6HAD

Human transketolase variant E160Q


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.04 Å
  • R-Value Free: 0.130 
  • R-Value Work: 0.111 
  • R-Value Observed: 0.111 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


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

  • DOI: https://doi.org/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.


  • Organizational Affiliation

    Department of Molecular Enzymology, Göttingen Centre for Molecular Biosciences and Albrecht-von-Haller Institute, Georg-August University Göttingen, Göttingen, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transketolase637Homo sapiensMutation(s): 1 
EC: 2.2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P29401 (Homo sapiens)
Explore P29401 
Go to UniProtKB:  P29401
PHAROS:  P29401
GTEx:  ENSG00000163931 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29401
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.04 Å
  • R-Value Free: 0.130 
  • R-Value Work: 0.111 
  • R-Value Observed: 0.111 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.71α = 90
b = 85.49β = 127.85
c = 73.61γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyFOR 1296/TP3

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-21
    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
  • Version 2.0: 2021-08-04
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-05-15
    Changes: Data collection, Database references