Evidence map›Paper›PMID 26056269›Full record

ArticleProceedings of the National Academy of Sciences of the United States of America2015

Structural basis of a Ni acquisition cycle for [NiFe] hydrogenase by Ni-metallochaperone HypA and its enhancer.

Satoshi Watanabe, Takumi Kawashima, Yuichi Nishitani, Tamotsu Kanai, Takehiko Wada, Kenji Inaba, Haruyuki Atomi, Tadayuki Imanaka, Kunio Miki

Open access · bronzeAbstract read
In one paragraph

Article in Proceedings of the National Academy of Sciences of the United States of America, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.

0numbers the graph read from it
0cells of the map it votes in
27citing papers in PubMed
2.6field-weighted citation impact, top 10% 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

27 citing papers in PubMed, 58 citations in OpenAlex.

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  9. The requirement for cobalt in vitamin BBiochimica et biophysica acta. Molecular cell research · 2021
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  10. Article
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  12. Bimodal Nickel-Binding Site onInorganic chemistry · 2019
    Article
  13. Article
  14. Article
  15. Structure and dynamics of Helicobacter pylori nickel-chaperone HypA: an integrated approach using NMR spectroscopy, functional assays and computational tools.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2018
    Article
  16. Crystal structures of a [NiFe] hydrogenase large subunit HyhL in an immature state in complex with a Ni chaperone HypA.Proceedings of the National Academy of Sciences of the United States of America · 2018
    Article
  17. 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

9 authors at 3 institutions in 1 country.

Satoshi WatanabeDepartment of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan; Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan;
Takumi KawashimaDepartment of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan;
Yuichi NishitaniDepartment of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan;
Tamotsu KanaiDepartment of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan; Japan Science and Technology Agency, CREST, 7, Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan;
Takehiko WadaInstitute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan;
Kenji InabaInstitute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan;
Haruyuki AtomiDepartment of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan; Japan Science and Technology Agency, CREST, 7, Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan;
Tadayuki ImanakaJapan Science and Technology Agency, CREST, 7, Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan; Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu 525-8577, Japan.
Kunio MikiDepartment of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan; miki@kuchem.kyoto-u.ac.jp.
Kyoto University · JPJapan Science and Technology Agency · JPTohoku University · JP

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The Ni atom at the catalytic center of [NiFe] hydrogenases is incorporated by a Ni-metallochaperone, HypA, and a GTPase/ATPase, HypB. We report the crystal structures of the transient complex formed between HypA and ATPase-type HypB (HypBAT) with Ni ions. Transient association between HypA and HypBAT is controlled by the ATP hydrolysis cycle of HypBAT, which is accelerated by HypA. Only the ATP-bound form of HypBAT can interact with HypA and induces drastic conformational changes of HypA. Consequently, upon complex formation, a conserved His residue of HypA comes close to the N-terminal conserved motif of HypA and forms a Ni-binding site, to which a Ni ion is bound with a nearly square-planar geometry. The Ni binding site in the HypABAT complex has a nanomolar affinity (Kd = 7 nM), which is in contrast to the micromolar affinity (Kd = 4 µM) observed with the isolated HypA. The ATP hydrolysis and Ni binding cause conformational changes of HypBAT, affecting its association with HypA. These findings indicate that HypA and HypBAT constitute an ATP-dependent Ni acquisition cycle for [NiFe]-hydrogenase maturation, wherein HypBAT functions as a metallochaperone enhancer and considerably increases the Ni-binding affinity of HypA.

Indexed as

Adenosine TriphosphateBinding SitesCarrier ProteinsCrystallography, X-RayEscherichia coli ProteinsHydrogenaseHydrolysisIntracellular Signaling Peptides and ProteinsModels, MolecularNickelProtein ConformationAdenosine TriphosphateCarrier ProteinsEscherichia coli ProteinsHydrogenaseHypA protein, E coliIntracellular Signaling Peptides and ProteinsNickelnickel-iron hydrogenasemetallochaperonemetalloproteintransient complexX-ray crystallography

Identifiers

PMID26056269
PMCPMC4485131
OpenAlexW1928485567

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.