Evidence map›Paper›PMID 33839679›Full record

ArticleThe Journal of biological chemistry

Crystal structure of higher plant heme oxygenase-1 and its mechanism of interaction with ferredoxin.

Rei Tohda, Hideaki Tanaka, Risa Mutoh, Xuhong Zhang, Young-Ho Lee, Tsuyoshi Konuma, Takahisa Ikegami, Catharina T Migita, Genji Kurisu

Open access · hybridAbstract read
In one paragraph

Article in The Journal of biological chemistry. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing papers in PubMed
0.6field-weighted citation impact, top 34% 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

6 citing papers in PubMed, 17 citations in OpenAlex.

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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

9 authors at 5 institutions in 2 countries.

Rei TohdaInstitute for Protein Research, Osaka University, Suita, Osaka, Japan; Department of Macromolecular Science, Osaka University, Toyonaka, Osaka, Japan.
Hideaki TanakaInstitute for Protein Research, Osaka University, Suita, Osaka, Japan; Department of Macromolecular Science, Osaka University, Toyonaka, Osaka, Japan.
Risa MutohInstitute for Protein Research, Osaka University, Suita, Osaka, Japan.
Xuhong ZhangGraduate School of Medical Science, Yamagata University, Yamagata, Yamagata, Japan.
Young-Ho LeeResearch Center of Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, Chungbuk, South Korea; Graduate School of Analytical Science and Technology, Chungnam National University, Yuseong-gu, Daejeon, South Korea; Research Headquarters, Korea Brain Research Institute, Dong-gu, Daegu, South Korea; Bio-Analytical Science, University of Science and Technology, Yuseong-gu, Daejeon, South Korea.
Tsuyoshi KonumaGraduate School of Medical Life Science, Yokohama City University, Tsurumi-ku, Yokohama, Japan.
Takahisa IkegamiGraduate School of Medical Life Science, Yokohama City University, Tsurumi-ku, Yokohama, Japan.
Catharina T MigitaDepartment of Biological Chemistry, Yamaguchi University, Yoshida, Yamaguchi, Japan.
Genji KurisuInstitute for Protein Research, Osaka University, Suita, Osaka, Japan; Department of Macromolecular Science, Osaka University, Toyonaka, Osaka, Japan. Electronic address: gkurisu@protein.osaka-u.ac.jp.
Protein Research Foundation · JPYokohama City University · JPChungnam National University · KRYamagata University · JPYamaguchi University · JP

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Heme oxygenase (HO) converts heme to carbon monoxide, biliverdin, and free iron, products that are essential in cellular redox signaling and iron recycling. In higher plants, HO is also involved in the biosynthesis of photoreceptor pigment precursors. Despite many common enzymatic reactions, the amino acid sequence identity between plant-type and other HOs is exceptionally low (∼19.5%), and amino acids that are catalytically important in mammalian HO are not conserved in plant-type HOs. Structural characterization of plant-type HO is limited to spectroscopic characterization by electron spin resonance, and it remains unclear how the structure of plant-type HO differs from that of other HOs. Here, we have solved the crystal structure of Glycine max (soybean) HO-1 (GmHO-1) at a resolution of 1.06 Å and carried out the isothermal titration calorimetry measurements and NMR spectroscopic studies of its interaction with ferredoxin, the plant-specific electron donor. The high-resolution X-ray structure of GmHO-1 reveals several novel structural components: an additional irregularly structured region, a new water tunnel from the active site to the surface, and a hydrogen-bonding network unique to plant-type HOs. Structurally important features in other HOs, such as His ligation to the bound heme, are conserved in GmHO-1. Based on combined data from X-ray crystallography, isothermal titration calorimetry, and NMR measurements, we propose the evolutionary fine-tuning of plant-type HOs for ferredoxin dependency in order to allow adaptation to dynamic pH changes on the stroma side of the thylakoid membrane in chloroplast without losing enzymatic activity under conditions of fluctuating light.

Indexed as

Amino Acid SequenceBiliverdineCarbon MonoxideCatalytic DomainChloroplastsCloning, MolecularCrystallography, X-RayEscherichia coliFerredoxinsGene ExpressionGenetic VectorsGlycine maxHemeHeme Oxygenase-1Hydrogen BondingIronBiliverdineCarbon MonoxideFerredoxinsHemeHeme Oxygenase-1IronPlant ProteinsRecombinant Proteinsheme oxygenaseITCNMR spectroscopystructural biologyX-ray crystallography

Identifiers

PMID33839679
PMCPMC7948506
OpenAlexW3118021397

What OpenQuestion holds

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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.