scholarly journals Ammonium ion transport by the AMT/Rh homologue LeAMT1;1

2006 ◽  
Vol 396 (3) ◽  
pp. 431-437 ◽  
Author(s):  
Maria Mayer ◽  
Marek Dynowski ◽  
Uwe Ludewig
Keyword(s):  
Structural Data ◽  
Homology Model ◽  
Ammonium Transporter ◽  
Ammonium Ion ◽  
Molecular Architecture ◽  
Gas Channel ◽  
Domains Of Life ◽  
Single Positive ◽  
Key Residues ◽  
Related Proteins

AMT (ammonium transporter)/Rh (Rhesus) ammonium transporters/channels are identified in all domains of life and fulfil contrasting functions related either to ammonium acquisition or excretion. Based on functional and crystallographic high-resolution structural data, it was recently proposed that the bacterial AmtB (ammonium transporter B) is a gas channel for NH3 [Khademi, O'Connell, III, Remis, Robles-Colmenares, Miercke and Stroud (2004) Science 305, 1587–1594; Zheng, Kostrewa, Berneche, Winkler and Li (2004) Proc. Natl. Acad. Sci. U.S.A. 101, 17090–17095]. Key residues, proposed to be crucial for NH3 conduction, and the hydrophobic, but obstructed, pore were conserved in a homology model of LeAMT1;1 from tomato. Transport by LeAMT1;1 was affected by mutations of residues that were predicted to constitute the aromatic recruitment site for NH4+ at the external pore entrance. Despite the structural similarities, LeAMT1;1 was shown to transport only the ion; each transported 14C-methylammonium molecule carried a single positive elementary charge. Similarly, NH4+ (or H+/NH3) was transported, but NH3 conduction was excluded. It is concluded that related proteins and a similar molecular architecture can apparently support contrasting transport mechanisms.

scholarly journals Shared requirements for key residues in the antibiotic resistance enzymes ErmC and ErmE suggest a common mode of RNA recognition

2020 ◽  
Vol 295 (51) ◽  
pp. 17476-17485
Author(s):  
Sebastian J. Rowe ◽  
Ryan J. Mecaskey ◽  
Mohamed Nasef ◽  
Rachel C. Talton ◽  
Rory E. Sharkey ◽  
...  
Keyword(s):  
Structural Model ◽  
Structural Data ◽  
Multidrug Resistant ◽  
Saturation Mutagenesis ◽  
23S Rrna ◽  
Binding Assays ◽  
Erythromycin Resistance ◽  
Functional Studies ◽  
Key Residues ◽  
Related Proteins

Erythromycin-resistance methyltransferases are SAM dependent Rossmann fold methyltransferases that convert A2058 of 23S rRNA to m62A2058. This modification sterically blocks binding of several classes of antibiotics to 23S rRNA, resulting in a multidrug-resistant phenotype in bacteria expressing the enzyme. ErmC is an erythromycin resistance methyltransferase found in many Gram-positive pathogens, whereas ErmE is found in the soil bacterium that biosynthesizes erythromycin. Whether ErmC and ErmE, which possess only 24% sequence identity, use similar structural elements for rRNA substrate recognition and positioning is not known. To investigate this question, we used structural data from related proteins to guide site-saturation mutagenesis of key residues and characterized selected variants by antibiotic susceptibility testing, single turnover kinetics, and RNA affinity–binding assays. We demonstrate that residues in α4, α5, and the α5-α6 linker are essential for methyltransferase function, including an aromatic residue on α4 that likely forms stacking interactions with the substrate adenosine and basic residues in α5 and the α5-α6 linker that likely mediate conformational rearrangements in the protein and cognate rRNA upon interaction. The functional studies led us to a new structural model for the ErmC or ErmE-rRNA complex.

scholarly journals HPF1 remodels the active site of PARP1 to enable the serine ADP-ribosylation of histones

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Fa-Hui Sun ◽  
Peng Zhao ◽  
Nan Zhang ◽  
Lu-Lu Kong ◽  
Catherine C. L. Wong ◽  
...  
Keyword(s):  
Dna Damage ◽  
Dna Repair ◽  
Active Site ◽  
Negative Charge ◽  
Structural Data ◽  
Dna Breaks ◽  
Adp Ribosylation ◽  
Local Conformation ◽  
Key Residues ◽  
Structural Insights

AbstractUpon binding to DNA breaks, poly(ADP-ribose) polymerase 1 (PARP1) ADP-ribosylates itself and other factors to initiate DNA repair. Serine is the major residue for ADP-ribosylation upon DNA damage, which strictly depends on HPF1. Here, we report the crystal structures of human HPF1/PARP1-CAT ΔHD complex at 1.98 Å resolution, and mouse and human HPF1 at 1.71 Å and 1.57 Å resolution, respectively. Our structures and mutagenesis data confirm that the structural insights obtained in a recent HPF1/PARP2 study by Suskiewicz et al. apply to PARP1. Moreover, we quantitatively characterize the key residues necessary for HPF1/PARP1 binding. Our data show that through salt-bridging to Glu284/Asp286, Arg239 positions Glu284 to catalyze serine ADP-ribosylation, maintains the local conformation of HPF1 to limit PARP1 automodification, and facilitates HPF1/PARP1 binding by neutralizing the negative charge of Glu284. These findings, along with the high-resolution structural data, may facilitate drug discovery targeting PARP1.

Characterization of a novel promoter insertion in the c-rel locus

1990 ◽  
Vol 10 (9) ◽  
pp. 4788-4794
Author(s):  
N Kabrun ◽  
N Bumstead ◽  
M J Hayman ◽  
P J Enrietto
Keyword(s):  
Molecular Weight ◽  
Alternative Splicing ◽  
Structural Data ◽  
Wild Type ◽  
Repeat Sequences ◽  
Myc Gene ◽  
A Cell ◽  
Related Proteins ◽  
Genetic Events

Avian leukosis virus (ALV)-induced neoplasias are commonly found associated with integrations of proviral DNA in proximity to the myc gene. However, studies suggest that other genetic events are necessary for the complete neoplastic phenotype. A cell line (HP46) derived from an ALV-induced tumor has been analyzed and found to contain, in addition to an alteration in the myc gene, a promoter insertion in the c-rel locus. Both loci expressed large amounts of mRNA coding for their respective proteins. Several rel-related transcripts were expressed in the HP46 line, and four rel-related proteins of lower molecular weight than the wild-type p68c-rel product were detected. At least two of these transcripts contained U5 long terminal repeat sequences on the 5' end of the RNA. Structural data suggest that the messages may have evolved by an alternative splicing mechanism. This is the first example of a promoter insertion in the c-rel locus, a gene whose viral counterpart v-rel is responsible for the induction of lymphoid tumors.

scholarly journals Proteasomes: unfoldase-assisted protein degradation machines

2019 ◽  
Vol 401 (1) ◽  
pp. 183-199 ◽  
Author(s):  
Parijat Majumder ◽  
Wolfgang Baumeister
Keyword(s):  
Stress Response ◽  
Molecular Machines ◽  
Molecular Architecture ◽  
Core Particle ◽  
Protein Substrates ◽  
Macromolecular Assemblies ◽  
Current State ◽  
Intracellular Proteins ◽  
Domains Of Life ◽  
Aaa Atpases

Abstract Proteasomes are the principal molecular machines for the regulated degradation of intracellular proteins. These self-compartmentalized macromolecular assemblies selectively degrade misfolded, mistranslated, damaged or otherwise unwanted proteins, and play a pivotal role in the maintenance of cellular proteostasis, in stress response, and numerous other processes of vital importance. Whereas the molecular architecture of the proteasome core particle (CP) is universally conserved, the unfoldase modules vary in overall structure, subunit complexity, and regulatory principles. Proteasomal unfoldases are AAA+ ATPases (ATPases associated with a variety of cellular activities) that unfold protein substrates, and translocate them into the CP for degradation. In this review, we summarize the current state of knowledge about proteasome – unfoldase systems in bacteria, archaea, and eukaryotes, the three domains of life.

Ammonium utilization in Bacillus subtilis: transport and regulatory functions of NrgA and NrgB

Microbiology ◽  
2003 ◽  
Vol 149 (11) ◽  
pp. 3289-3297 ◽  
Author(s):  
Christian Detsch ◽  
Jörg Stülke
Keyword(s):  
Bacillus Subtilis ◽  
Large Fraction ◽  
Glutamate Synthase ◽  
Nitrogen Sources ◽  
Covalent Modification ◽  
Ammonium Transporter ◽  
Ammonium Ion ◽  
Ammonium Transport ◽  
Low Concentrations ◽  
Regulatory Functions

Bacillus subtilis uses glutamine as the best source of nitrogen. In the absence of glutamine, alternative nitrogen sources such as ammonium can be used. Ammonium utilization involves the uptake of the gas or the ammonium ion, the synthesis of glutamine by the glutamine synthetase and the recycling of the glutamate by the glutamate synthase. In this work, ammonium transport in B. subtilis was studied. At high ammonium concentrations, a large fraction of the ammonium is present as ammonia, which may enter the cell via diffusion. In contrast, the ammonium transporter NrgA is required for ammonium utilization at low concentrations or at low pH values when the equilibrium between uncharged ammonia and the ammonium ion is shifted towards ammonium. Moreover, a functional NrgA is essential for the transport of the ammonium analogue methylammonium. NrgA is encoded in the nrgAB operon. The product of the second gene, NrgB, is a member of the PII family of regulatory proteins. In contrast to PII proteins from other organisms, there is no indication for a covalent modification of NrgB in response to the nitrogen supply of the cell. It is demonstrated here that NrgB is localized at the membrane, most likely in association with the ammonium transporter NrgA. The presence of a functional NrgB is required for full-level expression of the nrgAB operon in response to nitrogen limitation, suggesting that NrgB might relay the information on ammonium availability to downstream regulatory factors and thus fine-tune their activity.

The monovalent cation leak in overhydrated stomatocytic red blood cells results from amino acid substitutions in the Rh-associated glycoprotein

Blood ◽  
2009 ◽  
Vol 113 (6) ◽  
pp. 1350-1357 ◽  
Author(s):  
Lesley J. Bruce ◽  
Hélène Guizouarn ◽  
Nicholas M. Burton ◽  
Nicole Gabillat ◽  
Joyce Poole ◽  
...  
Keyword(s):  
Dna Analysis ◽  
Monovalent Cation ◽  
Ammonium Transporter ◽  
Xenopus Laevis Oocytes ◽  
Red Cell ◽  
Wild Type ◽  
Gas Channel ◽  
Transporter Family ◽  
Red Cell Membranes ◽  
Conserved Amino Acids

Abstract Overhydrated hereditary stomatocytosis (OHSt) is a rare dominantly inherited hemolytic anemia characterized by a profuse membrane leak to monovalent cations. Here, we show that OHSt red cell membranes contain slightly reduced amounts of Rh-associated glycoprotein (RhAG), a putative gas channel protein. DNA analysis revealed that the OHSt patients have 1 of 2 heterozygous mutations (t182g, t194c) in RHAG that lead to substitutions of 2 highly conserved amino acids (Ile61Arg, Phe65Ser). Unexpectedly, expression of wild-type RhAG in Xenopus laevis oocytes induced a monovalent cation leak; expression of the mutant RhAG proteins induced a leak about 6 times greater than that in wild type. RhAG belongs to the ammonium transporter family of proteins that form pore-like structures. We have modeled RhAG on the homologous Nitrosomonas europaea Rh50 protein and shown that these mutations are likely to lead to an opening of the pore. Although the function of RhAG remains controversial, this first report of functional RhAG mutations supports a role for RhAG as a cation pore.

Homology Model for Oncostatin M Based on NMR Structural Data

Biochemistry ◽  
1998 ◽  
Vol 37 (30) ◽  
pp. 10581-10588 ◽  
Author(s):  
Douglas Kitchen ◽  
Ross C. Hoffman ◽  
Franklin J. Moy ◽  
Robert Powers
Keyword(s):  
Structural Data ◽  
Homology Model ◽  
Oncostatin M

scholarly journals Structural and Functional Specialization of OSBP-Related Proteins

Contact ◽  
2020 ◽  
Vol 3 ◽  
pp. 251525642094662
Author(s):  
Vanessa Delfosse ◽  
William Bourguet ◽  
Guillaume Drin
Keyword(s):  
Structural Features ◽  
Eukaryotic Cell ◽  
Molecular Architecture ◽  
Lipid Transfer ◽  
Cellular Functions ◽  
Membrane Contact Sites ◽  
Close Proximity ◽  
Tightly Coupled ◽  
And Function ◽  
Related Proteins

Lipids are precisely distributed in the eukaryotic cell where they help to define organelle identity and function, in addition to their structural role. Once synthesized, many lipids must be delivered to other compartments by non-vesicular routes, a process that is undertaken by proteins called Lipid Transfer Proteins (LTPs). OSBP and the closely-related ORP and Osh proteins constitute a major, evolutionarily conserved family of LTPs in eukaryotes. Most of these target one or more subcellular regions, and membrane contact sites in particular, where two organelle membranes are in close proximity. It was initially thought that such proteins were strictly dedicated to sterol sensing or transport. However, over the last decade, numerous studies have revealed that these proteins have many more functions, and we have expanded our understanding of their mechanisms. In particular, many of them are lipid exchangers that exploit PI(4)P or possibly other phosphoinositide gradients to directionally transfer sterol or PS between two compartments. Importantly, these transfer activities are tightly coupled to processes such as lipid metabolism, cellular signalling and vesicular trafficking. This review describes the molecular architecture of OSBP/ORP/Osh proteins, showing how their specific structural features and internal configurations impart unique cellular functions.

scholarly journals Shared and Group-Specific Features of the Rotavirus RNA Polymerase Reveal Potential Determinants of Gene Reassortment Restriction

2009 ◽  
Vol 83 (12) ◽  
pp. 6135-6148 ◽  
Author(s):  
Sarah M. McDonald ◽  
Daniel Aguayo ◽  
Fernando D. Gonzalez-Nilo ◽  
John T. Patton
Keyword(s):  
Rna Polymerase ◽  
Protein A ◽  
Three Dimensional ◽  
Structural Data ◽  
Homology Model ◽  
Recognition Mechanism ◽  
Shell Protein ◽  
And Function ◽  
Gene Reassortment

ABSTRACT Rotaviruses (RVs) are nonenveloped, 11-segmented, double-stranded RNA viruses that are major pathogens associated with acute gastroenteritis. Group A, B, and C RVs have been isolated from humans; however, intergroup gene reassortment does not occur for reasons that remain unclear. This restriction might reflect the failure of the viral RNA-dependent RNA polymerase (RdRp; VP1) to recognize and replicate the RNA of a different group. To address this possibility, we contrasted the sequences, structures, and functions of RdRps belonging to RV groups A, B, and C (A-VP1, B-VP1, and C-VP1, respectively). We found that conserved amino acid residues are located within the hollow center of VP1 near the active site, whereas variable, group-specific residues are mostly surface exposed. By creating a three-dimensional homology model of C-VP1 with the A-VP1 crystallographic data, we provide evidence that these RV RdRps are nearly identical in their tertiary folds and that they have the same RNA template recognition mechanism that differs from that of B-VP1. Consistent with the structural data, recombinant A-VP1 and C-VP1 are capable of replicating one another's RNA templates in vitro. Nonetheless, the activity of both RdRps is strictly dependent upon the presence of cognate RV core shell protein A-VP2 or C-VP2, respectively. Together, the results of this study provide unprecedented insight into the structure and function of RV RdRps and support the notion that VP1 interactions may influence the emergence of reassortant viral strains.

Sign in / Sign up

Export Citation Format

Share Document