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Structural Motif

In an unbranched, chain-like biological molecule, such as a protein or a strand of RNA, a structural motif is a three-dimensional structural element or fold within the chain, which appears also in a variety of other molecules. In the context of proteins, the term is sometimes used interchangeably with "structural domain," although a domain need not be a motif nor, if it contains a motif, need not be made up of only one.

Structural alignment is a major method for discovering significant structural motifs.

Some motifs exhibit both tertiary and secondary structure, and may be regarded as a configuration of secondary structures. Such a description is the basis for many of the names that structural biologists give to particular kinds, such as the helix-turn-helix motif. This is not always true, however, as in the case of the EF-hand.

Other motifs, especially in proteins, consist of only a small number of amino acids, functional groups or functional atoms and do not depend on any secondary structure. These motifs are often directly involved in a protein's function. For example the catalytic triad made up of a serine, histidine, and aspartic acid is observed in the structures of the unrelated proteins trypsin and subtilisin.

Because the relationship between primary structure and tertiary structure is not straightforward, two biopolymers may share the same motif yet lack appreciable primary structure similarity. In other words, a structural motif does not need to be associated with a sequence motif. Also, the existence of a sequence motif does not necessarily imply a distinctive structure. In most DNA motifs, for example, it is assumed that the DNA of that sequence does not deviate from the normal "double helical" structure.

Structural motifs in proteins

In proteins, structure motifs usually consist of just a few elements, e.g. the 'helix-turn-helix' has just three. Note that while the spatial sequence of elements is the same in all instances of a motif, they may be encoded in any order within the underlying gene. Protein structural motifs often include loops of variable length and unspecified structure, which in effect create the "slack" necessary to bring together in space two elements that are not encoded by immediately adjacent DNA sequences in a gene. Note also that even when two genes encode secondary structural elements of a motif in the same order, nevertheless they may specify somewhat different sequences of amino acids. This is true not only because of the complicated relationship between tertiary and primary structure, but because the size of the elements varies from one protein and the next.

Examples of motif types in proteins

Extremely common. Two antiparallel beta strands connected by a tight turn of a few amino acids between them. 4 beta strands folded over into a sandwich shape. a loop where the residues that make up the beginning and end of the loop are very close together. Consists of alpha helices bound by a looping stretch of amino acids. Important in DNA binding proteins. Two beta strands with an alpha helix end folded over to bind a zinc ion. This motif is seen in transcription factors.
See also: structural domain

See also

References

polymer is a substance composed of molecules with large molecular mass composed of repeating structural units, or monomers, connected by covalent chemical bonds. The word is derived from the Greek, πολυ, polu, "many"; and μέρος, meros,
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molecule is defined as a sufficiently stable electrically neutral group of at least two atoms in a definite arrangement held together by strong chemical bonds.[1][2] In organic chemistry and biochemistry, the term molecule
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Proteins are large organic compounds made of amino acids arranged in a linear chain and joined together by peptide bonds between the carboxyl and amino groups of adjacent amino acid residues.
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Left: An RNA strand, with its nitrogenous bases. Right: Double-stranded DNA.]] Ribonucleic acid or RNA is a nucleic acid polymer consisting of nucleotide monomers, which plays several important roles in the processes of translating genetic information from
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Protein folding is the physical process by which a polypeptide folds into its characteristic three-dimensional structure.[1] Each protein begins as a polypeptide, translated from a sequence of mRNA as a linear chain of amino acids.
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citation, footnoting or external linking.


A structural domain is an element of overall structure within a protein that is self-stabilizing and often folds independently of the rest of the protein chain.
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Structural alignment is a form of sequence alignment based on comparison of shape. These alignments attempt to establish equivalences between two or more polymer structures based on their shape and three-dimensional conformation.
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In biochemistry and chemistry, the tertiary structure of a protein or any other macromolecule is its three-dimensional structure, as defined by the atomic coordinates.[1]

Relationship to primary sequence


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secondary structure is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids (DNA/RNA). It does not, however, describe specific atomic positions in three-dimensional space, which are considered to be tertiary structure.
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Structural biology is a branch of molecular biology concerned with the study of the architecture and shape of biological macromolecules—proteins and nucleic acids in particular—and what causes them to have the structures they have.
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Calmodulin (CaM) is a ubiquitous, calcium-binding protein that can bind to and regulate a multitude of different protein targets, thereby affecting many different cellular functions.
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A catalytic triad commonly refers to the three amino acid residues found inside the active site of certain protease enzymes: serine (S), aspartate (D) and histidine (H). They work together to break peptide bonds on polypeptides.
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Serine (abbreviated as Ser or S)[1] is an organic compound with the formula HO2CCH(NH2)CH2OH. It is one of the 20 naturally occurring proteinogenic amino acids. Its codons are UCU, UCC, UCA, UCG, AGU and AGC.
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Histidine (abbreviated as His or H)[1] is one of the 20 most common natural amino acids present in proteins. In the nutritional sense, in humans, histidine is considered an essential amino acid, but mostly only in children.
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Aspartic acid or aspartate (abbreviated as Asp or D; Asx or B represent either aspartic acid or asparagine)[1] is an α-amino acid with the chemical formula HO2CCH(NH2)CH2CO2H.
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Identifiers
Symbol PRSS2

Entrez 5645
HUGO 9483
OMIM 601564

RefSeq NM_002770
UniProt P07478
Other data

Locus Chr. 7 q35

protease, serine, 3 (mesotrypsin)


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Subtilisin (serine endopeptidase) is a proteolytic enzyme initially obtained from Bacillus subtilis. It is secreted in large amounts from many Bacillus species.

The structure of subtilisin has been determined by X-ray crystallography.
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primary structure of a biological molecule is the exact specification of its atomic composition and the chemical bonds connecting those atoms (including stereochemistry). For a typical unbranched, un-crosslinked biopolymer (such as a molecule of DNA, RNA or typical intracellular
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In genetics, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and has, or is conjectured to have, a biological significance. For proteins, a sequence motif is distinguished from a structural motif, a motif formed by the three dimensional
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For a non-technical introduction to the topic, see .
A gene is a locatable region of genomic sequence, corresponding to a unit of inheritance, which is associated with regulatory regions, transcribed regions and/or other functional sequence regions.
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DNA sequence or genetic sequence is a succession of letters representing the primary structure of a real or hypothetical DNA molecule or strand, with the capacity to carry information.
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amino acid is a molecule that contains both amine and carboxyl functional groups. In biochemistry, this term refers to alpha-amino acids with the general formula H2NCHRCOOH, where R is an organic substituent.
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Greek key refers to a kind of supersecondary structure or motif of a protein (amino-acid) sequence. It is named for its resemblance to the Greek key meander pattern in art.
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The omega loop is a protein motif. It consists of a loop of any length and any amino acid sequence. The only requirement is that residues that make up the beginning and end of the loop are very close together.
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basic-helix-loop-helix (bHLH) is a protein structural motif that characterizes a family of transcription factors.

Structure

The motif is characterized by two α helices connected by a loop.
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zinc finger is a protein domain that can bind to DNA. A zinc finger consists of two antiparallel β sheets, and an α helix. The zinc ion is crucial for the stability of this domain type - in absence of the metal ion the domain unfolds as it is too small to have a
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citation, footnoting or external linking.


A structural domain is an element of overall structure within a protein that is self-stabilizing and often folds independently of the rest of the protein chain.
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helix-turn-helix (HTH) is a major structural motif capable of binding DNA. It is composed of two α helices joined by a short strand of amino acids and is found in many proteins that regulate gene expression.
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The beta hairpin (or beta-beta unit) structural motif is the simplest protein motif involving two beta strands that look like a hairpin. The motif consists of two strands that are adjacent in primary sequence oriented in an antiparallel arrangement (where the
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