scholarly journals Structure and Function of 4-Hydroxyphenylacetate Decarboxylase and Its Cognate Activating Enzyme

2016 ◽  
Vol 26 (1-3) ◽  
pp. 76-91 ◽  
Author(s):  
Brinda Selvaraj ◽  
Wolfgang Buckel ◽  
Bernard T. Golding ◽  
G. Matthias Ullmann ◽  
Berta M. Martins
Keyword(s):  
Small Subunit ◽  
Structure And Function ◽  
Binding Motif ◽  
Prosthetic Group ◽  
New Class ◽  
Glycyl Radical ◽  
Open Questions ◽  
Substrate Conversion ◽  
And Function ◽  
A Site

4-Hydroxyphenylacetate decarboxylase (4Hpad) is the prototype of a new class of Fe-S cluster-dependent glycyl radical enzymes (Fe-S GREs) acting on aromatic compounds. The two-enzyme component system comprises a decarboxylase responsible for substrate conversion and a dedicated activating enzyme (4Hpad-AE). The decarboxylase uses a glycyl/thiyl radical dyad to convert 4-hydroxyphenylacetate into <i>p</i>-cresol (4-methylphenol) by a biologically unprecedented Kolbe-type decarboxylation. In addition to the radical dyad prosthetic group, the decarboxylase unit contains two [4Fe-4S] clusters coordinated by an extra small subunit of unknown function. 4Hpad-AE reductively cleaves S-adenosylmethionine (SAM or AdoMet) at a site-differentiated [4Fe-4S]<sup>2+/+</sup> cluster (RS cluster) generating a transient 5′-deoxyadenosyl radical that produces a stable glycyl radical in the decarboxylase by the abstraction of a hydrogen atom. 4Hpad-AE binds up to two auxiliary [4Fe-4S] clusters coordinated by a ferredoxin-like insert that is C-terminal to the RS cluster-binding motif. The ferredoxin-like domain with its two auxiliary clusters is not vital for SAM-dependent glycyl radical formation in the decarboxylase, but facilitates a longer lifetime for the radical. This review describes the 4Hpad and cognate AE families and focuses on the recent advances and open questions concerning the structure, function and mechanism of this novel Fe-S-dependent class of GREs.

Depletion and Reconstitution of Active E. Coli Ribosomes

1975 ◽  
Vol 33 ◽  
pp. 640-641
Author(s):  
M. Boublik ◽  
W. Hellmann ◽  
F. Jenkins
Keyword(s):  
Protein Biosynthesis ◽  
Large Subunit ◽  
High Resolution Electron Microscopy ◽  
Small Subunit ◽  
Structure And Function ◽  
Biologically Active ◽  
Biological Macromolecules ◽  
E Coli ◽  
Resolution Electron ◽  
And Function

Correlations between structure and function of biological macromolecules have been studied intensively for many years, mostly by indirect methods. High resolution electron microscopy is a unique tool which can provide such information directly by comparing the conformation of biopolymers in their biologically active and inactive state. We have correlated the structure and function of ribosomes, ribonucleoprotein particles which are the site of protein biosynthesis. 70S E. coli ribosomes, used in this experiment, are composed of two subunits - large (50S) and small (30S). The large subunit consists of 34 proteins and two different ribonucleic acid molecules. The small subunit contains 21 proteins and one RNA molecule. All proteins (with the exception of L7 and L12) are present in one copy per ribosome.This study deals with the changes in the fine structure of E. coli ribosomes depleted of proteins L7 and L12. These proteins are unique in many aspects.

scholarly journals A Rubisco-binding protein is required for normal pyrenoid number and starch sheath morphology inChlamydomonas reinhardtii

2019 ◽  
Vol 116 (37) ◽  
pp. 18445-18454 ◽  
Author(s):  
Alan K. Itakura ◽  
Kher Xing Chan ◽  
Nicky Atkinson ◽  
Leif Pallesen ◽  
Lianyong Wang ◽  
...  
Keyword(s):  
Surface Area ◽  
Structure And Function ◽  
Binding Motif ◽  
Starch Granules ◽  
Wild Type ◽  
Bisphosphate Carboxylase ◽  
Biophysical Mechanism ◽  
Mechanism Function ◽  
And Function

A phase-separated, liquid-like organelle called the pyrenoid mediates CO2fixation in the chloroplasts of nearly all eukaryotic algae. While most algae have 1 pyrenoid per chloroplast, here we describe a mutant in the model algaChlamydomonasthat has on average 10 pyrenoids per chloroplast. Characterization of the mutant leads us to propose a model where multiple pyrenoids are favored by an increase in the surface area of the starch sheath that surrounds and binds to the liquid-like pyrenoid matrix. We find that the mutant’s phenotypes are due to disruption of a gene, which we call StArch Granules Abnormal 1 (SAGA1) because starch sheath granules, or plates, in mutants lacking SAGA1 are more elongated and thinner than those of wild type. SAGA1 contains a starch binding motif, suggesting that it may directly regulate starch sheath morphology. SAGA1 localizes to multiple puncta and streaks in the pyrenoid and physically interacts with the small and large subunits of the carbon-fixing enzyme Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase), a major component of the liquid-like pyrenoid matrix. Our findings suggest a biophysical mechanism by which starch sheath morphology affects pyrenoid number and CO2-concentrating mechanism function, advancing our understanding of the structure and function of this biogeochemically important organelle. More broadly, we propose that the number of phase-separated organelles can be regulated by imposing constraints on their surface area.

scholarly journals Theoretical ribosomal protein mass distribution of Pseudomonas aeruginosa PAO1

2018 ◽  
Author(s):  
Wenfa Ng
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Ribosomal Protein ◽  
Ribosomal Proteins ◽  
Small Subunit ◽  
Structure And Function ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
And Function ◽  
Unique Mass ◽  
Tof Ms

Ribosomes are the protein synthesis factories of a cell and thus are evolutionary conserved in structure and function. Comprising a large and small subunit, the ribosome is further made up of ribosomal proteins that give structure and function to different parts of the macromolecular complex. Current methods for isolating the ribosome include density gradient ultracentrifugation that separates the ribosome into the large and small subunit. Separation of the various ribosomal proteins that comprise each of the subunit would require a solubilization step followed by the use of sodium dodecyl sulphate and polyacrylamide gel electrophoresis (SDS-PAGE). However, possibility exists for the use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to profile the set of ribosomal proteins that could be solubilized from each ribosome subunit. Using ribosomal protein amino acid sequence information from Kyoto Encyclopaedia of Genes and Genomes (KEGG), the molecular weight of each ribosomal protein from Pseudomonas aeruginosa PAO1 was calculated in this report. Obtained results revealed that each ribosomal protein had a unique mass that could be detected by mid-range MALDI-TOF MS instruments. More importantly, the mass of ribosomal proteins constitutes a unique mass fingerprint of each ribosome subunit, which accounts for the different structure and functions of the large and small ribosome subunit. Overall, current mass resolution of MALDI-TOF MS instruments could resolve ribosomal proteins and thus provides a tool for profiling the set of ribosomal proteins that constitute the large and small subunit of the ribosome.

scholarly journals Restoration of Both Structure and Function to a Defective Poly(A) Site byin VitroSelection

1996 ◽  
Vol 271 (52) ◽  
pp. 33654-33663 ◽  
Author(s):  
Brenton R. Graveley ◽  
Elizabeth S. Fleming ◽  
Gregory M. Gilmartin
Keyword(s):  
Structure And Function ◽  
And Function ◽  
A Site

scholarly journals Reconstructed evolutionary adaptive paths give polymerases accepting reversible terminators for sequencing and SNP detection

2010 ◽  
Vol 107 (5) ◽  
pp. 1948-1953 ◽  
Author(s):  
Fei Chen ◽  
Eric A. Gaucher ◽  
Nicole A. Leal ◽  
Daniel Hutter ◽  
Stephanie A. Havemann ◽  
...  
Keyword(s):  
Open Space ◽  
Dna Polymerases ◽  
Structure And Function ◽  
Primer Extension ◽  
Snp Detection ◽  
Parallel Sequencing ◽  
New Class ◽  
Dna Analyses ◽  
History Of ◽  
And Function

Any system, natural or human-made, is better understood if we analyze both its history and its structure. Here we combine structural analyses with a “Reconstructed Evolutionary Adaptive Path” (REAP) analysis that used the evolutionary and functional history of DNA polymerases to replace amino acids to enable polymerases to accept a new class of triphosphate substrates, those having their 3′-OH ends blocked as a 3′-ONH2 group (dNTP-ONH2). Analogous to widely used 2′,3′-dideoxynucleoside triphosphates (ddNTPs), dNTP-ONH2s terminate primer extension. Unlike ddNTPs, however, primer extension can be resumed by cleaving an O-N bond to restore an -OH group to the 3′-end of the primer. REAP combined with crystallographic analyses identified 35 sites where replacements might improve the ability of Taq to accept dNTP-ONH2s. A library of 93 Taq variants, each having replacements at three or four of these sites, held eight variants having improved ability to accept dNTP-ONH2 substrates. Two of these (A597T, L616A, F667Y, E745H, and E520G, K540I, L616A) performed notably well. The second variant incorporated both dNTP-ONH2sand ddNTPs faithfully and efficiently, supporting extension-cleavage-extension cycles applicable in parallel sequencing and in SNP detection through competition between reversible and irreversible terminators. Dissecting these results showed that one replacement (L616A), not previously identified, allows Taq to incorporate both reversible and irreversible terminators. Modeling showed how L616A might open space behind Phe-667, allowing it to move to accommodate the larger 3′-substituent. This work provides polymerases for DNA analyses and shows how evolutionary analyses help explore relationships between structure and function in proteins.

scholarly journals Mammalian DNA methyltransferases: new discoveries and open questions

2018 ◽  
Vol 46 (5) ◽  
pp. 1191-1202 ◽  
Author(s):  
Humaira Gowher ◽  
Albert Jeltsch
Keyword(s):  
Dna Methylation ◽  
Dna Methyltransferases ◽  
Structure And Function ◽  
Future Research ◽  
Ongoing Research ◽  
Cpg Sites ◽  
Open Questions ◽  
High Preference ◽  
And Function ◽  
Methylation Patterns

As part of the epigenetic network, DNA methylation is a major regulator of chromatin structure and function. In mammals, it mainly occurs at palindromic CpG sites, but asymmetric methylation at non-CpG sites is also observed. Three enzymes are involved in the generation and maintenance of DNA methylation patterns. DNMT1 has high preference for hemimethylated CpG sites, and DNMT3A and DNMT3B equally methylate unmethylated and hemimethylated DNA, and also introduce non-CpG methylation. Here, we review recent observations and novel insights into the structure and function of mammalian DNMTs (DNA methyltransferases), including new structures of DNMT1 and DNMT3A, data on their mechanism, regulation by post-translational modifications and on the function of DNMTs in cells. In addition, we present news findings regarding the allosteric regulation and targeting of DNMTs by chromatin modifications and chromatin proteins. In combination, the recent publications summarized here impressively illustrate the intensity of ongoing research in this field. They provide a deeper understanding of key mechanistic properties of DNMTs, but they also document still unsolved issues, which need to be addressed in future research.

The tegument in Hemiuridae (Digenea: Hemiuroidea): structure and function in the adult

1988 ◽  
Vol 62 (4) ◽  
pp. 305-316 ◽  
Author(s):  
B. F. Matthews ◽  
R. A. Matthews
Keyword(s):  
Phosphatase Activity ◽  
Mechanical Damage ◽  
Strong Acid ◽  
Structure And Function ◽  
The Body ◽  
Physico Chemical ◽  
Chemical Conditions ◽  
And Function ◽  
A Site ◽  
Outer Plasma Membrane

AbstractThe teleost stomach, as a site of strong acid proteolytic digestion at pH 1–4, is a hostile environment rarely chosen as a habitat by parasites. Several Hemiuroidea have nevertheless invaded this niche, notably the Hemiuridae, a family in which the body is characterized by a retractile “tail”, or ecsoma. The structure and function of the latter has been studied in three hemiurid species, namely Hemiurus communis, Lecithochirium rufoviride and L. fusiforme, using ultrastructural, histochemical and autoradiographic techniques. Results indicate a clear demarcation between the function of the tegument covering the ecsoma and that of the rest of the body, or soma. No mitochondria have been observed in the ecsomal tegument, and intense acid phosphatase activity was detected in association with its outer plasma membrane. Uptake of 3H-tyrosine occurred within the excretory vesicle, which may serve for transport of nutrients forwards into the soma. In contrast, the thickened, dense somal tegument, with few mitochondria largely confined to ridges or plications in H. communis, showed neither phosphatase activity nor uptake of tyrosine. Glucose uptake was not detected in any part of the body. That the somal tegument serves not for absorption but for protection against both physico-chemical conditions and mechanical damage by prey entering the host's stomach is discussed.

scholarly journals Structure and function of a new class of human prolactin antagonists

2009 ◽  
Vol 66 (2) ◽  
pp. 121-130 ◽  
Author(s):  
Laura DePalatis ◽  
Colleen M. Almgren ◽  
Jypji Patmastan ◽  
Mark Troyer ◽  
Todd Woodrich ◽  
...  
Keyword(s):  
Structure And Function ◽  
New Class ◽  
Human Prolactin ◽  
And Function
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