5OLK

Crystal structure of the ATP-cone-containing NrdB from Leeuwenhoekiella blandensis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Novel ATP-cone-driven allosteric regulation of ribonucleotide reductase via the radical-generating subunit.

Rozman Grinberg, I.Lundin, D.Hasan, M.Crona, M.Jonna, V.R.Loderer, C.Sahlin, M.Markova, N.Borovok, I.Berggren, G.Hofer, A.Logan, D.T.Sjoberg, B.M.

(2018) Elife 7

  • DOI: https://doi.org/10.7554/eLife.31529
  • Primary Citation of Related Structures:  
    5OLK

  • PubMed Abstract: 

    Ribonucleotide reductases (RNRs) are key enzymes in DNA metabolism, with allosteric mechanisms controlling substrate specificity and overall activity. In RNRs, the activity master-switch, the ATP-cone, has been found exclusively in the catalytic subunit. In two class I RNR subclasses whose catalytic subunit lacks the ATP-cone, we discovered ATP-cones in the radical-generating subunit. The ATP-cone in the Leeuwenhoekiella blandensis radical-generating subunit regulates activity via quaternary structure induced by binding of nucleotides. ATP induces enzymatically competent dimers, whereas dATP induces non-productive tetramers, resulting in different holoenzymes. The tetramer forms by interactions between ATP-cones, shown by a 2.45 Å crystal structure. We also present evidence for an Mn III Mn IV metal center. In summary, lack of an ATP-cone domain in the catalytic subunit was compensated by transfer of the domain to the radical-generating subunit. To our knowledge, this represents the first observation of transfer of an allosteric domain between components of the same enzyme complex.


  • Organizational Affiliation

    Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonucleoside-diphosphate reductase, beta subunit 1
A, B, C, D
430Leeuwenhoekiella blandensis MED217Mutation(s): 0 
Gene Names: MED217_17135
EC: 1.17.4.1
UniProt
Find proteins for A3XHF9 (Leeuwenhoekiella blandensis (strain CECT 7118 / CCUG 51940 / KCTC 22103 / MED217))
Explore A3XHF9 
Go to UniProtKB:  A3XHF9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3XHF9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DTP (Subject of Investigation/LOI)
Query on DTP

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
K [auth B]
L [auth B]
Q [auth C]
E [auth A],
F [auth A],
K [auth B],
L [auth B],
Q [auth C],
R [auth C],
W [auth D],
X [auth D]
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
SUYVUBYJARFZHO-RRKCRQDMSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
BA [auth D],
J [auth A],
P [auth B],
V [auth C]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
MN (Subject of Investigation/LOI)
Query on MN

Download Ideal Coordinates CCD File 
AA [auth D]
H [auth A]
I [auth A]
N [auth B]
O [auth B]
AA [auth D],
H [auth A],
I [auth A],
N [auth B],
O [auth B],
T [auth C],
U [auth C],
Z [auth D]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth A],
M [auth B],
S [auth C],
Y [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.003α = 110.78
b = 90.542β = 98.99
c = 90.948γ = 114.11
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Cancer SocietySwedenCAN 2016/670
Swedish Research CouncilSweden2016-01920
Swedish Research CouncilSweden2016-04855

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-10
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Source and taxonomy
  • Version 1.2: 2018-02-14
    Changes: Database references
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description