6YJO | pdb_00006yjo

Structure of FgChi7B

• PDB DOI: https://doi.org/10.2210/pdb6YJO/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Fusarium graminearum PH-1
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2020-04-04 Released: 2021-03-03 
• Deposition Author(s): Haddad Momeni, M., Fredslund, F., Berrin, J.G., Abou Hachem, M., Welner, D.H.
• Funding Organization(s): Novo Nordisk Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 
  0.238 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

Discovery of fungal oligosaccharide-oxidising flavo-enzymes with previously unknown substrates, redox-activity profiles and interplay with LPMOs.

Haddad Momeni, M., Fredslund, F., Bissaro, B., Raji, O., Vuong, T.V., Meier, S., Nielsen, T.S., Lombard, V., Guigliarelli, B., Biaso, F., Haon, M., Grisel, S., Henrissat, B., Welner, D.H., Master, E.R., Berrin, J.G., Abou Hachem, M.

(2021) Nat Commun 12: 2132-2132

• PubMed: 33837197 
• DOI: https://doi.org/10.1038/s41467-021-22372-0
• Primary Citation Related Structures: 
  6YJI, 6YJO


• PubMed Abstract: 
  

  Oxidative plant cell-wall processing enzymes are of great importance in biology and biotechnology. Yet, our insight into the functional interplay amongst such oxidative enzymes remains limited. Here, a phylogenetic analysis of the auxiliary activity 7 family (AA7), currently harbouring oligosaccharide flavo-oxidases, reveals a striking abundance of AA7-genes in phytopathogenic fungi and Oomycetes. Expression of five fungal enzymes, including three from unexplored clades, expands the AA7-substrate range and unveils a cellooligosaccharide dehydrogenase activity, previously unknown within AA7. Sequence and structural analyses identify unique signatures distinguishing the strict dehydrogenase clade from canonical AA7 oxidases. The discovered dehydrogenase directly is able to transfer electrons to an AA9 lytic polysaccharide monooxygenase (LPMO) and fuel cellulose degradation by LPMOs without exogenous reductants. The expansion of redox-profiles and substrate range highlights the functional diversity within AA7 and sets the stage for harnessing AA7 dehydrogenases to fine-tune LPMO activity in biotechnological conversion of plant feedstocks.

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Organizational Affiliation: 
• Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark.
INRAE, Aix Marseille Univ, Biodiversité et Biotechnologie Fongiques (BBF), Marseille, France.
The Novo Nordisk Center for Biosustainability, Lyngby, Denmark.
Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada.
Department of Chemistry, Technical University of Denmark, Lyngby, Denmark.
Architecture et Fonction des Macromolécules Biologiques, UMR 7257 CNRS, USC 1408, Aix Marseille Univ, Marseille, France.
Aix-Marseille Univ, CNRS, UMR7281 Unité de Bioénergétique et Ingénierie des Protéines (BIP), Marseille, France.
INRAE, USC1408 Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille, France.
Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland.
INRAE, Aix Marseille Univ, Biodiversité et Biotechnologie Fongiques (BBF), Marseille, France. [e-mail].
Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 57.66 kDa 
• Atom Count: 3,870 
• Modeled Residue Count: 475 
• Deposited Residue Count: 512 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FAD-binding PCMH-type domain-containing protein	A	512	Fusarium graminearum PH-1	Mutation(s): 0  Gene Names: FGRAMPH1_01T15319
UniProt
Find proteins for A0A098DND1 (Gibberella zeae (strain ATCC MYA-4620 / CBS 123657 / FGSC 9075 / NRRL 31084 / PH-1)) Explore A0A098DND1  Go to UniProtKB:  A0A098DND1
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD (Subject of Investigation/LOI)	C [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free:  0.238 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.6	α = 90
b = 67.455	β = 116.31
c = 85.082	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-03-03 
Deposition Author(s): Haddad Momeni, M., Fredslund, F., Berrin, J.G., Abou Hachem, M., Welner, D.H.

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Funding Organization	Location	Grant Number
Novo Nordisk Foundation	Denmark	NNF17OC0025642

Revision History  

• Version 1.0: 2021-03-03
  Type: Initial release
  
• Version 2.0: 2021-03-31
  Changes: Atomic model, Database references, Structure summary
• Version 2.1: 2021-04-21
  Changes: Database references
• Version 2.2: 2021-04-28
  Changes: Structure summary
• Version 2.3: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 2.4: 2024-10-23
  Changes: Structure summary