5V08

Crystal structure of human exonuclease 1 Exo1 (D173A) in complex with 5' recessed-end DNA (rVI)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.812 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I.

Shi, Y.Hellinga, H.W.Beese, L.S.

(2017) Proc. Natl. Acad. Sci. U.S.A. 114: 6010-6015

  • DOI: 10.1073/pnas.1704845114
  • Primary Citation of Related Structures:  5UZV, 5V04, 5V05, 5V06, 5V07, 5V09, 5V0A, 5V0B, 5V0C, 5V0D, 5V0E

  • PubMed Abstract: 
  • Human exonuclease 1 (hExo1) is a member of the RAD2/XPG structure-specific 5'-nuclease superfamily. Its dominant, processive 5'-3' exonuclease and secondary 5'-flap endonuclease activities participate in various DNA repair, recombination, and replica ...

    Human exonuclease 1 (hExo1) is a member of the RAD2/XPG structure-specific 5'-nuclease superfamily. Its dominant, processive 5'-3' exonuclease and secondary 5'-flap endonuclease activities participate in various DNA repair, recombination, and replication processes. A single active site processes both recessed ends and 5'-flap substrates. By initiating enzyme reactions in crystals, we have trapped hExo1 reaction intermediates that reveal structures of these substrates before and after their exo- and endonucleolytic cleavage, as well as structures of uncleaved, unthreaded, and partially threaded 5' flaps. Their distinctive 5' ends are accommodated by a small, mobile arch in the active site that binds recessed ends at its base and threads 5' flaps through a narrow aperture within its interior. A sequence of successive, interlocking conformational changes guides the two substrate types into a shared reaction mechanism that catalyzes their cleavage by an elaborated variant of the two-metal, in-line hydrolysis mechanism. Coupling of substrate-dependent arch motions to transition-state stabilization suppresses inappropriate or premature cleavage, enhancing processing fidelity. The striking reduction in flap conformational entropy is catalyzed, in part, by arch motions and transient binding interactions between the flap and unprocessed DNA strand. At the end of the observed reaction sequence, hExo1 resets without relinquishing DNA binding, suggesting a structural basis for its processivity.


    Organizational Affiliation

    Department of Biochemistry, Duke University Medical Center, Durham, NC 27710.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Exonuclease 1
Z
352Homo sapiensGene Names: EXO1 (EXOI, HEX1)
EC: 3.1.-.-
Find proteins for Q9UQ84 (Homo sapiens)
Go to Gene View: EXO1
Go to UniProtKB:  Q9UQ84
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*CP*TP*AP*GP*TP*CP*GP*AP*CP*AP*T)-3')A13synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*TP*CP*GP*AP*CP*TP*AP*GP*CP*G)-3')B10synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
Z
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
B, Z
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.812 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.215 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 74.259α = 90.00
b = 74.259β = 90.00
c = 179.385γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-02-28 
  • Released Date: 2017-05-24 
  • Deposition Author(s): Shi, Y., Beese, L.S.

Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01 GM091487
National Institutes of Health/National Cancer InstituteUnited StatesP01 CA092584

Revision History 

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2017-06-07
    Type: Database references
  • Version 1.2: 2017-06-21
    Type: Database references
  • Version 1.3: 2017-09-13
    Type: Author supporting evidence