Evidence map›Paper›PMID 12837785›Full record

ArticleJournal of bacteriology2003

Structure of a coenzyme A pyrophosphatase from Deinococcus radiodurans: a member of the Nudix family.

Lin-Woo Kang, Sandra B Gabelli, Mario A Bianchet, Wen Lian Xu, Maurice J Bessman, L Mario Amzel

Open access · greenAbstract read
In one paragraph

Article in Journal of bacteriology, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.

0numbers the graph read from it
0cells of the map it votes in
18citing papers in PubMed
1.0field-weighted citation impact, top 25% 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

18 citing papers in PubMed, 36 citations in OpenAlex.

  1. Article
  2. Article
  3. Review
  4. A cryptic activity in the Nudix hydrolase superfamily.Protein science : a publication of the Protein Society · 2019
    Article
  5. Article
  6. Article
  7. Article
  8. Article
  9. Article
  10. Article
  11. Structure of an N-terminally truncated Nudix hydrolase DR2204 from Deinococcus radiodurans.Acta crystallographica. Section F, Structural biology and crystallization communications · 2009
    Article
  12. Article
  13. Four enzymes define the incorporation of coenzyme A in thienamycin biosynthesis.Proceedings of the National Academy of Sciences of the United States of America · 2008
    Article
  14. Article
  15. Article
  16. Overexpression, crystallization and preliminary X-ray crystallographic analysis of Nudix hydrolase Orf141 from Escherichia coli K-1.Acta crystallographica. Section F, Structural biology and crystallization communications · 2007
    Article
  17. Article
  18. 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

6 authors at 2 institutions in 1 country.

Lin-Woo KangDepartment of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.
Sandra B Gabelli
Mario A Bianchet
Wen Lian Xu
Maurice J Bessman
L Mario Amzel
Johns Hopkins University · USJohns Hopkins Medicine · US

Funding

ENZYMATIC SYNTHESIS OF NUCLEOTIDES AND DNAR01GM018649 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI BESSMAN, MAURICE J · 1985 to 2006
$2.3M
STRUCTURE OF ANTIBODY COMPLEXES WITH BIOACTIVE PEPTIDESP01GM051362 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI BERG, JEREMY M. · 1996 to 2000
$1.2M
Structure, Function and Mechanism of Nudix HydrolasesR01GM066895 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI AMZEL, L. MARIO · 2003 to 2006
$1.1M
COMPACT STRUCTURE IN A DENATURED PROTEINF32GM018649 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI SINCLAIR, JAMES F · 1997 to 1998
–
NIGMS NIH HHS F32 GM018649NIGMS NIH HHS GM18649NIGMS NIH HHS GM51362NIGMS NIH HHS GM66895NIGMS NIH HHS R01 GM018649NIGMS NIH HHS R01 GM066895
6 · The paper itself

Abstract

Gene Dr1184 from Deinococcus radiodurans codes for a Nudix enzyme (DR-CoAse) that hydrolyzes the pyrophosphate moiety of coenzyme A (CoA). Nudix enzymes with the same specificity have been found in yeast, humans, and mice. The three-dimensional structure of DR-CoAse, the first of a Nudix hydrolase with this specificity, reveals that this enzyme contains, in addition to the fold observed in other Nudix enzymes, insertions that are characteristic of a CoA-hydrolyzing Nudix subfamily. The structure of the complex of the enzyme with Mg(2+), its activating cation, reveals the position of the catalytic site. A helix, part of the N-terminal insertion, partially occludes the binding site and has to change its position to permit substrate binding. Comparison of the structure of DR-CoAse to those of other Nudix enzymes, together with the location in the structure of the sequence characteristic of CoAses, suggests a mode of binding of the substrate to the enzyme that is compatible with all available data.

Indexed as

Amino Acid SequenceBinding SitesCations, DivalentCoenzyme ACrystallography, X-RayDeinococcusHumansModels, MolecularMolecular Sequence DataProtein ConformationProtein FoldingPyrophosphatasesSequence AlignmentSubstrate SpecificityCations, DivalentCoenzyme APyrophosphatases

Identifiers

PMID12837785
PMCPMC164880
OpenAlexW2157882710

What OpenQuestion holds

Textmetadata
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.