4JKR

Crystal Structure of E. coli RNA Polymerase in complex with ppGpp


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.20 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.250 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

The mechanism of E. coli RNA polymerase regulation by ppGpp is suggested by the structure of their complex.

Zuo, Y.Wang, Y.Steitz, T.A.

(2013) Mol Cell 50: 430-436

  • DOI: 10.1016/j.molcel.2013.03.020
  • Primary Citation of Related Structures:  
    4JKR

  • PubMed Abstract: 
  • Guanosine tetraphosphate (ppGpp) is an alarmone that enables bacteria to adapt to their environment. It has been known for years that ppGpp acts directly on RNA polymerase (RNAP) to alter the rate of transcription, but its exact target site is still under debate ...

    Guanosine tetraphosphate (ppGpp) is an alarmone that enables bacteria to adapt to their environment. It has been known for years that ppGpp acts directly on RNA polymerase (RNAP) to alter the rate of transcription, but its exact target site is still under debate. Here we report a crystal structure of Escherichia coli RNAP holoenzyme in complex with ppGpp at 4.5 Å resolution. The structure reveals that ppGpp binds at an interface between the shelf and core modules on the outer surface of RNAP, away from the catalytic center and the nucleic acid binding path. Bound ppGpp connects these two pivotal modules that may restrain the opening of the RNAP cleft. A detailed mechanism of action of ppGpp is proposed in which ppGpp prevents the closure of the active center that is induced by the binding of NTP, which could slow down nucleotide addition cycles and destabilize the initial transcription complexes.


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaA, B, G, H329Escherichia coli O104:H4 str. 2009EL-2071Mutation(s): 0 
Gene Names: ECDH10B_3470O3O_23125rpoA
EC: 2.7.7.6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaC, I1,342Escherichia coli DH1Mutation(s): 0 
Gene Names: ECDH1ME8569_3846EcDH1_4008O3K_23925rpoB
EC: 2.7.7.6
UniProt
Find proteins for A0A0E0Y7A2 (Escherichia coli O104:H4 (strain 2011C-3493))
Explore A0A0E0Y7A2 
Go to UniProtKB:  A0A0E0Y7A2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0E0Y7A2
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE SUBUNIT BETA'D, J1,416Escherichia coli BW2952Mutation(s): 0 
Gene Names: BWG_3647O3O_01425rpoC
EC: 2.7.7.6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaE, K90Escherichia coli DH1Mutation(s): 0 
Gene Names: ECDH1ME8569_3534EcDH1_0056O3O_25075rpoZ
EC: 2.7.7.6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase sigma factor RpoDF, L628Escherichia coli K-12Mutation(s): 0 
Gene Names: altb3067JW3039rpoD
UniProt
Find proteins for P00579 (Escherichia coli (strain K12))
Explore P00579 
Go to UniProtKB:  P00579
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00579
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G4P
Query on G4P

Download Ideal Coordinates CCD File 
P [auth D],
Z [auth K]
GUANOSINE-5',3'-TETRAPHOSPHATE
C10 H17 N5 O17 P4
BUFLLCUFNHESEH-UUOKFMHZSA-N
 Ligand Interaction
SR
Query on SR

Download Ideal Coordinates CCD File 
M [auth A],
N [auth C],
O [auth C],
S [auth D],
T [auth E],
M [auth A],
N [auth C],
O [auth C],
S [auth D],
T [auth E],
U [auth F],
V [auth I],
Y [auth J]
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
Q [auth D],
R [auth D],
W [auth J],
X [auth J]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.20 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.250 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 187.575α = 90
b = 206.164β = 90
c = 311.062γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-15
    Type: Initial release
  • Version 1.1: 2013-10-23
    Changes: Database references