Evidence map›Paper›PMID 29147002›Full record

ArticleNature communications2017

Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.

Takehiko Tosha, Takashi Nomura, Takuma Nishida, Naoya Saeki, Kouta Okubayashi, Raika Yamagiwa, Michihiro Sugahara, Takanori Nakane, Keitaro Yamashita, Kunio Hirata and 25 more

Abstract read
In one paragraph

Article in Nature communications, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.

0numbers the graph read from it
0cells of the map it votes in
54citing papers in PubMed
–field-weighted citation impact
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

54 citing papers in PubMed.

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  18. The time revolution in macromolecular crystallography.Structural dynamics (Melville, N.Y.) · 2024
    Article
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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

35 authors.

Takehiko ToshaRIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan.
Takashi NomuraRIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan.
Takuma NishidaDepartment of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamighori, Akoh, Hyogo, 678-1297, Japan.
Naoya SaekiDepartment of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamighori, Akoh, Hyogo, 678-1297, Japan.
Kouta OkubayashiDepartment of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamighori, Akoh, Hyogo, 678-1297, Japan.
Raika YamagiwaRIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan.
Michihiro SugaharaRIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan.
Takanori NakaneDepartment of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.ORCID http://orcid.org/0000-0003-2697-2767
Keitaro YamashitaRIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan.ORCID http://orcid.org/0000-0002-5442-7582
Kunio HirataRIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan.
Go UenoRIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan.
Tetsunari KimuraDepartment of Chemistry, Graduate School of Science, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, 657-8501, Japan.
Tamao HisanoRIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan.
Kazumasa MuramotoDepartment of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamighori, Akoh, Hyogo, 678-1297, Japan.
Hitomi SawaiDepartment of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamighori, Akoh, Hyogo, 678-1297, Japan.
Hanae TakedaRIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan.
Eiichi MizohataDepartment of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.
Ayumi YamashitaRIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan.
Yusuke KanematsuGraduate School of Information Sciences, Hiroshima City University, 3-4-1 Asa-Minami-ku, Hiroshima, 731-3194, Japan.
Yu TakanoGraduate School of Information Sciences, Hiroshima City University, 3-4-1 Asa-Minami-ku, Hiroshima, 731-3194, Japan.
Eriko NangoRIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan.
Rie TanakaRIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan.
Osamu NurekiDepartment of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.
Osami ShojiDepartment of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan.
Yuka IkemotoJapan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo, 679-5198, Japan.
Hironori MurakamiJapan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo, 679-5198, Japan.
Shigeki OwadaRIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan.
Kensuke TonoJapan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo, 679-5198, Japan.
Makina YabashiRIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan.ORCID http://orcid.org/0000-0002-2472-1684
Masaki YamamotoRIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan.
Hideo AgoRIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan.
So IwataRIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan.
Hiroshi SugimotoRIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan. sugimoto@spring8.or.jp.
Yoshitsugu ShiroRIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan. yshiro@sci.u-hyogo.ac.jp.
Minoru KuboRIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan. minoru.kubo@riken.jp.ORCID http://orcid.org/0000-0002-1470-942X

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Time-resolved serial femtosecond crystallography using an X-ray free electron laser (XFEL) in conjunction with a photosensitive caged-compound offers a crystallographic method to track enzymatic reactions. Here we demonstrate the application of this method using fungal NO reductase, a heme-containing enzyme, at room temperature. Twenty milliseconds after caged-NO photolysis, we identify a NO-bound form of the enzyme, which is an initial intermediate with a slightly bent Fe-N-O coordination geometry at a resolution of 2.1 Å. The NO geometry is compatible with those analyzed by XFEL-based cryo-crystallography and QM/MM calculations, indicating that we obtain an intact Fe

Identifiers

PMID29147002
PMCPMC5691058

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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.