4ERM

Crystal structure of the dATP inhibited E. coli class Ia ribonucleotide reductase complex at 4 Angstroms resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.95 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.259 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Tangled up in knots: structures of inactivated forms of E. coli class Ia ribonucleotide reductase.

Zimanyi, C.M.Ando, N.Brignole, E.J.Asturias, F.J.Stubbe, J.Drennan, C.L.

(2012) Structure 20: 1374-1383

  • DOI: https://doi.org/10.1016/j.str.2012.05.009
  • Primary Citation of Related Structures:  
    4ERM, 4ERP

  • PubMed Abstract: 

    Ribonucleotide reductases (RNRs) provide the precursors for DNA biosynthesis and repair and are successful targets for anticancer drugs such as clofarabine and gemcitabine. Recently, we reported that dATP inhibits E. coli class Ia RNR by driving formation of RNR subunits into α4β4 rings. Here, we present the first X-ray structure of a gemcitabine-inhibited E. coli RNR and show that the previously described α4β4 rings can interlock to form an unprecedented (α4β4)2 megacomplex. This complex is also seen in a higher-resolution dATP-inhibited RNR structure presented here, which employs a distinct crystal lattice from that observed in the gemcitabine-inhibited case. With few reported examples of protein catenanes, we use data from small-angle X-ray scattering and electron microscopy to both understand the solution conditions that contribute to concatenation in RNRs as well as present a mechanism for the formation of these unusual structures.


  • Organizational Affiliation

    Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonucleoside-diphosphate reductase 1 subunit alpha
A, B, C, D
761Escherichia coli K-12Mutation(s): 0 
Gene Names: b2234dnaFJW2228nrdA
EC: 1.17.4.1
UniProt
Find proteins for P00452 (Escherichia coli (strain K12))
Explore P00452 
Go to UniProtKB:  P00452
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00452
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonucleoside-diphosphate reductase 1 subunit beta
E, F, G, H
375Escherichia coli K-12Mutation(s): 0 
Gene Names: b2235ftsBJW2229nrdB
EC: 1.17.4.1
UniProt
Find proteins for P69924 (Escherichia coli (strain K12))
Explore P69924 
Go to UniProtKB:  P69924
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69924
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DTP
Query on DTP

Download Ideal Coordinates CCD File 
I [auth A]
K [auth A]
M [auth B]
O [auth B]
Q [auth C]
I [auth A],
K [auth A],
M [auth B],
O [auth B],
Q [auth C],
S [auth C],
U [auth D],
W [auth D]
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
SUYVUBYJARFZHO-RRKCRQDMSA-N
DAT
Query on DAT

Download Ideal Coordinates CCD File 
J [auth A],
N [auth B],
R [auth C],
V [auth D]
2'-DEOXYADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O9 P2
DAEAPNUQQAICNR-RRKCRQDMSA-N
FEO
Query on FEO

Download Ideal Coordinates CCD File 
AA [auth G],
BA [auth H],
Y [auth E],
Z [auth F]
MU-OXO-DIIRON
Fe2 O
NPMYUMBHPJGBFA-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
L [auth A],
P [auth B],
T [auth C],
X [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.95 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.259 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 280.471α = 90
b = 155.744β = 119.07
c = 166.919γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-04
    Type: Initial release
  • Version 1.1: 2012-10-24
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description