6JQO

Structure of PaaZ, a bifunctional enzyme in complex with NADP+ and CCoA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Molecular basis for metabolite channeling in a ring opening enzyme of the phenylacetate degradation pathway.

Sathyanarayanan, N.Cannone, G.Gakhar, L.Katagihallimath, N.Sowdhamini, R.Ramaswamy, S.Vinothkumar, K.R.

(2019) Nat Commun 10: 4127-4127

  • DOI: 10.1038/s41467-019-11931-1
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Substrate channeling is a mechanism for the internal transfer of hydrophobic, unstable or toxic intermediates from the active site of one enzyme to another. Such transfer has previously been described to be mediated by a hydrophobic tunnel, the use o ...

    Substrate channeling is a mechanism for the internal transfer of hydrophobic, unstable or toxic intermediates from the active site of one enzyme to another. Such transfer has previously been described to be mediated by a hydrophobic tunnel, the use of electrostatic highways or pivoting and by conformational changes. The enzyme PaaZ is used by many bacteria to degrade environmental pollutants. PaaZ is a bifunctional enzyme that catalyzes the ring opening of oxepin-CoA and converts it to 3-oxo-5,6-dehydrosuberyl-CoA. Here we report the structures of PaaZ determined by electron cryomicroscopy with and without bound ligands. The structures reveal that three domain-swapped dimers of the enzyme form a trilobed structure. A combination of small-angle X-ray scattering (SAXS), computational studies, mutagenesis and microbial growth experiments suggests that the key intermediate is transferred from one active site to the other by a mechanism of electrostatic pivoting of the CoA moiety, mediated by a set of conserved positively charged residues.


    Organizational Affiliation

    Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK.,Institute for Stem Cell Science and Regenerative Medicine, GKVK Campus, Bellary Road, Bangalore, India.,National Centre for Biological Sciences TIFR, GKVK Campus, Bellary Road, Bangalore, India.,Institute for Stem Cell Science and Regenerative Medicine, GKVK Campus, Bellary Road, Bangalore, India. ramas@instem.res.in.,Protein Crystallography Facility and Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.,Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences TIFR, GKVK Campus, Bellary Road, Bangalore, India.,National Centre for Biological Sciences TIFR, GKVK Campus, Bellary Road, Bangalore, India. vkumar@ncbs.res.in.,Institute of Trans-Disciplinary Health Sciences and Technology (TDU), Bangalore, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bifunctional protein PaaZ
A, B, C, D, E, F
688Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: paaZ (maoC, ydbN)
Find proteins for P77455 (Escherichia coli (strain K12))
Go to UniProtKB:  P77455
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download SDF File 
Download CCD File 
A, B, C, D, E, F
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
COO
Query on COO

Download SDF File 
Download CCD File 
A, B, C, D, E, F
CROTONYL COENZYME A
C25 H40 N7 O17 P3 S
KFWWCMJSYSSPSK-XBTRWLRFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Biotechnology (India)IndiaDBT/PR12422/MED/31/287/2014
Council of Scientific & Industrial ResearchIndiaCSIR/37/1606/13/EMR-II
Department of Biotechnology (India)IndiaBT/PR5081/INF/22/156/2012
Medical Research Council (United Kingdom)United KingdomU105184322

Revision History 

  • Version 1.0: 2019-09-11
    Type: Initial release
  • Version 1.1: 2019-09-25
    Type: Data collection, Database references