6H6V

Structure of the UbiD-class enzyme HmfF from Pelotomaculum thermopropionicum in complex with FMN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.66 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Enzymatic Carboxylation of 2-Furoic Acid Yields 2,5-Furandicarboxylic Acid (FDCA).

Payne, K.A.P.Marshall, S.A.Fisher, K.Cliff, M.J.Cannas, D.M.Yan, C.Heyes, D.J.Parker, D.A.Larrosa, I.Leys, D.

(2019) ACS Catal 9: 2854-2865

  • DOI: https://doi.org/10.1021/acscatal.8b04862
  • Primary Citation of Related Structures:  
    6H6V, 6H6X

  • PubMed Abstract: 

    The biological production of FDCA is of considerable value as a potential replacement for petrochemical-derived monomers such as terephthalate, used in polyethylene terephthalate (PET) plastics. HmfF belongs to an uncharacterized branch of the prenylated flavin (prFMN) dependent UbiD family of reversible (de)carboxylases and is proposed to convert 2,5-furandicarboxylic acid (FDCA) to furoic acid in vivo. We present a detailed characterization of HmfF and demonstrate that HmfF can catalyze furoic acid carboxylation at elevated CO 2 levels in vitro. We report the crystal structure of a thermophilic HmfF from Pelotomaculum thermopropionicum , revealing that the active site located above the prFMN cofactor contains a furoic acid/FDCA binding site composed of residues H296-R304-R331 specific to the HmfF branch of UbiD enzymes. Variants of the latter are compromised in activity, while H296N alters the substrate preference to pyrrole compounds. Solution studies and crystal structure determination of an engineered dimeric form of the enzyme revealed an unexpected key role for a UbiD family wide conserved Leu residue in activity. The structural insights into substrate and cofactor binding provide a template for further exploitation of HmfF in the production of FDCA plastic precursors and improve our understanding of catalysis by members of the UbiD enzyme family.


  • Organizational Affiliation

    Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases
A, B, C, D, E
A, B, C, D, E, F
448Pelotomaculum thermopropionicum SIMutation(s): 0 
Gene Names: UbiDPTH_0496
UniProt
Find proteins for A5D4Z9 (Pelotomaculum thermopropionicum (strain DSM 13744 / JCM 10971 / SI))
Explore A5D4Z9 
Go to UniProtKB:  A5D4Z9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5D4Z9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN (Subject of Investigation/LOI)
Query on FMN

Download Ideal Coordinates CCD File 
AA [auth F]
G [auth A]
K [auth B]
O [auth C]
S [auth D]
AA [auth F],
G [auth A],
K [auth B],
O [auth C],
S [auth D],
W [auth E]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
CA [auth F]
I [auth A]
M [auth B]
Q [auth C]
U [auth D]
CA [auth F],
I [auth A],
M [auth B],
Q [auth C],
U [auth D],
Y [auth E]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
DA [auth F]
J [auth A]
N [auth B]
R [auth C]
V [auth D]
DA [auth F],
J [auth A],
N [auth B],
R [auth C],
V [auth D],
Z [auth E]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
BA [auth F]
H [auth A]
L [auth B]
P [auth C]
T [auth D]
BA [auth F],
H [auth A],
L [auth B],
P [auth C],
T [auth D],
X [auth E]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.66 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.91α = 90
b = 139.25β = 93.74
c = 136.88γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MLPHAREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilUnited Kingdompre-FAB 695013

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-27
    Type: Initial release
  • Version 1.1: 2019-05-15
    Changes: Data collection, Database references