6HAF

Pyruvate oxidase variant E59Q from L. plantarum in complex with phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.134 
  • R-Value Observed: 0.135 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 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: 10.1038/s41586-019-1581-9
  • Primary Citation of Related Structures:  
    6HAD, 6HAF, 6HA3, 6RJC, 6RJB

  • 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 ...

    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 Structural Dynamics, Max-Planck-Institute for Biophysical Chemistry Göttingen, Göttingen, Germany. ktittma@gwdg.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pyruvate oxidaseA, B603Lactiplantibacillus plantarumMutation(s): 1 
Gene Names: spxBC4O30_12890CUR48_03890
EC: 1.2.3.3
UniProt
Find proteins for P37063 (Lactobacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1))
Explore P37063 
Go to UniProtKB:  P37063
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
C [auth A], O [auth B]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
TPP (Subject of Investigation/LOI)
Query on TPP

Download Ideal Coordinates CCD File 
F [auth A], R [auth B]THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
N [auth A], X [auth B]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A] , H [auth A] , I [auth A] , J [auth A] , K [auth A] , L [auth A] , M [auth A] , S [auth B] , 
G [auth A],  H [auth A],  I [auth A],  J [auth A],  K [auth A],  L [auth A],  M [auth A],  S [auth B],  T [auth B],  U [auth B],  V [auth B],  W [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
D [auth A], P [auth B]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A], Q [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.134 
  • R-Value Observed: 0.135 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.18α = 90
b = 154.35β = 90
c = 165.52γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



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, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Structure summary