4UD8 | pdb_00004ud8

AtBBE15

• PDB DOI: https://doi.org/10.2210/pdb4UD8/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Arabidopsis thaliana
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2014-12-09 Released: 2015-06-10 
• Deposition Author(s): Daniel, B., Steiner, B., Pavkov-Keller, T., Dordic, A., Gutmann, A., Sensen, C.W., Nidetzky, B., van der Graaff, E., Wallner, S., Gruber, K., Macheroux, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 
  0.221 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Oxidation of Monolignols by Members of the Berberine Bridge Enzyme Family Suggests a Role in Cell Wall Metabolism.

Daniel, B., Pavkov-Keller, T., Steiner, B., Dordic, A., Gutmann, A., Nidetzky, B., Sensen, C.W., Van Der Graaff, E., Wallner, S., Gruber, K., Macheroux, P.

(2015) J Biological Chem 290: 18770

• PubMed: 26037923 
• DOI: https://doi.org/10.1074/jbc.M115.659631
• Primary Citation Related Structures: 
  4UD8


• PubMed Abstract: 
  

  Plant genomes contain a large number of genes encoding for berberine bridge enzyme (BBE)-like enzymes. Despite the widespread occurrence and abundance of this protein family in the plant kingdom, the biochemical function remains largely unexplored. In this study, we have expressed two members of the BBE-like enzyme family from Arabidopsis thaliana in the host organism Komagataella pastoris. The two proteins, termed AtBBE-like 13 and AtBBE-like 15, were purified, and their catalytic properties were determined. In addition, AtBBE-like 15 was crystallized and structurally characterized by x-ray crystallography. Here, we show that the enzymes catalyze the oxidation of aromatic allylic alcohols, such as coumaryl, sinapyl, and coniferyl alcohol, to the corresponding aldehydes and that AtBBE-like 15 adopts the same fold as vanillyl alcohol oxidase as reported previously for berberine bridge enzyme and other FAD-dependent oxidoreductases. Further analysis of the substrate range identified coniferin, the glycosylated storage form of coniferyl alcohol, as a substrate of the enzymes, whereas other glycosylated monolignols were rather poor substrates. A detailed analysis of the motifs present in the active sites of the BBE-like enzymes in A. thaliana suggested that 14 out of 28 members of the family might catalyze similar reactions. Based on these findings, we propose a novel role of BBE-like enzymes in monolignol metabolism that was previously not recognized for this enzyme family.

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Organizational Affiliation: 
• From the Institutes of Biochemistry.
the Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria, the ACIB GmbH, 8010 Graz, Austria, and.
Biotechnology and Biochemical Engineering, and.
Molecular Biotechnology, Graz University of Technology, 8010 Graz, Austria.
the Section for Crop Sciences, Copenhagen University, 2630 Copenhagen, Denmark.
the Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria.
From the Institutes of Biochemistry, [e-mail].

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 123.2 kDa 
• Atom Count: 8,808 
• Modeled Residue Count: 997 
• Deposited Residue Count: 1,064 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FAD-BINDING AND BBE DOMAIN-CONTAINING PROTEIN	A, B	532	Arabidopsis thaliana	Mutation(s): 0  EC: 1.1.99
UniProt
Find proteins for O64743 (Arabidopsis thaliana) Explore O64743  Go to UniProtKB:  O64743
Glycosylation
Glycosylation Sites: 2

Oligosaccharides

Help  

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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	E [auth A], I [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
PE5	G [auth A], K [auth B]	3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL C18 H38 O9 CUDPPTPIUWYGFI-UHFFFAOYSA-N
NAG	F [auth A], J [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
K	L [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
NA	H [auth A], M [auth B], N [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free:  0.221 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.596	α = 90
b = 94.742	β = 90
c = 188.298	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-06-10 
Deposition Author(s): Daniel, B., Steiner, B., Pavkov-Keller, T., Dordic, A., Gutmann, A., Sensen, C.W., Nidetzky, B., van der Graaff, E., Wallner, S., Gruber, K., Macheroux, P.

Revision History  

• Version 1.0: 2015-06-10
  Type: Initial release
  
• Version 1.1: 2015-08-12
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 2.1: 2023-12-20
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-20
  Changes: Structure summary