7CT4 | pdb_00007ct4

Crystal structure of D-amino acid oxidase from Rasamsonia emersonii strain YA

PDB DOI: https://doi.org/10.2210/pdb7CT4/pdb

Classification: FLAVOPROTEIN
Organism(s): Rasamsonia emersonii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-08-18 Released: 2020-11-11
Deposition Author(s): Shimekake, Y., Hirato, Y., Okazaki, S., Funabashi, R., Goto, M., Furuichi, T., Suzuki, H., Takahashi, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.246 (Depositor), 0.233 (DCC)
R-Value Work:
0.206 (Depositor)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

X-ray structure analysis of a unique D-amino-acid oxidase from the thermophilic fungus Rasamsonia emersonii strain YA.

Shimekake, Y., Hirato, Y., Funabashi, R., Okazaki, S., Goto, M., Furuichi, T., Suzuki, H., Kera, Y., Takahashi, S.

(2020) Acta Crystallogr F Struct Biol Commun 76: 517-523

PubMed: 33135670 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S2053230X20013333
Primary Citation Related Structures:
7CT4

PubMed Abstract:
D-Amino-acid oxidases (DAAOs) catalyze the oxidative deamination of neutral and basic D-amino acids. The DAAO from the thermophilic fungus Rasamsonia emersonii strain YA (ReDAAO) has a high thermal stability and a unique broad substrate specificity that includes the acidic D-amino acid D-Glu as well as various neutral and basic D-amino acids. In this study, ReDAAO was crystallized by the hanging-drop vapor-diffusion method and its crystal structure was determined at a resolution of 2.00 Å. The crystal structure of the enzyme revealed that unlike other DAAOs, ReDAAO forms a homotetramer and contains an intramolecular disulfide bond (Cys230-Cys285), suggesting that this disulfide bond is involved in the higher thermal stability of ReDAAO. Moreover, the structure of the active site and its vicinity in ReDAAO indicates that Arg97, Lys99, Lys114 and Ser231 are candidates for recognizing the side chain of D-Glu.

Organizational Affiliation

Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan.

Macromolecule Content

Total Structure Weight: 173.2 kDa
Atom Count: 10,965
Modeled Residue Count: 1,376
Deposited Residue Count: 1,552
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-amino acid oxidase	A, B, C, D	388	Rasamsonia emersonii	Mutation(s): 0 Gene Names: ReDAO EC: 1.4.3.3
UniProt
Find proteins for A0A499UB99 (Rasamsonia emersonii) Explore A0A499UB99 Go to UniProtKB: A0A499UB99
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A499UB99
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth D] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth D] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth C], H [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.246 (Depositor), 0.233 (DCC)
R-Value Work: 0.206 (Depositor)
R-Value Observed: 0.208 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.13	α = 90
b = 79.13	β = 90
c = 366.673	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PDB_EXTRACT	data extraction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-11-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-11-11
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary