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Kringles definition: Triple-looped protein domains linked by disulfide bonds. These common structural domains, so-named for their resemblance to Danish pastries known as kringlers, play a role in binding membranes, proteins, and phospholipids as well as in regulating proteolysis. Kringles are also present in coagulation-related and fibrinolytic proteins and other plasma proteinases.
Kringle Domain definition: Kringles are autonomous structural domains, found throughout the blood clotting and fibrinolytic proteins. Kringle domains are believed to play a role in binding mediators (e.g., membranes, other proteins or phospholipids), and in the regulation of proteolytic activity. Kringle domains are characterised by a triple loop, 3-disulphide bridge structure, whose conformation is defined by a number of hydrogen bonds and small pieces of anti-parallel beta-sheet. They are found in a varying number of copies, in some serine proteases and plasma proteins.
Immunodominant Epitopes definition: Subunits of the antigenic determinant that are most easily recognized by the immune system and thus most influence the specificity of the induced antibody.
Protein Structure, Tertiary definition: The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.
Tertiary Protein Structure definition: Tertiary structure describes the folding of the polypeptide chain to assemble the different secondary structure elements in a particular arrangement.
SH2 Domain definition: A region of protein sequence similarity among members of the SRC family of cytoplasmic tyrosine kinases, and other proteins. The SH2 domain usually mediates binding to phosphotyrosine and neighboring residues of target proteins.
SH3 Domain definition: A region of protein sequence similarity among members of the SRC family of cytoplasmic tyrosine kinases, and other proteins. The SH3 domain is a protein-binding domain that interacts with cytoskeletal proteins.
src Homology Domains definition: Regions of AMINO ACID SEQUENCE similarity in the SRC-FAMILY TYROSINE KINASES that fold into specific functional tertiary structures. The SH1 domain is a CATALYTIC DOMAIN. SH2 and SH3 domains are protein interaction domains. SH2 usually binds PHOSPHOTYROSINE-containing proteins and SH3 interacts with CYTOSKELETAL PROTEINS.
Catalytic Domain definition: The region of an enzyme that interacts with its substrate to cause the enzymatic reaction.
LIM Domains Containing 1 definition: LIM Domains Containing 1 is encoded by the LIMD1 gene. LIM domains consist of a cysteine-rich consensus sequence containing two distinct zinc-binding subdomains, which mediate protein-protein interactions. The predicted protein sequence reveals three LIM domains located at the C-terminal end, which indicates that it belongs to the group 3 of the gene family encoding LIM motifs. The LIM motif has been previously identified in many developmentally important factors from various eukaryotes. These factors have been shown to play a role in intracellular signaling, transcriptional regulation and cellular differentiation during development. The LIMD1 gene may have a role in tumor suppression. (from PubMed)
HMG-Box Domains definition: DNA-binding domains present in proteins of the HMG-box superfamily including the archetypal HMGB PROTEINS, a number of sequence specific TRANSCRIPTION FACTORS, and other DNA-BINDING PROTEINS. The domains consist of 70-80 amino acids that form an L-shaped fold from three alpha-helical segments. The domain has the capacity to recognize and/or induce specific DNA structures and effect the accessibility of the DNA to other proteins involved in transcription, recombination, or DNA repair. (Note that not all HIGH MOBILITY GROUP PROTEINS contain this domain.)
BAG4 Gene definition: This gene plays a role in receptor signaling and the inhibition of apoptosis.
FHL2 Gene definition: This gene is involved in cellular signaling and the mediation of protein-protein interactions.
Four and a Half LIM Domains 2 Protein definition: Members of the four-and-a-half-LIM domain (FHL) protein family, which are expressed in a tissue- and stage-specific manner, have been reported to function as transcriptional coactivators. Expression of DRAL (FHL2) results in enhancement of NF-kappaB activation. DRAL (FHL2) is a p53-responsive gene implicated in induction of apoptosis. DRAL may participate in a regulatory mechanism that coordinates cellular responses controlled by NF-kappaB transcription factor. (from J Biol Chem 2002;277:37045-53 and FEBS Lett 2002;521(1-3):165-9)
LIMD1 Gene definition: This gene is involved in intracellular signaling, which effects several cellular processes during development.
CHFR Gene definition: This gene is involved in the mitotic checkpoint.
Chromatin Loop definition: A higher order chromatin structure above the level of the chromatin fiber. The organization of chromatin into loops permits the partitioning of chromatin into topologically independent domains, and is thought to facilitate its compartmentation into functionally independent regions.
RING Finger Domains definition: A zinc-binding domain defined by the sequence Cysteine-X2-Cysteine-X(9-39)-Cysteine-X(l-3)-His-X(2-3)-Cysteine-X2-Cysteine -X(4-48)-Cysteine-X2-Cysteine, where X is any amino acid. The RING finger motif binds two atoms of zinc, with each zinc atom ligated tetrahedrally by either four cysteines or three cysteines and a histidine. The motif also forms into a unitary structure with a central cross-brace region and is found in many proteins that are involved in protein-protein interactions. The acronym RING stands for Really Interesting New Gene.
Ring Finger Domain definition: The RING finger is a specialized type of Zn-finger consisting of 40 to 60 residues that binds two atoms of zinc, and is involved in mediating protein-protein interactions. The RING domain mediates the interaction with the appropriate E2 enzyme. Unlike HECT E3 enzymes that form a thiol-ester with ubiquitin, RING fingers likely mediate ubiquitination by facilitating the direct transfer of ubiquitin from E2 enzyme to lysine residues on the target substrate. (NCI)
Ring Finger Domain definition: RING finger domains are defined by the consensus sequence CX2CX(9-39)CX(1-3)HX(2-3)C/HX2CX(4-48)CX2C with the Cys and His representing zinc binding residues. RING fingers are further divided into RING-HC and RING-H2, depending on whether a Cys or His occupies the fifth coordination site. While RING fingers are structurally diverse, all contain two interleaved Zn2+ binding sites. Binding of the Cbl RING domain to the E2 protein, UbcH7, occurs between a groove within the RING domain and two loops in the E2 fold of UbcH7. Van der Waals interactions involving hydrophobic residues in both the E2 and RING domains support the Cbl-UbcH7 binding, though this is not universal as the RING-E2 pair of Rad18p and Rad6p/Ubc2p interact by hydrogen bonding of polar residues.
Protein Interaction Domains and Motifs definition: Protein modules with conserved ligand-binding surfaces which mediate specific interaction functions in SIGNAL TRANSDUCTION PATHWAYS and the specific BINDING SITES of their cognate protein LIGANDS.
Protein Interaction Domains definition: Recognition modules in proteins that mediate interactions between specific proteins involved in SIGNAL TRANSDUCTION PATHWAYS. They fold to form recognition pockets complementary to the short interaction sequence motifs on their LIGANDS.
PDZ Domains definition: Protein interaction domains of about 70-90 amino acid residues, named after a common structure found in PSD-95, Discs Large, and Zona Occludens 1 proteins. PDZ domains are involved in the recruitment and interaction of proteins, and aid the formation of protein scaffolds and signaling networks. This is achieved by sequence-specific binding between a PDZ domain in one protein and a PDZ motif in another protein.
Proline-Rich Protein Domains definition: Protein domains that are enriched in PROLINE. The cyclical nature of proline causes the peptide bonds it forms to have a limited degree of conformational mobility. Therefore the presence of multiple prolines in close proximity to each other can convey a distinct conformational arrangement to a peptide chain.