Crystal structure of binary and ternary complexes of serine hydroxymethyltransferase from Bacillus stearothermophilus: insights into the catalytic mechanism.
Vishal Trivedi,Amrita Gupta,Venkatakrishna R. Jala,P. Saravanan,G.S. Jagannatha Rao,N. Appaji Rao,Handanahal S. Savithri,Hosahalli Subramanya +7 more
TLDR
In this paper, the first structure of the serine-bound form of SHMT has been presented, which allows identification of residues involved in serine binding and catalysis and provides evidence for a direct displacement mechanism for the hydroxymethyl transfer rather than a retroaldol cleavage.About:
This article is published in Journal of Biological Chemistry.The article was published on 2002-05-10 and is currently open access. It has received 72 citations till now. The article focuses on the topics: Serine hydroxymethyltransferase & Serine binding.read more
Citations
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Book ChapterDOI
Folate-mediated one-carbon metabolism.
TL;DR: This chapter focuses on the current understanding of mammalian folate-mediated one-carbon metabolism, its cellular compartmentation, and knowledge gaps that limit the understanding of one- carbon metabolism and its regulation.
Journal ArticleDOI
Gut microbiota role in dietary protein metabolism and health-related outcomes: The two sides of the coin
Kevin J. Portune,Martin Beaumont,Anne-Marie Davila,Daniel Tomé,François Blachier,Yolanda Sanz +5 more
TL;DR: An up-to-date description of the dominant pathways/genes involved in amino acid metabolism in gut bacteria are provided, and an inventory of metabolic intermediates derived from bacterial protein fermentation that may affect human health are provided.
Journal ArticleDOI
Serine hydroxymethyltransferase revisited.
TL;DR: Molecular modeling revealed how a variety of substrates could be accommodated in the folate-independent cleavage of 3-hydroxyamino acids and shed light on the mechanism of this reaction.
Journal ArticleDOI
Structure-function relationship in serine hydroxymethyltransferase.
TL;DR: The mutational analysis of scSHMT along with the structure of recombinant Bacillus stearothermophilus SHMT and its substrate(s) complexes was used to provide evidence for a direct transfer mechanism rather than retro-aldol cleavage for the reaction catalyzed by SHMT.
Journal ArticleDOI
How pyridoxal 5'-phosphate differentially regulates human cytosolic and mitochondrial serine hydroxymethyltransferase oligomeric state.
Giorgio Giardina,Paolo Brunotti,Alessio Fiascarelli,Alessandra Cicalini,Mauricio G. S. Costa,Ashley M. Buckle,Martino L. di Salvo,Alessandra Giorgi,Marina Marani,Alessio Paone,Serena Rinaldo,Alessandro Paiardini,Roberto Contestabile,Francesca Cutruzzolà +13 more
TL;DR: An unexpected structural difference is indicated between the two human SHMT isoforms, which opens new perspectives for understanding their differing behaviours, roles or regulation mechanisms in response to PLP availability in vivo.
References
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Journal ArticleDOI
Clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
TL;DR: The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved and modifications are incorporated into a new program, CLUSTAL W, which is freely available.
Book ChapterDOI
Processing of X-ray diffraction data collected in oscillation mode
Zbyszek Otwinowski,Wladek Minor +1 more
TL;DR: The methods presented in the chapter have been applied to solve a large variety of problems, from inorganic molecules with 5 A unit cell to rotavirus of 700 A diameters crystallized in 700 × 1000 × 1400 A cell.
Journal ArticleDOI
PROCHECK: a program to check the stereochemical quality of protein structures
TL;DR: The PROCHECK suite of programs as mentioned in this paper provides a detailed check on the stereochemistry of a protein structure and provides an assessment of the overall quality of the structure as compared with well refined structures of the same resolution.
Journal ArticleDOI
The CCP4 suite: programs for protein crystallography
TL;DR: The CCP4 (Collaborative Computational Project, number 4) program suite is a collection of programs and associated data and subroutine libraries which can be used for macromolecular structure determination by X-ray crystallography.
Journal ArticleDOI
Refinement of macromolecular structures by the maximum-likelihood method.
TL;DR: The likelihood function for macromolecular structures is extended to include prior phase information and experimental standard uncertainties and the results derived are consistently better than those obtained from least-squares refinement.