The DOI matches its Crossref record; 37 of the 37 references it cites were found in a registry or an index.
The role of the conserved Lys68*:Glu265 intersubunit salt bridge in aspartate aminotransferase kinetics: Multiple forced covariant amino acid substitutions in natural variants
Open accessAbstract
The role of the Lys68*Residues pertaining to the opposite subunit. :Glu265 intersubunit salt bridge that is conserved (Csb) in all known aspartate aminotransferases (AATases), except those of animal cytosolic, Ac (His68*:Glu265), and plant mitochondrial, Pm (Met68*:Gln265), origins, was evaluated in the Escherichia coli AATase. Two double‐mutant cycles, to K68M/E265Q and the charge reversed K68E/E265K, were characterized with the context dependence (C) and impact (I) formalism, previously defined for functional chimeric analysis. Mutations of Lys68* with Glu265 fixed are generally more deleterious than the converse mutations of Glu265 with Lys68* fixed, showing that buried negative charges have greater effects than buried positive charges in this context. Replacement of the charged Lys68*:Glu265 with the K68M/E265Q neutral pair introduces relatively small effects on the kinetic parameters. The differential sensitivity of kcat/KM, L‐Asp and kcat/KM, α‐KG to salt bridge mutagenic replacements is shown by a linear‐free energy relationship, in which the logarithms of the latter second order rate constants are generally decreased by a factor of two more than are those of the former. Thus, kcat/KM, L‐Asp and kcat/KM, α‐KG are 133 and 442 mM−1 s−1 for the wild‐type (WT) enzyme, respectively, but their relative order is reversed in the more severely compromised mutants (14.8 and 5.3 mM−1 s−1 for K68E). A Venn diagram illustrates apparent forced covariances of groups of amino acids that accompany the naturally occurring salt bridge replacements in the Pm and Ac classes. The more deeply rooted tree indicates that the Csb variant was the ancestral specie.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“Before and after nitrogen upshift, AST's two substrate binding sites (one for the four carbon compounds oxaloacetate and aspartate, and the other for the five carbon compounds glutamate and α-ketoglutarate) are both saturated, largely with aspartate and glutamate (Powell and Morrison, 1978; Deu et al, 2002).”
From Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli (2009) · cites this paper as Deu et al, 2002
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
PCR protocols — A guide to methods and applications
U.G. (1990) · Trends in Biochemical Sciences · doi:10.1016/0968-0004(90)90252-7 · Cited by 11,751
Higuchi, R. (1990) · Elsevier eBooks · doi:10.1016/b978-0-12-372180-8.50026-3 · Cited by 425
A Kinetic and Equilibrium Analysis of the Glutamic Oxaloacetate Transaminase Mechanism
Velick, S. F., & Vavra, J. D. (1962) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)63406-x · Cited by 350
Double-mutant cycles: a powerful tool for analyzing protein structure and function.
Horovitz, A. (1996) · Folding & design · doi:10.1016/s1359-0278(96)00056-9 · Cited by 322
The role of compensatory neutral mutations in molecular evolution
Kimura, M. (1985) · Journal of Genetics · doi:10.1007/bf02923549 · Cited by 275
Ford, G. C., Eichele, G., & Jansonius, J. N. (1980) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.77.5.2559 · Cited by 240
Malcolm, B. A., Wilson, K. P., Matthews, B. W., Kirsch, J. F., & Wilson, A. C. (1990) · Nature · doi:10.1038/345086a0 · Cited by 226
Self-citationEFFECTS OF SITE-SPECIFIC AMINO ACID MODIFICATION ON PROTEIN INTERACTIONS AND BIOLOGICAL FUNCTION
Ackers, G. K., & Smith, F. R. (1985) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.54.070185.003121 · Cited by 226
X-ray structure refinement and comparison of three forms of mitochondrial aspartate aminotransferase
McPhalen, C. A., Vincent, M. G., & Jansonius, J. N. (1992) · Journal of Molecular Biology · doi:10.1016/0022-2836(92)90935-d · Cited by 204
Crystal Structures of Escherichia coli Aspartate Aminotransferase in Two Conformations
Jäger, J., Moser, M., Sauder, U., & Jansonius, J. N. (1994) · Journal of Molecular Biology · doi:10.1006/jmbi.1994.1368 · Cited by 188
Research works printed but not linked: 2
- Arnone A., 1985, Transaminases, 138
- 10.1021/bi980382 · DOI
Cited by
Sorted by citations
Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli
Yuan, J., Doucette, C. D., Fowler, W. U., Feng, X., Piazza, M., Rabitz, H. A., Wingreen, N. S., & Rabinowitz, J. D. (2009) · Molecular Systems Biology · doi:10.1038/msb.2009.60 · Cited by 178
Metadata
- Authors
- Deu, E., Koch, K. A., & Kirsch, J. F.
- Affiliations
- University of California, Berkeley (US)
- Triad National Security (United States) (US)
- Corresponding author
- Kirsch, Jack F.
- Venue
- Protein Science
- Publisher
- Wiley
- Published
- 2002-05
- Volume
- 11
- Issue
- 5
- Pages
- 1062-1073
- ISSN
- 0961-8368 (ISSN-L)
- 1469-896X
- PMC
- PMC2373551
- OpenAlex
- W2034621068
- Cited by
- 15
- References
- 37
- Citations by year
- 2021: 1 · 2019: 1 · 2016: 1 · 2013: 3
- FWCI
- 0.32
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Protein Science (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health
- National Institute of General Medical Sciences (GM35393, F32GM020585, R01GM035393, GM 20585)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biochemistry › Amino Acid Enzymes and Metabolism
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Keywords
- aspartate aminotransferase, enzyme kinetics, double mutant cycles, context sensitivity, linear free energy relationships, natural variants, Escherichia coli enzyme, ancestral state reconstruction
- MeSH terms
- Amino Acid Sequence, Aspartate Aminotransferases, Kinetics, Models, Biological, Molecular Sequence Data, Phylogeny, Substrate Specificity, Sequence Alignment, Amino Acid Substitution, Protein Structure, Quaternary
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
