6RS7

X-ray crystal structure of LsAA9B (deglycosylated form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.155 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 3.0 of the entry. See complete history


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

  • DOI: 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 ...

    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.


    Organizational Affiliation

    Department of Chemistry, University of Copenhagen, 2100 Copenhagen, Denmark leila@chem.ku.dk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
AA9A221Panus similisMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB 2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download Ideal Coordinates CCD File 
C [auth A]alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
PGE
Query on PGE

Download Ideal Coordinates CCD File 
M [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download Ideal Coordinates CCD File 
D [auth A](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NO3
Query on NO3

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.155 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.08α = 90
b = 72.99β = 90
c = 79.06γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Danish Agency for Science Technology and InnovationDenmark12-134922
Danish Agency for Science Technology and InnovationDenmark12-134923
Novo Nordisk FoundationDenmarkNNF17SA0027704
European Communitys Seventh Framework ProgrammeDenmarkBioStruct-X (grant agreement N283570)
European CommissionDenmarkCF16-0673 - The Carlsberg Foundation
European CommissionDenmarkCF17-0533 - The Carlsberg Foundation
European CommissionFranceAgreenSkills+ (Marie-Curie FP7 COFUND People Programme under grant agreement 609398)

Revision History  (Full details and data files)

  • 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: Advisory, 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