Structural proteins are now known to be as necessary for controlling cell division and cell shape in prokaryotes as they are in eukaryotes. Bacterial ParM and MreB not only have atomic structures that resemble eukaryotic actin and form similar filaments, but they are also equivalent in function: the assembly of ParM drives intracellular motility and MreB maintains the shape of the cell. FtsZ re...

The nucleotide sequences of two DNA segments from Pseudomonas sp. strain CBS3 that code for two different haloalkanoic acid halidohydrolases were determined. Two open reading frames with coding capacities of 227 amino acids (corresponding to a molecular mass of 25,401 Da) and 229 amino acids (corresponding to a molecular mass of 25,683 Da) were identified as structural genes of 2-haloalkanoic a...

MOTIVATION Detecting homologous proteins is one of the fundamental problems in computational biology. Many tools to solve this problem have been developed, but development of a simple, effective and generally applicable method is still desirable. RESULTS We propose a simple but effective information retrieval approach, named SIMPRO, to identify homology relationship between proteins. The key ...

Computational methods for homology detection between protein sequences have become a central component in genome analysis. Nowadays, sequences of unknown function are routinely searched against databases of known proteins, providing an important aid for sequence annotation and for guiding laboratory experiments. Although homology identification through pairwise sequence matching [1, 2] is still...

After the atomic coordinates themselves, the most important data in a homology model are the spatial reliability estimates associated with each of the atoms (atom annotation). Recent blind homology modeling predictions have demonstrated that principally correct sequence-structure alignments are achievable to sequence identities as low as 25% [Martin, A.C., MacArthur, M.W., Thornton, J.M., 1997....

Ribosomal proteins of the model gram-positive bacterium B. subtilis 168 were extensively characterized in a proteomic study. Mass spectra of the 52 proteins expected to be constitutive components of the 70S ribosome were recorded. Peptide MS/MS analysis with an average sequence coverage of 85% supported the identification of these proteins and facilitated the unambiguous assignment of post-tran...

Oncostatin M (OM) is a member of the cytokine family which regulates the proliferation and differentiation of a variety of cell types and includes interleukin-6 (IL-6), leukemia inhibitory factor (LIF), and granulocyte-colony stimulating factor (G-CSF). This family of proteins adopts a four-helix bundle fold with up-up-down-down topology and contains intramolecular disulfide bonds. Since an X-r...

As a part of a structural genomics program, the 2.2 angstroms resolution crystal structure of the PurC gene product from Thermotoga maritima has been solved. This 26.2 kDa protein belongs to the phophoribosylaminoimidazole-succinocarboxamide or SAICAR synthase family of enzymes, the members of which are involved in de novo purine biosynthesis. SAICAR synthase can be divided into three subdomain...

Post-translational modification by ubiquitin (ubiquitination, ubiquitylation, ubiquitinylation) is used as a robust signaling mechanism in a variety of processes that are essential for cell homeostasis. Its signaling specificity is conferred by the inherent dynamics of ubiquitin, the multivalency of ubiquitin chains, and its subcellular context, often defined by ubiquitin receptors and the subs...

Paralogous genes are genes which descend from a progenitor gene which has duplicated as an ancestral gene, each copy having diverged prior to speciation. With comprehensive information available on functions of Escherichia coli proteins, analysis of sequence-related E. coli paralogous proteins can give information on the early ancestors of families of proteins now residing in many contemporary ...