Mutations in theTetrahymenaRibozyme Internal Guide Sequence:  Effects on Docking of the P1 Helix into the Catalytic Core and Correlation with Catalytic Activity†

The histone acetyl transferases CREB-binding protein (CBP) and its paralog p300 play a critical role in numerous cellular processes. Dysregulation of their catalytic activity is associated with several human diseases. Previous work has elucidated the regulatory mechanisms of p300 acetyltransferase activity, but it is not known whether CBP activity is controlled similarly. Here, we present the crystal structure of the CBP catalytic core encompassing the bromodomain (BRD), CH2 (comprising PHD and RING), HAT, and ZZ domains at 2.4-Å resolution. The BRD, PHD, and HAT domains form an integral structural unit to which the RING and ZZ domains are flexibly attached. The structure of the apo-CBP HAT domain is similar to that of acyl-CoA–bound p300 HAT complexes and shows that the acetyl-CoA binding site is stably formed in the absence of cofactor. The BRD, PHD, and ZZ domains interact with small ubiquitin-like modifier 1 (SUMO-1) and Ubc9, and function as an intramolecular E3 ligase for SUMOylation of the cell cycle regulatory domain 1 (CRD1) of CBP, which is located adjacent to the BRD. In vitro HAT assays suggest that the RING domain, the autoregulatory loop (AL) within the HAT domain, and the ZZ domain do not directly influence catalytic activity, whereas the BRD is essential for histone H3 acetylation in nucleosomal substrates. Several lysine residues in the intrinsically disordered AL are autoacetylated by the HAT domain. Upon autoacetylation, acetyl-K1596 (Ac-K1596) binds intramolecularly to the BRD, competing with histones for binding to the BRD and acting as a negative regulator that inhibits histone H3 acetylation.

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Porphyrin in prebiotic catalysis: Ascertaining a route for the emergence of early metalloporphyrins

10.1101/2021.12.20.473587 ◽

2021 ◽

Author(s):

Shikha Dagar ◽

Susovan Sarkar ◽

Sudha Rajamani

Keyword(s):

Catalytic Activity ◽

Molecular Evolution ◽

Transition Metal ◽

Metal Ions ◽

Metal Ion ◽

Selective Advantage ◽

Metal Porphyrin ◽

Catalytic Core ◽

Prebiotic Catalysis ◽

Mediated Oxidation

Metal ions are known to catalyze certain prebiotic reactions. However, the transition from metal ions to extant metalloenzymes remains unclear. Porphyrins are found ubiquitously in the catalytic core of many ancient metalloenzymes. In this study, we evaluated the influence of porphyrin-based organic scaffold, on the catalysis, emergence and putative molecular evolution of prebiotic metalloporphyrins. We studied the effect of porphyrins on the transition metal ion-mediated oxidation of hydroquinone (HQ). We report a change in the catalytic activity of the metal ions in the presence of porphyrin. This was observed to be facilitated by the coordination between metal ions and porphyrins or by formation of non-coordinated complexes. The metal-porphyrin complexes also oxidized NADH, underscoring its versatility at oxidizing more than one substrate. Our study highlights the selective advantage that some of the metal ions would have had in the presence of porphyrin, underscoring their role in shaping the evolution of protometalloenzymes.

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One RNA plays three roles to provide catalytic activity to a group I intron lacking an endogenous internal guide sequence

Nucleic Acids Research ◽

10.1093/nar/gkp271 ◽

2009 ◽

Vol 37 (12) ◽

pp. 3981-3989 ◽

Cited By ~ 10

Author(s):

Nilesh Vaidya ◽

Niles Lehman

Keyword(s):

Catalytic Activity ◽

Group I Intron ◽

Group I ◽

Guide Sequence

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Tertiary interactions with the internal guide sequence mediate docking of the P1 helix into the catalytic core of the Tetrahymena ribozyme

Biochemistry ◽

10.1021/bi00212a027 ◽

1993 ◽

Vol 32 (49) ◽

pp. 13593-13604 ◽

Cited By ~ 60

Author(s):

Scott A. Strobel ◽

Thomas R. Cech

Keyword(s):

Catalytic Core ◽

Guide Sequence ◽

Tertiary Interactions

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A Unique Class of Conditional sir2 Mutants Displays Distinct Silencing Defects in Saccharomyces cerevisiae

Genetics ◽

10.1093/genetics/162.2.721 ◽

2002 ◽

Vol 162 (2) ◽

pp. 721-736 ◽

Cited By ~ 2

Author(s):

Sandra N Garcia ◽

Lorraine Pillus

Keyword(s):

Saccharomyces Cerevisiae ◽

Catalytic Activity ◽

Dna Binding Domain ◽

Catalytic Core ◽

Conserved Residues ◽

Mutant Proteins ◽

Mechanistic Insight ◽

Chromatin Proteins ◽

Insight Into ◽

Subtelomeric Regions

Abstract Silencing provides a critical means of repressing transcription through the assembly and modification of chromatin proteins. The NAD+-dependent deacetylation of histones by the Sir2p family of proteins lends mechanistic insight into how SIR2 contributes to silencing. Here we describe three locus-specific sir2 mutants that have a spectrum of silencing phenotypes in yeast. These mutants are dependent on SIR1 for silencing function at the HM silent mating-type loci, display distinct phenotypes at the rDNA, and have dominant silencing defects at the telomeres. Telomeric silencing is restored if the mutant proteins are directly tethered to subtelomeric regions, via a Gal4p DNA-binding domain (GBD), or are recruited by tethered GBD-Sir1p. These sir2 mutations are found within conserved residues of the SIR2 family and lead to defects in catalytic activity. Since one of the mutations lies outside the previously defined minimal catalytic core, our results show that additional regions of Sir2p can be important for enzymatic activity and that differences in levels of activity may have distinct effects at the silenced loci.

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Faculty Opinions recommendation of One RNA plays three roles to provide catalytic activity to a group I intron lacking an endogenous internal guide sequence.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1160651.622037 ◽

2009 ◽

Author(s):

Sabine Müller

Keyword(s):

Catalytic Activity ◽

Group I Intron ◽

Group I ◽

Guide Sequence

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New insights into the catalytic mechanism of histidine phosphatases revealed by a functionally essential arginine residue within the active site of the Sts phosphatases

Biochemical Journal ◽

10.1042/bj20121769 ◽

2013 ◽

Vol 453 (1) ◽

pp. 27-35 ◽

Cited By ~ 5

Author(s):

Boris San Luis ◽

Nicolas Nassar ◽

Nick Carpino

Keyword(s):

Catalytic Activity ◽

T Cell ◽

T Cell Receptor ◽

T Cell Activation ◽

Active Site ◽

Cell Receptor ◽

Catalytic Core ◽

Receptor Signalling ◽

Arginine Residues ◽

Histidine Phosphatases

Sts (suppressor of T-cell receptor signalling)-1 and Sts-2 are HPs (histidine phosphatases) that negatively regulate TCR (T-cell receptor) signalling pathways, including those involved in cytokine production. HPs play key roles in such varied biological processes as metabolism, development and intracellular signalling. They differ considerably in their primary sequence and substrate specificity, but possess a catalytic core formed by an invariant quartet of active-site residues. Two histidine and two arginine residues cluster together within the HP active site and are thought to participate in a two-step dephosphorylation reaction. To date there has been little insight into any additional residues that might play an important functional role. In the present study, we identify and characterize an additional residue within the Sts phosphatases (Sts-1 Arg383 or Sts-2 Arg369) that is critical for catalytic activity and intracellular function. Mutation of Sts-1 Arg383 to an alanine residue compromises the enzyme's activity and renders Sts-1 unable to suppress TCR-induced cytokine induction. Of the multiple amino acids substituted for Arg383, only lysine partially rescues the catalytic activity of Sts-1. Although Sts-1 Arg383 is conserved in all Sts homologues, it is only conserved in one of the two sub-branches of HPs. The results of the present study highlight an essential role for Sts-1 phosphatase activity in regulating T-cell activation and add a new dimension of complexity to our understanding of HP catalytic activity.

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High resolution electron microscopy of lanthanum phosphate crystals

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100108519 ◽

1978 ◽

Vol 36 (1) ◽

pp. 274-275

Author(s):

J. C. Wheatley ◽

J. M. Cowley

Keyword(s):

Electron Microscopy ◽

Catalytic Activity ◽

High Resolution ◽

Petroleum Industry ◽

High Resolution Electron Microscopy ◽

Lanthanum Phosphate ◽

Good Catalyst ◽

Resolution Electron ◽

Good Catalytic Activity ◽

Physical And Chemical

Rare-earth phosphates are of particular interest because of their catalytic properties associated with the hydrolysis of many aromatic chlorides in the petroleum industry. Lanthanum phosphates (LaPO4) which have been doped with small amounts of copper have shown increased catalytic activity (1). However the physical and chemical characteristics of the samples leading to good catalytic activity are not known.Many catalysts are amorphous and thus do not easily lend themselves to methods of investigation which would include electron microscopy. However, the LaPO4, crystals are quite suitable samples for high resolution techniques.The samples used were obtained from William L. Kehl of Gulf Research and Development Company. The electron microscopy was carried out on a JEOL JEM-100B which had been modified for high resolution microscopy (2). Standard high resolution techniques were employed. Three different sample types were observed: 669A-1-5-7 (poor catalyst), H-L-2 (good catalyst) and 27-011 (good catalyst).

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