5CNS

Crystal structure of the dATP inhibited E. coli class Ia ribonucleotide reductase complex bound to CDP and dATP at 2.97 Angstroms resolution

  • Classification: OXIDOREDUCTASE
  • Organism(s): Escherichia coli K-12
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2015-07-18 Released: 2016-01-20 
  • Deposition Author(s): Chen, P.Y.-T., Zimanyi, C.M., Funk, M.A., Drennan, C.L.
  • Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 


Literature

Molecular basis for allosteric specificity regulation in class Ia ribonucleotide reductase from Escherichia coli.

Zimanyi, C.M., Chen, P.Y., Kang, G., Funk, M.A., Drennan, C.L.

(2016) Elife 5: e07141-e07141

  • DOI: 10.7554/eLife.07141
  • Primary Citation of Related Structures:  
    5CNS, 5CNT, 5CNU, 5CNV

  • PubMed Abstract: 

    • Ribonucleotide reductase (RNR) converts ribonucleotides to deoxyribonucleotides, a reaction that is essential for DNA biosynthesis and repair. This enzyme is responsible for reducing all four ribonucleotide substrates, with specificity regulated by the binding of an effector to a distal allosteric site ...

    Ribonucleotide reductase (RNR) converts ribonucleotides to deoxyribonucleotides, a reaction that is essential for DNA biosynthesis and repair. This enzyme is responsible for reducing all four ribonucleotide substrates, with specificity regulated by the binding of an effector to a distal allosteric site. In all characterized RNRs, the binding of effector dATP alters the active site to select for pyrimidines over purines, whereas effectors dGTP and TTP select for substrates ADP and GDP, respectively. Here, we have determined structures of Escherichia coli class Ia RNR with all four substrate/specificity effector-pairs bound (CDP/dATP, UDP/dATP, ADP/dGTP, GDP/TTP) that reveal the conformational rearrangements responsible for this remarkable allostery. These structures delineate how RNR 'reads' the base of each effector and communicates substrate preference to the active site by forming differential hydrogen bonds, thereby maintaining the proper balance of deoxynucleotides in the cell.

    Organizational Affiliation: 

    Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, United States.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonucleoside-diphosphate reductase 1 subunit alphaA, B, C, D761Escherichia coli K-12Mutation(s): 0 
Gene Names: nrdA, dnaF, b2234, JW2228
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
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonucleoside-diphosphate reductase 1 subunit betaE, F, G, H375Escherichia coli K-12Mutation(s): 0 
Gene Names: nrdB, ftsB, b2235, JW2229
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DTP
Query on DTP
Download Ideal Coordinates CCD File 
AA [auth D],
L [auth A],
Q [auth B],
V [auth C]		2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
SUYVUBYJARFZHO-RRKCRQDMSA-N		 Ligand Interaction
DAT
Query on DAT
Download Ideal Coordinates CCD File 
J [auth A],
O [auth B],
T [auth C],
Y [auth D]		2'-DEOXYADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O9 P2
DAEAPNUQQAICNR-RRKCRQDMSA-N		 Ligand Interaction
CDP
Query on CDP
Download Ideal Coordinates CCD File 
I [auth A],
N [auth B],
S [auth C],
X [auth D]		CYTIDINE-5'-DIPHOSPHATE
C9 H15 N3 O11 P2
ZWIADYZPOWUWEW-XVFCMESISA-N		 Ligand Interaction
FEO
Query on FEO
Download Ideal Coordinates CCD File 
CA [auth E],
DA [auth F],
EA [auth G],
FA [auth H]		MU-OXO-DIIRON
Fe2 O
NPMYUMBHPJGBFA-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
BA [auth D],
K [auth A],
M [auth A],
P [auth B],
R [auth B],
BA [auth D],
K [auth A],
M [auth A],
P [auth B],
R [auth B],
U [auth C],
W [auth C],
Z [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 
  • Space Group: C 1 2 1
  • Diffraction Data DOI: 10.15785/SBGRID/236
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 274.154α = 90
b = 157.83β = 118.82
c = 164.251γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesP30-ES002109
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32GM08334
National Science Foundation (NSF, United States)United States0645960

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-20
    Type: Initial release
  • Version 1.1: 2016-05-11
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Derived calculations
  • Version 1.3: 2019-11-27
    Changes: Author supporting evidence