The main entity of this document is a entry with accession number PTHR10623

This region, found at the C-terminus of the APC proteins, binds the microtubule-associating protein EB-1 . At the C-terminus of the alignment is also a [pfam:PF00595] binding domain. A short motif in the middle of the region appears to be found in the APC2 proteins (e.g [swissprot:O95996]).

The EB-eye Search system is developed on top of the Apache Lucene project framework, which is an Open-source, high-performance, full-featured text search engine library written entirely in Java. It uses this technology to index EBI databases in various formats (e.g. flatfiles, XML dumps, OBO format, etc.) and provides very fast access to the EBI''s data resources. The system allows the user to search globally across all EBI databases or individually in selected resources by using an Advance search.

This entry represents the microtubule-associated protein RP/EB (MAPRE) family, including MAPRE1 (EB1), MAPRE2 (RP1, also known as EB2), MAPRE3 (EBF3, also known as EB3) and their homologues from eukaryotes. Despite their high protein sequence conservation, the individual EBs exhibit different regulatory and functional properties . For instance, EB1 and EB3, but not EB2, promote persistent microtubule growth by suppressing catastrophes .EB1 contains an N-terminal calponin homology (CH) domain that is responsible for the interaction with microtubules (MTs), and a C-terminal coiled coil domain that extends into a four-helix bundle, required for dimer formation . Through their C-terminal sequences, EBs interact with most other known +TIPs (plus end tracking proteins) and recruit many of them to the growing MT ends . EB1 is involved in MT anchoring at the centrosome and cell migration .EB2 is highly expressed in pancreatic cancer cells, and seems to be involved in perineural invasion .

The main entity of this document is a structure with accession number 1v5k

This domain has no known function. It is found in several C. elegans proteins. The domain contains 8 conserved cysteines that probably form four disulphide bridges. This domain is found associated with kunitz domains [pfam:PF00014].

The main entity of this document is a structure with accession number 4bj9

The MiT/TFE family of basic helix-loop-helix leucine zipper transcription factors includes MITF (microphthalmia-associated transcription factor) and related family members TFE3, TFEB and TFEC . The transcription factors heterodimerize with each other and recognise the same DNA sequences . They recognise and bind E-box sequences (3'-CANNTG-5').

A group of microtubule-associated proteins called +TIPs (plus end tracking proteins), including EB1 (end-binding protein 1) family proteins, label growing microtubules ends specifically in diverse organisms and are implicated in spindle dynamics, chromosome segregation, and directing microtubules toward cortical sites. EB1 members have a bipartite composition: the N-terminal CH domain ([interpro:IPR001715]) mediates microtubule plus end localization and a C-terminal cargo binding domain (EB1-C) that captures cell polarity determinants. The EB1-C domain comprises a unique EB1-like sequence motif that acts as a binding site for other +TIP proteins. It interacts with the carboxy terminus of the adenomatous polyposis coli (APC) tumor suppressor, a well conserved +TIP phosphoprotein with a pivotal function in cell cycle regulation. Another binding partner of the EB1-C domain is the well conserved +TIP protein dynactin, a component of the large cytoplasmic dynein/dynactin complex .The ~80-residue EB1-C domain starts with a long smoothly curved helix (alpha1), which is followed by a hairpin connection leading to a short second helix (alpha2) running antiparallel to alpha1. The two parallel alpha1 helices of the EB1-C domain dimer wrap around each other in a slightly left-handed supercoil. The two alpha2 helices run antiparallel to helices alpha1 and form a similar fork in the opposite orientation and rotated by 90 degrees. As a result, two helical segments from each monomer form a four-helix bundle. The side chain forming the hydrophobic core of this bundle are highly conserved .Some protein known to contain an EB1-C domain are listed below:Yeast protein BIM1.Fission yeast microtubule integrity protein mal3.Vertebrate microtubule-associated protein RP/EB family member 1 (EB1).Vertebrate microtubule-associated protein RP/EB family member 2 (EB2 or RP1).Vertebrate microtubule-associated protein RP/EB family member 3 (EBF3).

A group of microtubule-associated proteins called +TIPs (plus end tracking proteins), including EB1 (end-binding protein 1) family proteins, label growing microtubules ends specifically in diverse organisms and are implicated in spindle dynamics, chromosome segregation, and directing microtubules toward cortical sites. EB1 members have a bipartite composition: the N-terminal CH domain ([interpro:IPR001715]) mediates microtubule plus end localization and a C-terminal cargo binding domain (EB1-C) that captures cell polarity determinants. The EB1-C domain comprises a unique EB1-like sequence motif that acts as a binding site for other +TIP proteins. It interacts with the carboxy terminus of the adenomatous polyposis coli (APC) tumor suppressor, a well conserved +TIP phosphoprotein with a pivotal function in cell cycle regulation. Another binding partner of the EB1-C domain is the well conserved +TIP protein dynactin, a component of the large cytoplasmic dynein/dynactin complex .The ~80-residue EB1-C domain starts with a long smoothly curved helix (alpha1), which is followed by a hairpin connection leading to a short second helix (alpha2) running antiparallel to alpha1. The two parallel alpha1 helices of the EB1-C domain dimer wrap around each other in a slightly left-handed supercoil. The two alpha2 helices run antiparallel to helices alpha1 and form a similar fork in the opposite orientation and rotated by 90 degrees. As a result, two helical segments from each monomer form a four-helix bundle. The side chain forming the hydrophobic core of this bundle are highly conserved .Some protein known to contain an EB1-C domain are listed below:Yeast protein BIM1.Fission yeast microtubule integrity protein mal3.Vertebrate microtubule-associated protein RP/EB family member 1 (EB1).Vertebrate microtubule-associated protein RP/EB family member 2 (EB2 or RP1).Vertebrate microtubule-associated protein RP/EB family member 3 (EBF3).

Catalyzes the conversion of 6-deoxyerythronolide B (6-DEB) to erythronolide B (EB) by the insertion of an oxygen at the 6S position of 6-DEB. Requires the participation of a ferredoxin and a ferredoxin reductase for the transfer of electrons from NADPH to the monooxygenase

A group of microtubule-associated proteins called +TIPs (plus end trackingproteins), including EB1 (end-binding protein 1) family proteins, labelgrowing microtubules ends specifically in diverse organisms and are implicatedin spindle dynamics, chromosome segregation, and directing microtubules towardcortical sites. EB1 members have a bipartite composition: the N-terminal CHdomain mediates microtubule plus end localization and a C-terminal cargo binding domain (EB1-C) that captures cell polaritydeterminants. The EB1-C domain comprises a unique EB1-like sequence motif thatacts as a binding site for other +TIP proteins. It interacts with the carboxyterminus of the adenomatous polyposis coli (APC) tumor suppressor, a wellconserved +TIP phosphoprotein with a pivotal function in cell cycleregulation. Another binding partner of the EB1-C domain is the well conserved+TIP protein dynactin, a component of the large cytoplasmic dynein/dynactincomplex .The ~80-residue EB1-C domain starts with a long smoothly curved helix(alpha1), which is followed by a hairpin connection leading to a short secondhelix (alpha2) running antiparallel to alpha1. The twoparallel alpha1 helices of the EB1-C domain dimer wrap around each other in aslightly left-handed supercoil. The two alpha2 helices run antiparallel tohelices alpha1 and form a similar fork in the opposite orientation and rotatedby 90 degrees. As a result, two helical segments from each monomer form afour-helix bundle. The side chain forming the hydrophobic core of this bundleare highly conserved .Some protein known to contain a EB1-C domain are listed below: - Yeast protein BIM1. - Fission yeast microtubule integrity protein mal3. - Vertebrate microtubule-associated protein RP/EB family member 1 (EB1). - Vertebrate microtubule-associated protein RP/EB family member 2 (EB2 or RP1). - Vertebrate microtubule-associated protein RP/EB family member 3 (EBF3).The profile we developed covers the entire EB1-C domain.

Using Mycoplasma pneumoniae as a model organism, we conditionally depleted the two essential ATP-dependent proteases (Lon and FtsH) of this bacterium, by engineering three strains carrying a Lon and/or FtsH inducible expression locus. An integrative comparative study combining label-free shotgun proteomics and RNA-seq allowed us to decipher the global cellular response to Lon and FtsH depletion and to define protease substrates in this genome-reduced organism.

The obligate intracellular developmental cycle of Chlamydia trachomatis presents significant challenges in defining its proteome. In this study we have applied quantitative proteomics to both the intracellular reticulate body (RB) and the extracellular elementary body (EB) from C. trachomatis. We used C. trachomatis L2 which is a model chlamydial isolate for such a study since it has a high infectivity: particle ratio and there is an excellent quality genome sequence. EBs and RBs (>99% pure) were quantified by chromosomal and plasmid copy number using PCR to determine the concentrations of chlamydial proteins per bacterial cell. RBs harvested at 15h post infection (PI) were purified by three successive rounds of gradient centrifugation. This is the earliest possible time to obtain purified RBs, free from host cell components in quantity, within the constraints of the technology, EBs were purified at 48h PI. We then used two-dimensional reverse phase UPLC to fractionate RB or EB peptides before mass spectroscopic analysis, providing absolute amount estimates of chlamydial proteins.

Three cysteine-rich proteins (also believed to be lipoproteins) make up the extracellular matrix of the Chlamydial outer membrane . They are involved in the essential structural integrity of both the elementary body (EB) and recticulate body (RB) phase. As these bacteria lack the peptidoglycan layer common to most Gram-negative microbes, such proteins are highly important in the pathogenicity of the organism.The largest of these is the major outer membrane protein (MOMP), and constitutes around 60% of the total protein for the membrane . OMP6 is the second largest, with a molecular mass of 58kDa, while the OMP3 protein is ~15kDa . MOMP is believed to elicit the strongest immune response, and has recently been linked to heart disease through its sequence similarity to a murine heart-muscle specific alpha myosin .The OMP6 family plays a structural role in the outer membrane during the EB stage of the Chlamydial cell, and different biovars show a small, yet highly significant, change at peptide charge level . Members of this family include Chlamydia trachomatis, Chlamydia pneumoniae and Chlamydia psittaci.

Reversible phosphorylation of the transcription factor EB (TFEB) coordinates cellular responses to metabolic and other stresses. During nutrient replete and stressor-free conditions, phosphorylated TFEB is primarily localised to the cytoplasm. Stressor-mediated reduction of TFEB phosphorylation promotes its nuclear translocation and context-dependent transcriptional activity. In this study, we explored targeted dephosphorylation of TFEB as an approach to activate TFEB in the absence of nutrient deprivation or other cellular stress. Through an induction of proximity between TFEB and several phosphatases using the AdPhosphatase system, we demonstrate targeted dephosphorylation of TFEB in cells. Furthermore, by developing a heterobifunctional molecule BDPIC (bromoTAG-dTAG proximity-inducing chimera), we demonstrate targeted dephosphorylation of TFEB-dTAG through induced proximity to bromoTAG-PPP2CA. Targeted dephosphorylation of TFEB-dTAG by bromoTAG-PPP2CA with BDPIC at the endogenous levels is sufficient to induce nuclear translocation and some transcriptional activity of TFEB.

This entry represents DUF11 domain found in large cysteine-rich periplasmic protein OmcB proteins from bacteria and archaea. It adopts an Ig-like fold.Some members contain conserved N-terminal lysine and C-terminal asparagine with central aspartate/glutamate suggesting that these domains may contain an isopeptide bond.In C. trachomatis, three cysteine-rich proteins (also believed to be lipoproteins), MOMP, OMP6 and OMP3, make up the extracellular matrix of the outer membrane . They are involved in the essential structural integrity of both the elementary body (EB) and reticulate body (RB) phase. They are thought to be involved in porin formation and, as these bacteria lack the peptidoglycan layer common to most Gram-negative microbes, such proteins are highly important in the pathogenicity of the organism.In Methanothermobacter sp. CaT2, a DUF11-containing repeat hypothetical protein encoded by MTCT_1020 plays a key role as a membrane-bound adhesion protein in the aggregation of CaT2. DUF11-containing repeat domains are not involved in aggregation, but may be important for stabilizing the surface cell wall structures of CaT2 .

This entry represents a family of multi-SAM containing proteins (MSCPs) predominantly found in animals, including Ankyrin repeat and SAM domain-containing protein 1A (ANKS1A, also known as Odin), Ankyrin repeat and sterile alpha motif domain-containing protein 1B (ANKS1B, also known as AIDA-1 or EB-1) and Caskin-1/2. Structurally, ANKS1 proteins consist of N-terminal ankyrin motifs followed by tandem sterile alpha motif (SAM) domains and a carboxyl phosphotyrosine binding (PTB) domain while Caskin-1/2 show N-terminal ankyrin repeats, an SH3 domain, two SAM domains, and an extended Proline-rich C-terminal tail .