Evidence map›Paper›PMID 25363770›Full record

ArticleNature2015

Structure and mechanism of the tRNA-dependent lantibiotic dehydratase NisB.

Manuel A Ortega, Yue Hao, Qi Zhang, Mark C Walker, Wilfred A van der Donk, Satish K Nair

Open access · greenAbstract read
In one paragraph

Article in Nature, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 172 papers.

0numbers the graph read from it
0cells of the map it votes in
172citing papers in PubMed
13.4field-weighted citation impact, top 1% 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

172 citing papers in PubMed, 318 citations in OpenAlex.

  1. Leveraging latent space models for enzyme discovery and sampling.Proceedings of the National Academy of Sciences of the United States of America · 2026
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  15. Review
  16. Biosynthesis of Macrocyclic Peptides by Formation and Crosslinking ofbioRxiv : the preprint server for biology · 2025
    Article
  17. Substrate recognition by a peptide-aminoacyl-tRNA ligase.Proceedings of the National Academy of Sciences of the United States of America · 2025
    Article
  18. Article
  19. Article
  20. Article

112 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

6 authors at 1 institution in 1 country.

Manuel A OrtegaDepartment of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.
Yue HaoDepartment of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.
Qi ZhangDepartment of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.
Mark C WalkerDepartment of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.
Wilfred A van der Donk1] Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA [2] Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.
Satish K Nair1] Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA [2] Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.
University of Illinois Urbana-Champaign · US

Funding

Training Program in Chemistry-Interface with BiologyT32GM070421 · NIGMS · UNIVERSITY OF ILLINOIS URBANA-CHAMPAIGN · PI HERGENROTHER, PAUL · 2005 to 2019
$5.4M
Posttranslational Modifications in Natural Product BiosynthesisR01GM058822 · NIGMS · UNIVERSITY OF ILLINOIS URBANA-CHAMPAIGN · PI VAN DER DONK, WILFRED A. · 1999 to 2015
$3.8M
Structural /Mechanistic Study of Lantibiotic Biosynthetic Enzymes & AutoimmunityR01GM079038 · NIGMS · UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN · PI NAIR, SATISH K · 2006 to 2023
$3.7M
4800 Plus MALDI TOF/TOF AnalyzerS10RR027109 · NCRR · UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN · PI VAN DER DONK, WILFRED A. · 2010 to 2010
$395k
Targeting protein-protein interactions through directed evolution of lanthipeptidF32GM112284 · NIGMS · UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN · PI WALKER, MARK CHALFANT · 2014 to 2016
$164k
NCRR NIH HHS S10 RR027109NCRR NIH HHS S10 RR027109 ANIGMS NIH HHS 5T32-GM070421NIGMS NIH HHS F32 GM112284NIGMS NIH HHS R01 GM 058822NIGMS NIH HHS R01 GM058822NIGMS NIH HHS R01 GM079038NIGMS NIH HHS T32 GM070421
6 · The paper itself

Abstract

Lantibiotics are a class of peptide antibiotics that contain one or more thioether bonds. The lantibiotic nisin is an antimicrobial peptide that is widely used as a food preservative to combat food-borne pathogens. Nisin contains dehydroalanine and dehydrobutyrine residues that are formed by the dehydration of Ser/Thr by the lantibiotic dehydratase NisB (ref. 2). Recent biochemical studies revealed that NisB glutamylates Ser/Thr side chains as part of the dehydration process. However, the molecular mechanism by which NisB uses glutamate to catalyse dehydration remains unresolved. Here we show that this process involves glutamyl-tRNA(Glu) to activate Ser/Thr residues. In addition, the 2.9-Å crystal structure of NisB in complex with its substrate peptide NisA reveals the presence of two separate domains that catalyse the Ser/Thr glutamylation and glutamate elimination steps. The co-crystal structure also provides insights into substrate recognition by lantibiotic dehydratases. Our findings demonstrate an unexpected role for aminoacyl-tRNA in the formation of dehydroamino acids in lantibiotics, and serve as a basis for the functional characterization of the many lantibiotic-like dehydratases involved in the biosynthesis of other classes of natural products.

Indexed as

Bacterial ProteinsBacteriocinsCrystallography, X-RayEscherichia coliGlutamic AcidHydro-LyasesLactococcus lactisMembrane ProteinsModels, MolecularNisinPhylogenyProtein Structure, TertiaryRNA, Transfer, GluSerineThreonineBacterial ProteinsBacteriocinsGlutamic AcidHydro-LyasesMembrane ProteinsNisB protein, Lactococcus lactisNisinRNA, Transfer, GluSerineThreonine

Identifiers

PMID25363770
PMCPMC4430201
OpenAlexW2070424221

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.