or protein-bound DNA. All complexes are well poised for dCTP insertion. Our structures provide a view of cis-BP-N ² -dG adducts in a DNA polymerase active site, and offer a basis for understanding error-free replication of the BP-derived stereoisomeric guanine adducts.Benzo[a]pyrene (BP) is a carcinogen in cigarette smoke that upon metabolic activation reacts with guanine. Here, the authors present the structures of the translesion DNA synthesis polymerase Rev1 in complex with three of the four possible stereoisomeric BP-N ² -dG adducts, which gives insights how Rev1 achieves error-free replication.

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Organizational Affiliation: 
• Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, Box 1677, 1425 Madison Avenue, New York, NY, 10029, USA. [e-mail].
Department of Chemistry, New York University, 31 Washington Place, New York, NY, 10003-5180, USA.
Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, Box 1677, 1425 Madison Avenue, New York, NY, 10029, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 60.22 kDa 
• Atom Count: 4,555 
• Modeled Residue Count: 462 
• Deposited Residue Count: 463 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein REV1	C [auth A]	434	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: REV1, YOR346W, O6339 EC: 2.7.7
UniProt
Find proteins for P12689 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P12689  Go to UniProtKB:  P12689

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*GP*GP*TP*GP*TP*GP*GP*TP*AP*(DDG))-3')	A [auth P]	12	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*TP*CP*GP*CP*TP*AP*CP*CP*AP*CP*AP*CP*CP*CP*C)-3')	B [auth T]	17	synthetic construct

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DCP	J [auth A]	2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE C9 H16 N3 O13 P3 RGWHQCVHVJXOKC-SHYZEUOFSA-N
BAP	E [auth T]	1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE C20 H16 O3 GFANZDFKCCJYRF-NSISKUIASA-N
PEG	W [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	K [auth A], L [auth A], M [auth A], N [auth A], O [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	F [auth T], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	D [auth P], G [auth A], H [auth A], I [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.206 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.002	α = 90
b = 64.879	β = 90
c = 130.652	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-10-25 
Deposition Author(s): Rechkoblit, O., Kolbanovsky, A., Landes, H., Geacintov, N.E., Aggarwal, A.K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	R01 CA200575
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	R01 ES024050

Revision History  

• Version 1.0: 2017-10-25
  Type: Initial release
  
• Version 1.1: 2017-11-01
  Changes: Database references
• Version 1.2: 2019-12-18
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description