Evidence map›Paper›PMID 27406907›Full record

ArticleThe Journal of antibiotics2016

Crystal structure of SgcJ, an NTF2-like superfamily protein involved in biosynthesis of the nine-membered enediyne antitumor antibiotic C-1027.

Tingting Huang, Chin-Yuan Chang, Jeremy R Lohman, Jeffrey D Rudolf, Youngchang Kim, Changsoo Chang, Dong Yang, Ming Ma, Xiaohui Yan, Ivana Crnovcic and 8 more

Open access · bronzeAbstract read
In one paragraph

Article in The Journal of antibiotics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.

0numbers the graph read from it
0cells of the map it votes in
8citing papers in PubMed
0.3field-weighted citation impact, top 29% 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

8 citing papers in PubMed, 13 citations in OpenAlex.

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  6. Structural characterization of DynU16, a START/Bet v1-like protein involved in dynemicin biosynthesis.Acta crystallographica. Section F, Structural biology communications · 2021
    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

18 authors at 5 institutions in 1 country.

Tingting HuangDepartment of Chemistry, The Scripps Research Institute, Jupiter, FL, USA.
Chin-Yuan ChangDepartment of Chemistry, The Scripps Research Institute, Jupiter, FL, USA.
Jeremy R LohmanDepartment of Chemistry, The Scripps Research Institute, Jupiter, FL, USA.
Jeffrey D RudolfDepartment of Chemistry, The Scripps Research Institute, Jupiter, FL, USA.
Youngchang KimCenter for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL USA.
Changsoo ChangStructural Biology Center, Argonne National Laboratory, Argonne, IL, USA.
Dong YangDepartment of Chemistry, The Scripps Research Institute, Jupiter, FL, USA.
Ming MaDepartment of Chemistry, The Scripps Research Institute, Jupiter, FL, USA.
Xiaohui YanDepartment of Chemistry, The Scripps Research Institute, Jupiter, FL, USA.
Ivana CrnovcicDepartment of Chemistry, The Scripps Research Institute, Jupiter, FL, USA.
Lance BigelowMidwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL, USA.
Shonda ClancyMidwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL, USA.
Craig A BingmanDepartment of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
Ragothaman M YennamalliBioSciences at Rice and Department of Chemistry, Rice University, Houston, TX, USA.
Gyorgy BabniggCenter for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL USA.
Andrzej JoachimiakCenter for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL USA.
George N PhillipsBioSciences at Rice and Department of Chemistry, Rice University, Houston, TX, USA.
Ben ShenDepartment of Chemistry, The Scripps Research Institute, Jupiter, FL, USA.
Scripps Research Institute · USArgonne National Laboratory · USRice University · USUniversity of Chicago · USUniversity of Wisconsin–Madison · US

Funding

Midwest Center for Structural GenomicsU54GM094585 · NIGMS · UNIVERSITY OF CHICAGO · PI MINOR, WLADEK · 2010 to 2014
$33.7M
Enediyne Biosynthesis and EngineeringR01CA078747 · NCI · UNIVERSITY OF WISCONSIN-MADISON · PI SHEN, BEN · 1999 to 2015
$3.4M
Enzyme Discovery for Natural Product BiosynthesisU01GM098248 · NIGMS · UNIVERSITY OF WISCONSIN-MADISON · PI PHILLIPS, GEORGE NEAL · 2011 to 2015
$2.8M
Genome Mining for Enediyne Natural Products from ActinomycetalsR01GM115575 · NIGMS · SCRIPPS FLORIDA · PI SHEN, BEN · 2016 to 2019
$1.9M
Rigidity and flexibility of large bio-molecular assembliesR01GM109456 · NIGMS · SMITH COLLEGE · PI STREINU, ILEANA · 2013 to 2017
$1.4M
NCI NIH HHS R01 CA078747NIGMS NIH HHS R01 GM109456NIGMS NIH HHS R01 GM115575NIGMS NIH HHS U01 GM098248NIGMS NIH HHS U54 GM094585
6 · The paper itself

Abstract

Comparative analysis of the enediyne biosynthetic gene clusters revealed sets of conserved genes serving as outstanding candidates for the enediyne core. Here we report the crystal structures of SgcJ and its homologue NCS-Orf16, together with gene inactivation and site-directed mutagenesis studies, to gain insight into enediyne core biosynthesis. Gene inactivation in vivo establishes that SgcJ is required for C-1027 production in Streptomyces globisporus. SgcJ and NCS-Orf16 share a common structure with the nuclear transport factor 2-like superfamily of proteins, featuring a putative substrate binding or catalytic active site. Site-directed mutagenesis of the conserved residues lining this site allowed us to propose that SgcJ and its homologues may play a catalytic role in transforming the linear polyene intermediate, along with other enediyne polyketide synthase-associated enzymes, into an enzyme-sequestered enediyne core intermediate. These findings will help formulate hypotheses and design experiments to ascertain the function of SgcJ and its homologues in nine-membered enediyne core biosynthesis.

Indexed as

Amino Acid SequenceAminoglycosidesAntibiotics, AntineoplasticBacterial ProteinsDNA, BacterialEnediynesPolyenesPolyketide SynthasesProtein Structure, TertiaryStreptomycesAminoglycosidesAntibiotics, AntineoplasticBacterial ProteinsC 1027DNA, BacterialEnediynesPolyenesPolyketide Synthases

Identifiers

PMID27406907
PMCPMC5083130
OpenAlexW2472599504

What OpenQuestion holds

Textmetadata
LicenceTDM
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.