3EYA

Structural basis for membrane binding and catalytic activation of the peripheral membrane enzyme pyruvate oxidase from Escherichia coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Structural basis for membrane binding and catalytic activation of the peripheral membrane enzyme pyruvate oxidase from Escherichia coli.

Neumann, P.Weidner, A.Pech, A.Stubbs, M.T.Tittmann, K.

(2008) Proc Natl Acad Sci U S A 105: 17390-17395

  • DOI: 10.1073/pnas.0805027105
  • Primary Citation of Related Structures:  
    3EY9, 3EYA

  • PubMed Abstract: 
  • The thiamin- and flavin-dependent peripheral membrane enzyme pyruvate oxidase from E. coli catalyzes the oxidative decarboxylation of the central metabolite pyruvate to CO(2) and acetate. Concomitant reduction of the enzyme-bound flavin triggers membrane binding of the C terminus and shuttling of 2 electrons to ubiquinone 8, a membrane-bound mobile carrier of the electron transport chain ...

    The thiamin- and flavin-dependent peripheral membrane enzyme pyruvate oxidase from E. coli catalyzes the oxidative decarboxylation of the central metabolite pyruvate to CO(2) and acetate. Concomitant reduction of the enzyme-bound flavin triggers membrane binding of the C terminus and shuttling of 2 electrons to ubiquinone 8, a membrane-bound mobile carrier of the electron transport chain. Binding to the membrane in vivo or limited proteolysis in vitro stimulate the catalytic proficiency by 2 orders of magnitude. The molecular mechanisms by which membrane binding and activation are governed have remained enigmatic. Here, we present the X-ray crystal structures of the full-length enzyme and a proteolytically activated truncation variant lacking the last 23 C-terminal residues inferred as important in membrane binding. In conjunction with spectroscopic results, the structural data pinpoint a conformational rearrangement upon activation that exposes the autoinhibitory C terminus, thereby freeing the active site. In the activated enzyme, Phe-465 swings into the active site and wires both cofactors for efficient electron transfer. The isolated C terminus, which has no intrinsic helix propensity, folds into a helical structure in the presence of micelles.


    Organizational Affiliation

    Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes Strasse 3, D-06120 Halle/Saale, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pyruvate dehydrogenase [cytochrome]
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J, K, L
549Escherichia coliMutation(s): 0 
Gene Names: poxBb0871JW0855
EC: 1.2.2.2 (PDB Primary Data), 1.2.5.1 (UniProt)
UniProt
Find proteins for P07003 (Escherichia coli (strain K12))
Explore P07003 
Go to UniProtKB:  P07003
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
BB [auth G] , CA [auth C] , HA [auth D] , HB [auth H] , MB [auth I] , N [auth A] , RA [auth E] , RB [auth J] , 
BB [auth G], CA [auth C], HA [auth D], HB [auth H], MB [auth I], N [auth A], RA [auth E], RB [auth J], VB [auth K], W [auth B], WA [auth F], ZB [auth L]
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 
AB [auth G] , BA [auth C] , GA [auth D] , GB [auth H] , LB [auth I] , M [auth A] , QA [auth E] , QB [auth J] , 
AB [auth G], BA [auth C], GA [auth D], GB [auth H], LB [auth I], M [auth A], QA [auth E], QB [auth J], UB [auth K], V [auth B], VA [auth F], YB [auth L]
THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
AA [auth B] , BC [auth L] , CC [auth L] , DB [auth G] , DC [auth L] , EA [auth C] , EB [auth G] , EC [auth L] , 
AA [auth B], BC [auth L], CC [auth L], DB [auth G], DC [auth L], EA [auth C], EB [auth G], EC [auth L], FA [auth C], FB [auth G], FC [auth L], JA [auth D], JB [auth H], KA [auth D], KB [auth H], LA [auth D], MA [auth D], NA [auth D], OA [auth D], OB [auth I], P [auth A], PA [auth D], PB [auth I], Q [auth A], R [auth A], S [auth A], T [auth A], TA [auth E], TB [auth J], U [auth A], UA [auth E], XB [auth K], Y [auth B], YA [auth F], Z [auth B], ZA [auth F]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AC [auth L] , CB [auth G] , DA [auth C] , IA [auth D] , IB [auth H] , NB [auth I] , O [auth A] , SA [auth E] , 
AC [auth L], CB [auth G], DA [auth C], IA [auth D], IB [auth H], NB [auth I], O [auth A], SA [auth E], SB [auth J], WB [auth K], X [auth B], XA [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 203.243α = 90
b = 207.051β = 90
c = 214.542γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-11-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2021-08-18
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary