PROCOGNATE: a cognate ligand domain mapping for enzymes
نویسندگان
چکیده
PROCOGNATE is a database of protein cognate ligands for the domains in enzyme structures as described by CATH, SCOP and Pfam, and is available as an interactive website or a flat file. This article gives an overview of the database and its generation and presents a new website front end, as well as recent increased coverage in our dataset via inclusion of Pfam domains. We also describe navigation of the website and its features. The current version (1.3) of PROCOGNATE covers 4123, 4536, 5876 structures and 377, 326, 695 superfamilies/families in CATH, SCOP and Pfam, respectively. PROCOGNATE can be accessed at: http://www.ebi.ac.uk/thornton-srv/databases/procognate/
منابع مشابه
Substrate recruitment of γ-secretase and mechanism of clinical presenilin mutations revealed by photoaffinity mapping.
Intramembrane proteases execute fundamental biological processes ranging from crucial signaling events to general membrane proteostasis. Despite the availability of structural information on these proteases, it remains unclear how these enzymes bind and recruit substrates, particularly for the Alzheimer's disease-associated γ-secretase. Systematically scanning amyloid precursor protein substrat...
متن کاملSubstrate recruitment of c-secretase and mechanism of clinical presenilin mutations revealed by photoaffinity mapping
Intramembrane proteases execute fundamental biological processes ranging from crucial signaling events to general membrane proteostasis. Despite the availability of structural information on these proteases, it remains unclear how these enzymes bind and recruit substrates, particularly for the Alzheimer’s diseaseassociated c-secretase. Systematically scanning amyloid precursor protein substrate...
متن کاملMolecular dynamics simulation study of the binding of purine bases to the aptamer domain of the guanine sensing riboswitch
Riboswitches are a novel class of genetic control elements that function through the direct interaction of small metabolite molecules with structured RNA elements. The ligand is bound with high specificity and affinity to its RNA target and induces conformational changes of the RNA's secondary and tertiary structure upon binding. To elucidate the molecular basis of the remarkable ligand selecti...
متن کاملPhosphorylation and intramolecular stabilization of the ligand binding domain in the nuclear receptor steroidogenic factor 1.
Steroidogenic factor 1 (SF-1) is an orphan nuclear receptor with no known ligand. We showed previously that phosphorylation at serine 203 located N'-terminal to the ligand binding domain (LBD) enhanced cofactor recruitment, analogous to the ligand-mediated recruitment in ligand-dependent receptors. In this study, results of biochemical analyses and an LBD helix assembly assay suggest that the S...
متن کاملComplexity in ‘2-component’ signal transduction systems
The prototypical (Class I) sensory histidine kinase is comprised of a ligand binding domain coupled to an autokinase domain (Figure 1A). Ligand binding causes activation of the catalytic autokinase domain which hydrolyses ATP and autophosphorylates a conserved histidine residue located in a sub-domain of the histidine kinase. Transfer of this high energy phosphoryl group to a conserved aspartat...
متن کامل