Molecular Basis of eRF3 Recognition by the MLLE Domain of Poly(A)-Binding Protein

PABPC1 (cytosolic poly(A)-binding protein 1) is an RNA-binding protein that binds to the poly(A) tail of mRNAs to promote translation and mRNA turnover. In addition to RNA-binding domains, PABPC1 contains a unique protein-protein interaction domain, MLLE (also known as PABC) that binds regulatory proteins and translation factors that contain a conserved 12 amino acid peptide motif termed PAM2. Eukaryotic Release Factor 3 (eRF3/GSPT1) contains two overlapping PAM2 sequences, which are required for its activity. Here, we determined the crystal structures of the MLLE domain from PABPC1 in complex with the two PAM2 regions of eRF3. The structures reveal a mechanism of cooperativity between the two PAM2 sites that increases the binding affinity but prevents the binding of more than one molecule of eRF3 to PABPC1. Relative to previous structures, the high-resolution crystal structures force a re-evaluation of the PAM2 motif and improve our understanding of the molecular basis of MLLE peptide recognition

Structure of GlgS from Escherichia coli suggests a role in protein–protein interactions

BACKGROUND: The Escherichia coli protein GlgS is up-regulated in response to starvation stress and its overexpression was shown to stimulate glycogen synthesis. RESULTS: We solved the structure of GlgS from E. coli, a member of an enterobacterial protein family. The protein structure represents a bundle of three α-helices with a short hydrophobic helix sandwiched between two long amphipathic helices. CONCLUSION: GlgS shows structural homology to Huntingtin, elongation factor 3, protein phosphatase 2A, TOR1 motif domains and tetratricopeptide repeats, suggesting a possible role in protein–protein interactions

Structural insights into molecular function of the metastasis-associated phosphatase PRL-3.

Phosphatases and kinases are the cellular signal transduction enzymes that control protein phosphorylation. PRL phosphatases constitute a novel class of small (20 kDa), prenylated phosphatases with oncogenic activity. In particular, PRL-3 is consistently overexpressed in liver metastasis in colorectal cancer cells and represents a new therapeutic target. Here, we present the solution structure of PRL-3, the first structure of a PRL phosphatase. The structure places PRL phosphatases in the class of dual specificity phosphatases with closest structural homology to the VHR phosphatase. The structure, coupled with kinetic studies of site-directed mutants, identifies functionally important residues and reveals unique features, differentiating PRLs from other phosphatases. These differences include an unusually hydrophobic active site without the catalytically important serine/threonine found in most other phosphatases. The position of the general acid loop indicates the presence of conformational change upon catalysis. The studies also identify a potential regulatory role of Cys(49) that forms an intramolecular disulfide bond with the catalytic Cys(104) even under mildly reducing conditions. Molecular modeling of the highly homologous PRL-1 and PRL-2 phosphatases revealed unique surface elements that are potentially important for specificity

Reconstruction of diaminopimelic acid biosynthesis allows characterisation of Mycobacterium tuberculosis N-succinyl-L,L-diaminopimelic acid desuccinylase

With the increased incidence of tuberculosis (TB) caused by Mycobacterium tuberculosis there is an urgent need for new and better anti-tubercular drugs. N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE) is a key enzyme in the succinylase pathway for the biosynthesis of meso-diaminopimelic acid (meso-DAP) and L-lysine. DapE is a zinc containing metallohydrolase which hydrolyses N-succinyl L,L diaminopimelic acid (L,L-NSDAP) to L,L-diaminopimelic acid (L,L-DAP) and succinate. M. tuberculosis DapE (MtDapE) was cloned, over-expressed and purified as an N-terminal hexahistidine ((His)6) tagged fusion containing one zinc ion per DapE monomer. We redesigned the DAP synthetic pathway to generate L,L-NSDAP and other L,L-NSDAP derivatives and have characterised MtDapE with these substrates. In contrast to its other Gram negative homologues, the MtDapE was insensitive to inhibition by L-captopril which we show is consistent with novel mycobacterial alterations in the binding site of this drug

Solution structure of the PDZ2 domain from human phosphatase hPTP1E and its interactions with C-terminal peptides from the Fas receptor

NRC publication: Ye

Solution structure of the PDZ2 domain from human phosphatase hPTP1E and its interactions with C-terminal peptides from the Fas receptor

NRC publication: Ye

Structure of the non-catalytic domain of the protein disulfide isomerase-related protein (PDIR) reveals function in protein binding.

Protein disulfide isomerases comprise a large family of enzymes responsible for catalyzing the proper oxidation and folding of newly synthesized proteins in the endoplasmic reticulum (ER). Protein disulfide isomerase-related (PDIR) protein (also known as PDIA5) is a specialized member that participates in the folding of α1-antitrypsin and N-linked glycoproteins. Here, the crystal structure of the non-catalytic domain of PDIR was determined to 1.5 Å resolution. The structure adopts a thioredoxin-like fold stabilized by a structural disulfide bridge with a positively charged binding surface for interactions with the ER chaperones, calreticulin and ERp72. Crystal contacts between molecules potentially mimic the interactions of PDIR with misfolded substrate proteins. The results suggest that the non-catalytic domain of PDIR plays a key role in the recognition of protein partners and substrates

The structure of phosphate-bound Escherichia coli adenylosuccinate lyase identifies His171 as a catalytic acid

Here, the crystal structure of adenylosuccinate lyase from Escherichia coli was determined to 1.9 Å resolution

Sequence analysis of the PDIR non-catalytic domain.

<p>(A) Occurrence of the domain in protein disulfide isomerases and other proteins. Human ERp57 is shown for comparison. Catalytic motifs are shown in catalytically-active thioredoxin-like domains. (B) Rooted phylogenetic tree of proteins shown in panel (A). Sequences labeled WUBG_02370 and RNA methyltransferase are proteins from parasitic nematodes <i>Wuchereria bancrofti</i> (EJW86719) and <i>Brugia malayi</i> (XP_001896925); mosquito PDIR is from <i>Aedes aegypti</i> (XP_001659136). The N-terminal catalytic domain of ERp57 was used for the phylogenetic tree. The figure was generated with ClustalW <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062021#pone.0062021-Thompson1" target="_blank">[29]</a> and TreeViewPPC <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062021#pone.0062021-Page1" target="_blank">[30]</a>. (C) Sequence alignment of the non-catalytic domain from PDIR proteins from human (NP_006801), rabbit (XP_002716857), rattlesnake (AFJ50881), chicken (XP_422097), zebrafish (XP_001107048), frog (XP_001086600), fly (XP_609645), and sea urchin (XP_001200801) and the related sequence from <i>Brugia malayi</i> RNA methyltransferase (XP_001896925). The consensus sequence is shown below; the secondary structure elements are above the sequence.</p