Evidence map›Paper›PMID 33135670›Full record

ArticleActa crystallographica. Section F, Structural biology communications2020

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

Yuya Shimekake, Yuki Hirato, Rikako Funabashi, Sayoko Okazaki, Masaru Goto, Takehiro Furuichi, Hideyuki Suzuki, Yoshio Kera, Shouji Takahashi

Open access · greenAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Acta crystallographica. Section F, Structural biology communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
0.4field-weighted citation impact, top 39% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed, 8 citations in OpenAlex.

  1. Article
  2. Crystal structure of D-aspartate oxidase from Cryptococcus humicola UJ1.Acta crystallographica. Section F, Structural biology communications · 2025
    Article
  3. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors at 2 institutions in 1 country.

Yuya ShimekakeDepartment of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan.ORCID 0000-0002-9112-8530
Yuki HiratoDepartment of Biomolecular Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan.ORCID 0000-0002-5302-9005
Rikako FunabashiDepartment of Biomolecular Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan.
Sayoko OkazakiDepartment of Biomolecular Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan.
Masaru GotoDepartment of Biomolecular Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan.ORCID 0000-0002-9317-0521
Takehiro FuruichiDepartment of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan.ORCID 0000-0002-1778-6869
Hideyuki SuzukiDepartment of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan.
Yoshio KeraDepartment of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan.
Shouji TakahashiDepartment of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan.ORCID 0000-0002-0279-9173
Nagaoka University of Technology · JPToho University · JP

Funding

Japan Society for the Promotion of Science 16K07660
6 · The paper itself

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.

Indexed as

Amino Acid SubstitutionCatalytic DomainCrystallography, X-RayD-Amino-Acid OxidaseDisulfidesEnzyme StabilityEurotialesFungal ProteinsGlutamic AcidModels, MolecularProtein ConformationD-Amino-Acid OxidaseDisulfidesFungal ProteinsGlutamic Acidd-amino-acid oxidasesd-amino acidsflavoenzymesRasamsonia emersoniisubstrate specificitythermal stabilitythermophilic fungi

Identifiers

PMID33135670
PMCPMC7605106
OpenAlexW3094044715

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.