Evidence map›Paper›PMID 26134419›Full record

ArticleNature communications2015

Mechanistic insights into metal ion activation and operator recognition by the ferric uptake regulator.

Zengqin Deng, Qing Wang, Zhao Liu, Manfeng Zhang, Ana Carolina Dantas Machado, Tsu-Pei Chiu, Chong Feng, Qi Zhang, Lin Yu, Lei Qi and 9 more

Open access · goldAbstract read
In one paragraph

Article in Nature communications, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers.

0numbers the graph read from it
0cells of the map it votes in
76citing papers in PubMed
5.4field-weighted citation impact, top 3% 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

76 citing papers in PubMed, 112 citations in OpenAlex.

  1. Article
  2. Review
  3. Two ferric uptake regulator proteins inApplied and environmental microbiology · 2026
    Article
  4. Review
  5. Article
  6. Article
  7. Article
  8. Article
  9. Article
  10. Article
  11. Review
  12. Characterization of the ferric uptake regulatorApplied and environmental microbiology · 2024
    Article
  13. Article
  14. Review
  15. Article
  16. Article
  17. Review
  18. Article
  19. Review
  20. Article

16 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

19 authors at 4 institutions in 2 countries.

Zengqin DengState Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China.
Qing WangState Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China.
Zhao LiuExperimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China.
Manfeng ZhangState Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China.
Ana Carolina Dantas MachadoMolecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, California 90089, USA.
Tsu-Pei ChiuMolecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, California 90089, USA.
Chong FengState Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China.
Qi ZhangState Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China.
Lin YuState Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China.
Lei QiState Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China.
Jiangge ZhengState Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China.
Xu WangState Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China.
XinMei HuoInstitute of Apicultural Research, Key Laboratory of Pollinating Insect Biology, Chinese Academy of Agricultural Science, Beijing 100093, China.
Xiaoxuan QiState Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China.
Xiaorong LiState Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China.
Wei WuState Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China.
Remo RohsMolecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, California 90089, USA.
Ying LiState Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China.
Zhongzhou ChenState Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China.
China Agricultural University · CNUniversity of Southern California · USChinese Academy of Agricultural Sciences · CNChinese Academy of Medical Sciences & Peking Union Medical College · CN

Funding

Multi-scale modeling of genetic variation in a developmental networkU01GM103804 · NIGMS · UNIVERSITY OF SOUTHERN CALIFORNIA · PI DEPACE, ANGELA H, MARJORAM, PAUL · 2013 to 2016
$2.0M
Genome analysis based on the integration of DNA sequence and shapeR01GM106056 · NIGMS · UNIVERSITY OF SOUTHERN CALIFORNIA · PI ROHS, REMO · 2014 to 2017
$1.3M
NIGMS NIH HHS R01 GM106056NIGMS NIH HHS R01GM106056NIGMS NIH HHS U01 GM103804NIGMS NIH HHS U01GM103804
6 · The paper itself

Abstract

Ferric uptake regulator (Fur) plays a key role in the iron homeostasis of prokaryotes, such as bacterial pathogens, but the molecular mechanisms and structural basis of Fur-DNA binding remain incompletely understood. Here, we report high-resolution structures of Magnetospirillum gryphiswaldense MSR-1 Fur in four different states: apo-Fur, holo-Fur, the Fur-feoAB1 operator complex and the Fur-Pseudomonas aeruginosa Fur box complex. Apo-Fur is a transition metal ion-independent dimer whose binding induces profound conformational changes and confers DNA-binding ability. Structural characterization, mutagenesis, biochemistry and in vivo data reveal that Fur recognizes DNA by using a combination of base readout through direct contacts in the major groove and shape readout through recognition of the minor-groove electrostatic potential by lysine. The resulting conformational plasticity enables Fur binding to diverse substrates. Our results provide insights into metal ion activation and substrate recognition by Fur that suggest pathways to engineer magnetotactic bacteria and antipathogenic drugs.

Indexed as

Operator Regions, GeneticBacterial ProteinsCation Transport ProteinsCircular DichroismCrystallizationDNA-Binding ProteinsIronMagnetospirillumMicroscopy, Electron, TransmissionProtein ConformationPseudomonas aeruginosaReal-Time Polymerase Chain ReactionRepressor ProteinsSpectrum AnalysisBacterial ProteinsCation Transport ProteinsDNA-Binding Proteinsferric uptake regulating proteins, bacterialIronRepressor Proteins

Identifiers

PMID26134419
PMCPMC4506495
OpenAlexW2217928045

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.