Evidence map›Paper›PMID 34645869›Full record

ArticleScientific reports2021

Functional and structural analysis of catabolite control protein C that responds to citrate.

Wei Liu, Jinli Chen, Liming Jin, Zi-Yong Liu, Ming Lu, Ge Jiang, Qing Yang, Chunshan Quan, Ki Hyun Nam, Yongbin Xu

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Scientific reports, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
0.3field-weighted citation impact, top 50% 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

3 citing papers in PubMed, 4 citations in OpenAlex.

  1. Engineering theACS synthetic biology · 2026
    Article
  2. Regulation of tricarboxylate transport and metabolism inApplied and environmental microbiology · 2024
    Article
  3. Article
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

10 authors at 5 institutions in 2 countries.

Wei Liu *Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China.
Jinli Chen *School of Life Science and Biotechnology, Dalian University of Technology, No. 2 Linggong Road, Dalian, 116024, Liaoning, China.
Liming JinDepartment of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China.
Zi-Yong LiuShandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuel, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China.
Ming LuShandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuel, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China.
Ge JiangSchool of Life Science and Biotechnology, Dalian University, Dalian, 116622, Liaoning, China.
Qing YangSchool of Life Science and Biotechnology, Dalian University of Technology, No. 2 Linggong Road, Dalian, 116024, Liaoning, China.
Chunshan QuanDepartment of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China. mikyeken@dlnu.edu.cn.
Ki Hyun NamDepartment of Life Science, Pohang University of Science and Technology, Pohang, 35398, Republic of Korea. structures@postech.ac.kr.
Yongbin XuDepartment of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China. yongbinxu@dlnu.edu.cn.
Dalian Minzu University · CNDalian University of Technology · CNQingdao Institute of Bioenergy and Bioprocess Technology · CNDalian University · CNPohang University of Science and Technology · KR

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Catabolite control protein C (CcpC) belongs to the LysR-type transcriptional regulator (LTTR) family, which regulates the transcription of genes encoding the tricarboxylic acid branch enzymes of the TCA cycle by responding to a pathway-specific metabolite, citrate. The biological function of CcpC has been characterized several times, but the structural basis for the molecular function of CcpC remains elusive. Here, we report the characterization of a full-length CcpC from Bacillus amyloliquefaciens (BaCcpC-FL) and a crystal structure of the C-terminal inducer-binding domain (IBD) complexed with citrate. BaCcpC required both dyad symmetric regions I and II to recognize the citB promoter, and the presence of citrate reduced citB promoter binding. The crystal structure of CcpC-IBD shows two subdomains, IBD-I and IBD-II, and a citrate molecule buried between them. Ile100, two arginines (Arg147 and Arg260), and three serines (Ser129, Ser189, and Ser191) exhibit strong hydrogen-bond interactions with citrate molecules. A structural comparison of BaCcpC-IBD with its homologues showed that they share the same tail-to-tail dimer alignment, but the dimeric interface and the rotation between these molecules exhibit significant differences. Taken together, our results provide a framework for understanding the mechanism underlying the functional divergence of the CcpC protein.

Indexed as

Gene Expression Regulation, BacterialAconitate HydrataseArginineBacillus amyloliquefaciensBacillus subtilisBacterial ProteinsCitratesCitric AcidCitric Acid CycleCrystallography, X-RayCyclic AMP Receptor ProteinDimerizationDNA-Binding ProteinsHydrogen BondingMolecular Dynamics SimulationPromoter Regions, GeneticAconitate HydrataseArginineBacterial ProteinsCitratesCitric AcidCyclic AMP Receptor ProteinDNA-Binding ProteinsRepressor Proteins

Identifiers

PMID34645869
PMCPMC8514465
OpenAlexW3205273392

What OpenQuestion holds

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LicenceCC BY
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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.