4OPB | pdb_00004opb

AA13 Lytic polysaccharide monooxygenase from Aspergillus oryzae

• PDB DOI: https://doi.org/10.2210/pdb4OPB/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Aspergillus oryzae RIB40
• Expression System: Aspergillus oryzae
• Mutation(s): No 


• Deposited: 2014-02-05 Released: 2015-01-28 
• Deposition Author(s): Lo Leggio, L., Frandsen, K.H., Davies, G.J., Dupree, P., Walton, P., Henrissat, B., Stringer, M., Tovborg, M., De Maria, L., Johansen, K.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.170 (Depositor), 0.173 (DCC) 
• R-Value Work: 
  0.119 (Depositor), 0.122 (DCC) 
• R-Value Observed: 
  0.121 (Depositor) 

Literature

Structure and boosting activity of a starch-degrading lytic polysaccharide monooxygenase.

Lo Leggio, L., Simmons, T.J., Poulsen, J.C., Frandsen, K.E., Hemsworth, G.R., Stringer, M.A., von Freiesleben, P., Tovborg, M., Johansen, K.S., De Maria, L., Harris, P.V., Soong, C.L., Dupree, P., Tryfona, T., Lenfant, N., Henrissat, B., Davies, G.J., Walton, P.H.

(2015) Nat Commun 6: 5961-5961

• PubMed: 25608804 
• DOI: https://doi.org/10.1038/ncomms6961
• Primary Citation Related Structures: 
  4OPB


• PubMed Abstract: 
  

  Lytic polysaccharide monooxygenases (LPMOs) are recently discovered enzymes that oxidatively deconstruct polysaccharides. LPMOs are fundamental in the effective utilization of these substrates by bacteria and fungi; moreover, the enzymes have significant industrial importance. We report here the activity, spectroscopy and three-dimensional structure of a starch-active LPMO, a representative of the new CAZy AA13 family. We demonstrate that these enzymes generate aldonic acid-terminated malto-oligosaccharides from retrograded starch and boost significantly the conversion of this recalcitrant substrate to maltose by β-amylase. The detailed structure of the enzyme's active site yields insights into the mechanism of action of this important class of enzymes.

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Organizational Affiliation: 
• Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, Denmark.
Department of Biochemistry, University Of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK.
Department of Chemistry, University of York, York YO10 5DD, UK.
Novozymes A/S, Krogshoejvej 36, 2880 Bagsvaerd, Denmark.
Novozymes, Inc., 1445 Drew Avenue, Davis, California 95618, USA.
Novozymes North America Inc., 77 Perrys Chapel Church Road, Franklinton, North Carolina 27525, USA.
Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13288 Marseille, France.
1] Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13288 Marseille, France [2] Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.

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: 27.12 kDa 
• Atom Count: 2,150 
• Modeled Residue Count: 233 
• Deposited Residue Count: 233 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Predicted protein	A	233	Aspergillus oryzae RIB40	Mutation(s): 0  Gene Names: AO090701000246
UniProt
Find proteins for Q2U8Y3 (Aspergillus oryzae (strain ATCC 42149 / RIB 40)) Explore Q2U8Y3  Go to UniProtKB:  Q2U8Y3
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	I [auth A], J [auth A], L [auth A], M [auth A], O [auth A], P [auth A], Q [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	D [auth A], E [auth A], F [auth A], G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU	B [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
IPA	H [auth A], K [auth A]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N
ACT	N [auth A], R [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HIC	A	L-PEPTIDE LINKING	C7 H11 N3 O2		HIS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.170 (Depositor), 0.173 (DCC) 
• R-Value Work:  0.119 (Depositor), 0.122 (DCC) 
• R-Value Observed: 0.121 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.56	α = 90
b = 61.6	β = 90
c = 73.16	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
PHENIX	model building
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-28 
Deposition Author(s): Lo Leggio, L., Frandsen, K.H., Davies, G.J., Dupree, P., Walton, P., Henrissat, B., Stringer, M., Tovborg, M., De Maria, L., Johansen, K.S.

Revision History  

• Version 1.0: 2015-01-28
  Type: Initial release
  
• Version 1.1: 2015-03-04
  Changes: Database references, Experimental preparation
• Version 1.2: 2017-11-22
  Changes: Data collection, Refinement description
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2025-03-26
  Changes: Data collection, Database references, Structure summary