Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 149.38 kDa 
• Atom Count: 13032 
• Modelled Residue Count: 1332 
• Deposited Residue Count: 1338 
• Unique protein chains: 1

6RJC

E.coli transketolase apoenzyme

• PDB DOI: 10.2210/pdb6RJC/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-04-26 Released: 2019-09-11 
• Deposition Author(s): Rabe von Pappenheim, F., Tittmann, K.
• Funding Organization(s): German Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 0.123 
• R-Value Work: 0.104 
• R-Value Observed: 0.104 

Literature

Low-barrier hydrogen bonds in enzyme cooperativity.

Dai, S., Funk, L.M., von Pappenheim, F.R., Sautner, V., Paulikat, M., Schroder, B., Uranga, J., Mata, R.A., Tittmann, K.

(2019) Nature 573: 609-613

• PubMed: 31534226 
• DOI: 10.1038/s41586-019-1581-9
• Primary Citation of Related Structures:  
  6HA3, 6HAD, 6HAF, 6RJB, 6RJC


• PubMed Abstract: 
  

The underlying molecular mechanisms of cooperativity and allosteric regulation are well understood for many proteins, with haemoglobin and aspartate transcarbamoylase serving as prototypical examples ^1,2 . The binding of effectors typically causes a structural transition of the protein that is propagated through signalling pathways to remote sites and involves marked changes on the tertiary and sometimes even the quaternary level ^1-5 . However, the origin of these signals and the molecular mechanism of long-range signalling at an atomic level remain unclear ^5-8 . The different spatial scales and timescales in signalling pathways render experimental observation challenging; in particular, the positions and movement of mobile protons cannot be visualized by current methods of structural analysis. Here we report the experimental observation of fluctuating low-barrier hydrogen bonds as switching elements in cooperativity pathways of multimeric enzymes. We have observed these low-barrier hydrogen bonds in ultra-high-resolution X-ray crystallographic structures of two multimeric enzymes, and have validated their assignment using computational calculations. Catalytic events at the active sites switch between low-barrier hydrogen bonds and ordinary hydrogen bonds in a circuit that consists of acidic side chains and water molecules, transmitting a signal through the collective repositioning of protons by behaving as an atomistic Newton's cradle. The resulting communication synchronizes catalysis in the oligomer. Our studies provide several lines of evidence and a working model for not only the existence of low-barrier hydrogen bonds in proteins, but also a connection to enzyme cooperativity. This finding suggests new principles of drug and enzyme design, in which sequences of residues can be purposefully included to enable long-range communication and thus the regulation of engineered biomolecules.

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Organizational Affiliation: 

Department of Structural Dynamics, Max-Planck-Institute for Biophysical Chemistry Göttingen, Göttingen, Germany. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transketolase 1	A, B	669	Escherichia coli K-12	Mutation(s): 0  Gene Names: tktA, tkt, b2935, JW5478 EC: 2.2.1.1
UniProt
Find proteins for P27302 (Escherichia coli (strain K12)) Explore P27302  Go to UniProtKB:  P27302

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	BA [auth A], CA [auth A], DA [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], F [auth A], FA [auth B], G [auth A], GA [auth B], H [auth A], HA [auth B], I [auth A], IA [auth B], J [auth A], JA [auth B], K [auth A], KA [auth B], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], NA [auth B], O [auth A], OA [auth B], P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B], S [auth A], SA [auth B], T [auth A], TA [auth B], U [auth A], UA [auth B], V [auth A], VA [auth B], W [auth A], WA [auth B], X [auth A], XA [auth B], Y [auth A], YA [auth B], Z [auth A], ZA [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	C [auth A], EA [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	AA [auth A], AB [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 0.123 
• R-Value Work: 0.104 
• R-Value Observed: 0.104 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.905	α = 90
b = 102.048	β = 90
c = 132.933	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-04-26 
• Released Date: 2019-09-11 
Deposition Author(s): Rabe von Pappenheim, F., Tittmann, K.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	FOR 1296/TP3

Revision History  

• Version 1.0: 2019-09-11
  Type: Initial release
  
• Version 1.1: 2019-09-18
  Changes: Data collection, Database references
• Version 1.2: 2019-10-02
  Changes: Data collection, Database references
• Version 1.3: 2019-10-09
  Changes: Data collection, Database references