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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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: 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonucleoside-diphosphate reductase, beta subunit 1A, B, C, D430Leeuwenhoekiella 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 / MED217))
Explore A3XHF9 
Go to UniProtKB:  A3XHF9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3XHF9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / 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
 Ligand Interaction
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
 Ligand Interaction
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
 Ligand Interaction
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
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
DTP Binding MOAD:  5OLK Kd: 1000 (nM) from 1 assay(s)
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

View Full Validation Report



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