3AQL | pdb_00003aql

Structure of bacterial protein (apo form II)

• PDB DOI: https://doi.org/10.2210/pdb3AQL/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli DH1
• Expression System: Escherichia coli DH1
• Mutation(s): Yes 


• Deposited: 2010-11-09 Released: 2011-02-09 
• Deposition Author(s): Toh, Y., Takeshita, D., Tomita , K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.251 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.237 (Depositor), 0.237 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Literature

Mechanism for the alteration of the substrate specificities of template-independent RNA polymerases

Toh, Y., Takeshita, D., Nagaike, T., Numata, T., Tomita, K.

(2011) Structure 19: 232-243

• PubMed: 21300291 
• DOI: https://doi.org/10.1016/j.str.2010.12.006
• Primary Citation Related Structures: 
  3AQK, 3AQL, 3AQM, 3AQN


• PubMed Abstract: 
  

  PolyA polymerase (PAP) adds a polyA tail onto the 3'-end of RNAs without a nucleic acid template, using adenosine-5'-triphosphate (ATP) as a substrate. The mechanism for the substrate selection by eubacterial PAP remains obscure. Structural and biochemical studies of Escherichia coli PAP (EcPAP) revealed that the shape and size of the nucleobase-interacting pocket of EcPAP are maintained by an intra-molecular hydrogen-network, making it suitable for the accommodation of only ATP, using a single amino acid, Arg(197). The pocket structure is sustained by interactions between the catalytic domain and the RNA-binding domain. EcPAP has a flexible basic C-terminal region that contributes to optimal RNA translocation for processive adenosine 5'-monophosphate (AMP) incorporations onto the 3'-end of RNAs. A comparison of the EcPAP structure with those of other template-independent RNA polymerases suggests that structural changes of domain(s) outside the conserved catalytic core domain altered the substrate specificities of the template-independent RNA polymerases.

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Organizational Affiliation: 
• Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba-shi, Ibaraki 305-8566, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 96.26 kDa 
• Atom Count: 6,342 
• Modeled Residue Count: 776 
• Deposited Residue Count: 830 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly(A) polymerase	A, B	415	Escherichia coli DH1	Mutation(s): 1  Gene Names: EcDH1_3459 EC: 2.7.7.19

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A], E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	C [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.251 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.237 (Depositor), 0.237 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.012	α = 90
b = 133.012	β = 90
c = 176.845	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-02-09 
Deposition Author(s): Toh, Y., Takeshita, D., Tomita , K.

Revision History  

• Version 1.0: 2011-02-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2013-07-31
  Changes: Database references
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations