Evidence map›Paper›PMID 20400946›Full record

ArticleNature2010

X-ray crystal structure of the light-independent protochlorophyllide reductase.

Norifumi Muraki, Jiro Nomata, Kozue Ebata, Tadashi Mizoguchi, Tomoo Shiba, Hitoshi Tamiaki, Genji Kurisu, Yuichi Fujita

Abstract read
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Article in Nature, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers.

0numbers the graph read from it
0cells of the map it votes in
79citing papers in PubMed
8.5field-weighted citation impact, top 2% 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

79 citing papers in PubMed, 194 citations in OpenAlex.

  1. Article
  2. Review
  3. Article
  4. Review
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  6. Article
  7. Article
  8. Review
  9. Article
  10. Proteomic strategies to interrogate the Fe-S proteome.Biochimica et biophysica acta. Molecular cell research · 2024
    Review
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  14. Plastid Genome Evolution of Two Colony-Forming BenthicInternational journal of molecular sciences · 2023
    Article
  15. Transcriptomic and photosynthetic analyses ofFrontiers in plant science · 2023
    Article
  16. Review
  17. Proton-coupled electron transfer of macrocyclic ring hydrogenation: The chlorinphlorin.Proceedings of the National Academy of Sciences of the United States of America · 2022
    Article
  18. Article
  19. Article
  20. Article

19 more citing papers are in PubMed but not listed here.

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

8 authors at 5 institutions in 1 country.

Norifumi MurakiDepartment of Life Sciences, University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan.
Jiro Nomata
Kozue Ebata
Tadashi Mizoguchi
Tomoo Shiba
Hitoshi Tamiaki
Genji Kurisu
Yuichi Fujita
Nagoya University · JPRitsumeikan University · JPThe University of Tokyo · JPJapan Science and Technology Agency · JPProtein Research Foundation · JP

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Photosynthetic organisms adopt two different strategies for the reduction of the C17 = C18 double bond of protochlorophyllide (Pchlide) to form chlorophyllide a, the direct precursor of chlorophyll a (refs 1-4). The first involves the activity of the light-dependent Pchlide oxidoreductase, and the second involves the light-independent (dark-operative) Pchlide oxidoreductase (DPOR). DPOR is a nitrogenase-like enzyme consisting of two components, L-protein (a BchL dimer) and NB-protein (a BchN-BchB heterotetramer), which are structurally related to nitrogenase Fe protein and MoFe protein, respectively. Here we report the crystal structure of the NB-protein of DPOR from Rhodobacter capsulatus at a resolution of 2.3A. As expected, the overall structure is similar to that of nitrogenase MoFe protein: each catalytic BchN-BchB unit contains one Pchlide and one iron-sulphur cluster (NB-cluster) coordinated uniquely by one aspartate and three cysteines. Unique aspartate ligation is not necessarily needed for the cluster assembly but is essential for the catalytic activity. Specific Pchlide-binding accompanies the partial unwinding of an alpha-helix that belongs to the next catalytic BchN-BchB unit. We propose a unique trans-specific reduction mechanism in which the distorted C17-propionate of Pchlide and an aspartate from BchB serve as proton donors for C18 and C17 of Pchlide, respectively. Intriguingly, the spatial arrangement of the NB-cluster and Pchlide is almost identical to that of the P-cluster and FeMo-cofactor in nitrogenase MoFe-protein, illustrating that a common architecture exists to reduce chemically stable multibonds of porphyrin and dinitrogen.

Indexed as

Models, MolecularCrystallography, X-RayOxidoreductases Acting on CH-CH Group DonorsProtein Structure, TertiaryRhodobacter capsulatusOxidoreductases Acting on CH-CH Group Donorsprotochlorophyllide reductase

Identifiers

PMID20400946
OpenAlexW1991325941

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

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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.