1S0V

Structural basis for substrate selection by T7 RNA polymerase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.255 

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This is version 1.4 of the entry. See complete history


Literature

Structural basis for substrate selection by t7 RNA polymerase.

Temiakov, D.Patlan, V.Anikin, M.McAllister, W.T.Yokoyama, S.Vassylyev, D.G.

(2004) Cell 116: 381-391

  • DOI: https://doi.org/10.1016/s0092-8674(04)00059-5
  • Primary Citation of Related Structures:  
    1S0V

  • PubMed Abstract: 

    The mechanism by which nucleotide polymerases select the correct substrate is of fundamental importance to the fidelity of DNA replication and transcription. During the nucleotide addition cycle, pol I DNA polymerases undergo the transition from a catalytically inactive "open" to an active "closed" conformation. All known determinants of substrate selection are associated with the "closed" state. To elucidate if this mechanism is conserved in homologous single subunit RNA polymerases (RNAPs), we have determined the structure of T7 RNAP elongation complex with the incoming substrate analog. Surprisingly, the substrate specifically binds to RNAP in the "open" conformation, where it is base paired with the acceptor template base, while Tyr639 provides discrimination of ribose versus deoxyribose substrates. The structure therefore suggests a novel mechanism, in which the substrate selection occurs prior to the isomerization to the catalytically active conformation. Modeling of multisubunit RNAPs suggests that this mechanism might be universal for all RNAPs.


  • Organizational Affiliation

    Morse Institute for Molecular Genetics, Department of Microbiology, SUNY Health Science Center, 450 Clarkson Avenue, Brooklyn, New York 11203, USA.


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymeraseM [auth A],
N [auth B],
O [auth C],
P [auth D]
883Escherichia phage T7Mutation(s): 0 
Gene Names: 1
EC: 2.7.7.6
UniProt
Find proteins for P00573 (Escherichia phage T7)
Explore P00573 
Go to UniProtKB:  P00573
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00573
Sequence Annotations
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
5'-D(*G*GP*GP*AP*AP*TP*CP*GP*AP*TP*AP*TP*CP*GP*CP*CP*GP*C)-3'A [auth E],
D [auth H],
G [auth K],
J [auth N]
18N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
5'-R(*AP*AP*CP*U*GP*CP*GP*GP*CP*GP*AP*U)-3'B [auth F],
E [auth I],
H [auth L],
K [auth O]
12N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
5'-D(*GP*TP*CP*GP*AP*TP*TP*CP*CP*C)-3'C [auth G],
F [auth J],
I [auth M],
L [auth P]
10N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
APC
Query on APC

Download Ideal Coordinates CCD File 
BA [auth D],
S [auth A],
V [auth B],
Y [auth C]
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
C11 H18 N5 O12 P3
CAWZRIXWFRFUQB-IOSLPCCCSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth D]
Q [auth F]
R [auth A]
T [auth B]
U [auth B]
AA [auth D],
Q [auth F],
R [auth A],
T [auth B],
U [auth B],
W [auth C],
X [auth C],
Z [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.255 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.133α = 91.93
b = 87.703β = 91.02
c = 206.531γ = 110.66
Software Package:
Software NamePurpose
DENZOdata reduction
TRUNCATEdata reduction
CNSrefinement
CCP4data scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2004-02-24
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-04-04
    Changes: Data collection
  • Version 1.4: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description