2AQ4

Ternary complex of the catalytic core of REV1 with DNA and dCTP.

• PDB DOI: https://doi.org/10.2210/pdb2AQ4/pdb
• NAKB: 2AQ4

• Classification: TRANSFERASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2005-08-17 Released: 2005-10-04 
• Deposition Author(s): Nair, D.T., Johnson, R.E., Prakash, L., Prakash, S., Aggarwal, A.K.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 0.238 
• R-Value Work: 0.197 
• R-Value Observed: 0.199 

Literature

Rev1 employs a novel mechanism of DNA synthesis using a protein template.

Nair, D.T., Johnson, R.E., Prakash, L., Prakash, S., Aggarwal, A.K.

(2005) Science 309: 2219-2222

• PubMed: 16195463 
• DOI: https://doi.org/10.1126/science.1116336
• Primary Citation of Related Structures:  
  2AQ4


• PubMed Abstract: 
  

  The Rev1 DNA polymerase is highly specialized for the incorporation of C opposite template G. We present here the crystal structure of yeast Rev1 bound to template G and incoming 2'-deoxycytidine 5'-triphosphate (dCTP), which reveals that the polymerase itself dictates the identity of the incoming nucleotide, as well as the identity of the templating base. Template G and incoming dCTP do not pair with each other. Instead, the template G is evicted from the DNA helix, and it makes optimal hydrogen bonds with a segment of Rev1. Also, unlike other DNA polymerases, incoming dCTP pairs with an arginine rather than the templating base, which ensures the incorporation of dCTP over other incoming nucleotides. This mechanism provides an elegant means for promoting proficient and error-free synthesis through N2-adducted guanines that obstruct replication.

---

Organizational Affiliation: 

Structural Biology Program, Department of Physiology and Biophysics, Mount Sinai School of Medicine, 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.

Macromolecule Content

• Total Structure Weight: 58.54 kDa 
• Atom Count: 4,117 
• Modelled Residue Count: 456 
• Deposited Residue Count: 462 
• 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	Mutation(s): 0  Gene Names: REV1 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
5'-D(*AP*TP*CP*CP*TP*CP*CP*CP*CP*TP*AP*C)-3'	A [auth P]	12	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*TP*AP*AP*GP*GP*TP*AP*GP*GP*GP*GP*AP*GP*GP*AP*T)-3'	B [auth T]	16	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DCP	F [auth A]	2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE C9 H16 N3 O13 P3 RGWHQCVHVJXOKC-SHYZEUOFSA-N
MG	D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 0.238 
• R-Value Work: 0.197 
• R-Value Observed: 0.199 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 177.32	α = 90
b = 200.906	β = 90
c = 55.586	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-10-04 
Deposition Author(s): Nair, D.T., Johnson, R.E., Prakash, L., Prakash, S., Aggarwal, A.K.

Revision History  

• Version 1.0: 2005-10-04
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations