6RS9

X-ray crystal structure of LsAA9B (xylotetraose soak)

• PDB DOI:  https://doi.org/10.2210/pdb6RS9/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Panus similis
• Expression System: Aspergillus oryzae
• Mutation(s): No 


• Deposited: 2019-05-21 Released: 2019-09-11 
• Deposition Author(s): Frandsen, K.E.H., Tovborg, M., Poulsen, J.C.N., Johansen, K.S., Lo Leggio, L.
• Funding Organization(s): Danish Agency for Science Technology and Innovation, Novo Nordisk Foundation, European Communitys Seventh Framework Programme, European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.175 
• R-Value Work: 0.133 
• R-Value Observed: 0.135 

Literature

Insights into an unusual Auxiliary Activity 9 family member lacking the histidine brace motif of lytic polysaccharide monooxygenases.

Frandsen, K.E.H., Tovborg, M., Jorgensen, C.I., Spodsberg, N., Rosso, M.N., Hemsworth, G.R., Garman, E.F., Grime, G.W., Poulsen, J.N., Batth, T.S., Miyauchi, S., Lipzen, A., Daum, C., Grigoriev, I.V., Johansen, K.S., Henrissat, B., Berrin, J.G., Lo Leggio, L.

(2019) J Biol Chem 294: 17117-17130

• PubMed: 31471321 
• DOI: https://doi.org/10.1074/jbc.RA119.009223
• Primary Citation of Related Structures:  
  6RS6, 6RS7, 6RS8, 6RS9


• PubMed Abstract: 
  

Lytic polysaccharide monooxygenases (LPMOs) are redox-enzymes involved in biomass degradation. All characterized LPMOs possess an active site of two highly conserved histidine residues coordinating a copper ion (the histidine brace), which are essential for LPMO activity. However, some protein sequences that belong to the AA9 LPMO family display a natural N-terminal His to Arg substitution (Arg-AA9). These are found almost entirely in the phylogenetic fungal class Agaricomycetes , associated with wood decay, but no function has been demonstrated for any Arg-AA9. Through bioinformatics, transcriptomic, and proteomic analyses we present data, which suggest that Arg-AA9 proteins could have a hitherto unidentified role in fungal degradation of lignocellulosic biomass in conjunction with other secreted fungal enzymes. We present the first structure of an Arg-AA9, Ls AA9B, a naturally occurring protein from Lentinus similis The Ls AA9B structure reveals gross changes in the region equivalent to the canonical LPMO copper-binding site, whereas features implicated in carbohydrate binding in AA9 LPMOs have been maintained. We obtained a structure of Ls AA9B with xylotetraose bound on the surface of the protein although with a considerably different binding mode compared with other AA9 complex structures. In addition, we have found indications of protein phosphorylation near the N-terminal Arg and the carbohydrate-binding site, for which the potential function is currently unknown. Our results are strong evidence that Arg-AA9s function markedly different from canonical AA9 LPMO, but nonetheless, may play a role in fungal conversion of lignocellulosic biomass.

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Organizational Affiliation: 

Department of Chemistry, University of Copenhagen, 2100 Copenhagen, Denmark [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 24.55 kDa 
• Atom Count: 1,972 
• Modelled Residue Count: 221 
• Deposited Residue Count: 221 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AA9	A	221	Panus similis	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose	C	4		N/A
Glycosylation Resources
GlyTouCan:  G60650FG GlyCosmos:  G60650FG

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MAN	D [auth A]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
BCN	E [auth A]	BICINE C6 H13 N O4 FSVCELGFZIQNCK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.175 
• R-Value Work: 0.133 
• R-Value Observed: 0.135 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.41	α = 90
b = 72.79	β = 90
c = 78.59	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MxCuBE	data collection
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-09-11 
Deposition Author(s): Frandsen, K.E.H., Tovborg, M., Poulsen, J.C.N., Johansen, K.S., Lo Leggio, L.

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Funding Organization	Location	Grant Number
Danish Agency for Science Technology and Innovation	Denmark	12-134922
Danish Agency for Science Technology and Innovation	Denmark	12-134923
Novo Nordisk Foundation	Denmark	NNF17SA0027704
European Communitys Seventh Framework Programme	Denmark	BioStruct-X (grant agreement N283570)
European Commission	Denmark	CF16-0673 - The Carlsberg Foundation
European Commission	Denmark	CF17-0533 - The Carlsberg Foundation
European Commission	France	AgreenSkills+ (Marie-Curie FP7 COFUND People Programme under grant agreement 609398)

Revision History  

• Version 1.0: 2019-09-11
  Type: Initial release
  
• Version 1.1: 2019-11-20
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 3.0: 2021-11-10
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary