2PPB

Crystal structure of the T. thermophilus RNAP polymerase elongation complex with the ntp substrate analog and antibiotic streptolydigin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural basis for substrate loading in bacterial RNA polymerase.

Vassylyev, D.G.Vassylyeva, M.N.Zhang, J.Palangat, M.Artsimovitch, I.Landick, R.

(2007) Nature 448: 163-168

  • DOI: 10.1038/nature05931
  • Primary Citation of Related Structures:  
    2O5J, 2PPB

  • PubMed Abstract: 
  • The mechanism of substrate loading in multisubunit RNA polymerase is crucial for understanding the general principles of transcription yet remains hotly debated. Here we report the 3.0-A resolution structures of the Thermus thermophilus elongation complex (EC) with a non-hydrolysable substrate analogue, adenosine-5'-[(alpha,beta)-methyleno]-triphosphate (AMPcPP), and with AMPcPP plus the inhibitor streptolydigin ...

    The mechanism of substrate loading in multisubunit RNA polymerase is crucial for understanding the general principles of transcription yet remains hotly debated. Here we report the 3.0-A resolution structures of the Thermus thermophilus elongation complex (EC) with a non-hydrolysable substrate analogue, adenosine-5'-[(alpha,beta)-methyleno]-triphosphate (AMPcPP), and with AMPcPP plus the inhibitor streptolydigin. In the EC/AMPcPP structure, the substrate binds to the active ('insertion') site closed through refolding of the trigger loop (TL) into two alpha-helices. In contrast, the EC/AMPcPP/streptolydigin structure reveals an inactive ('preinsertion') substrate configuration stabilized by streptolydigin-induced displacement of the TL. Our structural and biochemical data suggest that refolding of the TL is vital for catalysis and have three main implications. First, despite differences in the details, the two-step preinsertion/insertion mechanism of substrate loading may be universal for all RNA polymerases. Second, freezing of the preinsertion state is an attractive target for the design of novel antibiotics. Last, the TL emerges as a prominent target whose refolding can be modulated by regulatory factors.


    Organizational Affiliation

    Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Schools of Medicine and Dentistry, 402B Kaul Genetics Building, 720 20th Street South, Birmingham, Alabama 35294, USA. dmitry@uab.edu



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase alpha chainG [auth A],
H [auth B],
L [auth K],
M [auth L]
315Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpoATTHA1664
EC: 2.7.7.6
UniProt
Find proteins for Q5SHR6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ5SHR6
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase beta chainI [auth C],
N [auth M]
1119Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpoBTTHA1813
EC: 2.7.7.6
UniProt
Find proteins for Q8RQE9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ8RQE9
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase beta' chainJ [auth D],
O [auth N]
1524Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpoCTTHA1812
EC: 2.7.7.6
UniProt
Find proteins for Q8RQE8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ8RQE8
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase omega chainK [auth E],
P [auth O]
99Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpoZTTHA1561
EC: 2.7.7.6
UniProt
Find proteins for Q8RQE7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ8RQE7
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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*CP*CP*CP*TP*GP*TP*CP*TP*GP*GP*CP*GP*TP*TP*CP*GP*CP*GP*CP*GP*CP*CP*G)-3')A [auth G],
D [auth X]
23N/A
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Entity ID: 2
MoleculeChainsLengthOrganismImage
RNA (5'-R(P*GP*AP*GP*UP*CP*UP*GP*CP*GP*GP*CP*GP*CP*GP*CP*G)-3')B [auth H],
E [auth Y]
16N/A
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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(*AP*AP*CP*GP*CP*CP*AP*GP*AP*CP*AP*GP*GP*G)-3')C [auth I],
F [auth Z]
14N/A
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Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
STD
Query on STD

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Q [auth D],
X [auth N]
STREPTOLYDIGIN
C32 H44 N2 O9
KVTPRMVXYZKLIG-NCAOFHFGSA-N
 Ligand Interaction
APC
Query on APC

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V [auth D],
W [auth M]
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
C11 H18 N5 O12 P3
CAWZRIXWFRFUQB-IOSLPCCCSA-N
 Ligand Interaction
ZN
Query on ZN

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R [auth D],
S [auth D],
Y [auth N],
Z [auth N]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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AA [auth N],
BA [auth N],
T [auth D],
U [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 155.379α = 90
b = 155.379β = 90
c = 496.992γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-07-17
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance