This entry represents a domain found in the C-terminal of bacterial type II CRISPR system Cas9 endonuclease. This domain adopts a novel protein fold that is unique to the Cas9 family. It is positioned in the structure-DNA-complex to recognise the PAM sequence on the non-complementary DNA strand of the crRNA. PAM sequence is protospacer-adjacent motifs on DNA. Cas9 carries two nuclease domains, HNH and RuvC, which cleave the DNA strands that are complementary and non-complementary to the 20 nucleotide guide sequence in crRNAs, respectively [].
Tim44 is an essential component of the PAM complex, which is required for the translocation of transit peptide-containing proteins from the inner membrane into the mitochondrial matrix in an ATP-dependent manner. It recruits mitochondrial HSP70 to drive protein translocation into the matrix using ATP as an energy source [].
This entry includes mitochondrial import inner membrane translocase subunit Tim44 andits bacterial homologues. All possess a Tim44-like domain.Tim44 is an essential component of the PAM complex, which is required for the translocation of transit peptide-containing proteins from the inner membrane into the mitochondrial matrix in an ATP-dependent manner. It recruits mitochondrial HSP70 to drive protein translocation into the matrix using ATP as an energy source [].
This domain is found in Cas9 proteins from some bacteria, such as Staphylococcus aureus. Cas9 cleaves double-stranded DNA targets with a protospacer adjacent motif (PAM) and complementarity to the guide RNA. When this domain is combined with the C-terminal domain it is called the Pam-interacting (PI) domain. The Cas9 orthologs from different microbes have highly divergent sequences but their PI domains share a conserved core fold andrecognize distinct PAM sequences [].
CRISPR (clustered regularly interspaced short palindromic repeat) is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA) to guide the silencing of invading nucleic acids. In type II CRISPR systems, correct processing of pre-crRNA requires a trans-encoded small RNA (tracrRNA), endogenous ribonuclease 3 (rnc) and this protein, Cas9 (Csn1) []. The tracrRNA serves as a guide for ribonuclease 3-aided processing of pre-crRNA. Subsequently Cas9/crRNA/tracrRNA endonucleolytically cleaves linear or circular dsDNA target complementary to the spacer []. Cas9 probably recognises a short motif in the CRISPR repeat sequences (the PAM or protospacer adjacent motif) to help distinguish self versus nonself.
This domain is called PHR as it was originally found in the E3 ubiquitin-protein ligase proteins PAM (), highwire () and RPM-1 () [].PHR proteins are conserved, large multi-domain E3 ubiquitin ligases with modular architecture. PHR proteins presynaptically control synaptic growth and axon guidance and postsynaptically regulate endocytosis of glutamate receptors. Dysfunction of neuronal ubiquitin-mediated proteasomal degradation is implicated in various neurodegenerative diseases. PHR proteins are characterised by the presence of two PHR domains near the N terminus, which are essential for proper localisation and function. The domain has a β-sandwich fold composed of 11 anti-parallel β-strands [].The C-terminal region of the protein BTBD1 includes the PHR domain and is known to interact with Topoisomerase I, an enzyme which relaxes DNA supercoils [].
This domain is called PHR as it was originally found in the E3 ubiquitin-protein ligase proteins PAM (), highwire () and RPM-1 () [].PHR proteins are conserved, large multi-domain E3 ubiquitin ligases with modular architecture. PHR proteins presynaptically control synaptic growth and axon guidance and postsynaptically regulate endocytosis of glutamate receptors. Dysfunction of neuronal ubiquitin-mediated proteasomal degradation is implicated in various neurodegenerative diseases. PHR proteins are characterised by the presence of two PHR domains near the N terminus, which are essential for proper localisation and function. The domain has a β-sandwich fold composed of 11 anti-parallel β-strands [].The C-terminal region of the protein BTBD1 includes the PHR domain and is known to interact with Topoisomerase I, an enzyme which relaxes DNA supercoils [].
The Ras association domain (RASSF) proteins are named due to the presence of a Ras association (RA) domain in their N or C terminus that can potentially interact with the Ras GTPase family of proteins. These GTPases control a variety of cellular processes, such as membrane trafficking, apoptosis, and proliferation. RASSF proteins contain several other functional domains that modulate associations with other proteins. RASSF proteins with the RA domain at the C terminus (which are termed C-terminal or classical RASSF) usually also include a Salvador-RASSF-Hippo (SARAH) domain involved in several protein-protein interactions and for homo- and heterodimerisation of RASSF isoforms. N-terminal RASSF proteins (with the RA domain in the N terminus) do not usually contain a SARAH domain [].At least 10 RASSF family members have been characterised (with multiple splice variants), many of which have been shown to play a role in tumour suppression. RASSF proteins also act as scaffolding agents in microtubule stability, regulate mitotic cell division, control cell migration and cell adhesion, and modulate NF-KB activity and the duration of inflammation. Loss of RASSF expression through promoter methylation has been shown in numerous types of cancer, including leukemia, melanoma, breast and prostate cancer [].RASSF9 is one of the N-terminal RASSF proteins, characterised by an RA domain in the N terminus. It was previously called P-CIP1 (peptidylglycine alpha-amidating monooxygenase (PAM) COOH-terminal interactor protein-1), and was believed to play a role in the regulation of PAM in endosomal pathways []. Very little else is known about the function of RASSF9, but it has been suggested to be involved in epidermal homeostasis [].
