5CNT

Crystal structure of the dATP inhibited E. coli class Ia ribonucleotide reductase complex bound to UDP and dATP at 3.25 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: 3.25 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 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: https://doi.org/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. 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: 

    Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonucleoside-diphosphate reductase 1 subunit alpha
A, B, C, D
761Escherichia 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
Sequence Annotations
Expand
  • 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: 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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DTP
Query on DTP
Download Ideal Coordinates CCD File 
BA [auth D]
DA [auth D]
EA [auth D]
J [auth A]
L [auth A]
BA [auth D],
DA [auth D],
EA [auth D],
J [auth A],
L [auth A],
M [auth A],
P [auth B],
R [auth B],
S [auth B],
V [auth C],
X [auth C],
Y [auth C]
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
SUYVUBYJARFZHO-RRKCRQDMSA-N
UDP
Query on UDP
Download Ideal Coordinates CCD File 
AA [auth D],
I [auth A],
O [auth B],
U [auth C]		URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
FEO
Query on FEO
Download Ideal Coordinates CCD File 
GA [auth E],
HA [auth F],
IA [auth G],
JA [auth H]		MU-OXO-DIIRON
Fe2 O
NPMYUMBHPJGBFA-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
CA [auth D]
FA [auth D]
K [auth A]
N [auth A]
Q [auth B]
CA [auth D],
FA [auth D],
K [auth A],
N [auth A],
Q [auth B],
T [auth B],
W [auth C],
Z [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 274.621α = 90
b = 157.34β = 119.3
c = 165.2γ = 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: 2017-08-23
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence
  • Version 1.4: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.5: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description