6P5U | pdb_00006p5u

Structure of an enoyl-CoA hydratase/aldolase isolated from a lignin-degrading consortium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.229 (Depositor), 0.195 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

The structure of a prokaryotic feruloyl-CoA hydratase-lyase from a lignin-degrading consortium with high oligomerization stability under extreme pHs.

Liberato, M.V.Araujo, J.N.Sodre, V.Goncalves, T.A.Vilela, N.Moraes, E.C.Garcia, W.Squina, F.M.

(2020) Biochim Biophys Acta Proteins Proteom 1868: 140344-140344

  • DOI: https://doi.org/10.1016/j.bbapap.2019.140344
  • Primary Citation Related Structures: 
    6P5U

  • PubMed Abstract: 

    In the context of increasing demand for renewable alternatives of fuels and chemicals, the valorization of lignin emerges as a value-adding strategy in biorefineries and an alternative to petroleum-derived molecules. One of the compounds derived from lignin is ferulic acid (FA), which can be converted into valuable molecules such as vanillin. In microorganisms, FA biotransformation into vanillin can occur via a two-step reaction catalyzed by the sequential activity of a feruloyl-CoA synthetase (FCS) and an feruloyl-CoA hydratase-lyase (FCHL), which could be exploited industrially. In this study, a prokaryotic FCHL derived from a lignin-degrading microbial consortium (named LM-FCHL) was cloned, successfully expressed in soluble form and purified. The crystal structure was solved and refined at 2.1 Å resolution. The LM-FCHL is a hexamer composed of a dimer of trimers, which showed to be quite stable under extreme pH conditions. Finally, small angle X-ray scattering corroborates the hexameric state in solution and indicates flexibility in the protein structure. The present study contributes to the field of lignin valorization to valuable molecules by establishing the biophysical and structural characterization for a novel FCHL member of unique characteristics.


  • Organizational Affiliation
    • Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, SP, Brazil.

Macromolecule Content 

  • Total Structure Weight: 192.81 kDa 
  • Atom Count: 12,510 
  • Modeled Residue Count: 1,446 
  • Deposited Residue Count: 1,698 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Enoyl-CoA hydratase
A, B, C, D, E
A, B, C, D, E, F
283uncultured organismMutation(s): 0 
Gene Names: Ech
UniProt
Find proteins for A0A2P1BT02 (uncultured organism)
Explore A0A2P1BT02 
Go to UniProtKB:  A0A2P1BT02
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2P1BT02
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
COA
(Subject of Investigation/LOI)

Query on COA



Download:Ideal Coordinates CCD File
G [auth A]
H [auth B]
J [auth C]
K [auth D]
L [auth E]
G [auth A],
H [auth B],
J [auth C],
K [auth D],
L [auth E],
M [auth F]
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
B3P

Query on B3P



Download:Ideal Coordinates CCD File
I [auth B]2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C11 H26 N2 O6
HHKZCCWKTZRCCL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.229 (Depositor), 0.195 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.28α = 90
b = 130.96β = 90.68
c = 115.91γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil2014/04105-4
Sao Paulo Research Foundation (FAPESP)Brazil2015/50590-4

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-08
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description