In a chain-like biological

molecule A molecule is a group of two or more atoms held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which satisfy this criterion. In quantum physics, organic chemistry, and b ...

, such as a

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, res ...

nucleic acid Nucleic acids are biopolymers, macromolecules, essential to all known forms of life. They are composed of nucleotides, which are the monomers made of three components: a 5-carbon sugar, a phosphate group and a nitrogenous base. The two main ...

, a structural motif is a common three-dimensional structure that appears in a variety of different, evolutionarily unrelated molecules. A structural motif does not have to be associated with a

sequence motif In biology, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and usually assumed to be related to biological function of the macromolecule. For example, an ''N''-glycosylation site motif can be defined as ' ...

; it can be represented by different and completely unrelated sequences in different proteins or RNA.

In nucleic acids

Depending upon the sequence and other conditions, nucleic acids can form a variety of structural motifs which is thought to have biological significance. ;

Stem-loop Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded RNA. The structure is also known as a hairpin or hairpin loop. It occurs when two regions of the same strand, usually complementary in nucleotide sequence wh ...

: Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded DNA or, more commonly, in RNA. The structure is also known as a hairpin or hairpin loop. It occurs when two regions of the same strand, usually complementary in nucleotide sequence when read in opposite directions, base-pair to form a double helix that ends in an unpaired loop. The resulting structure is a key building block of many RNA secondary structures. ; Cruciform DNA: Cruciform DNA is a form of non-B DNA that requires at least a 6

nucleotide Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecu ...

sequence of inverted repeats to form a structure consisting of a stem, branch point and loop in the shape of a cruciform, stabilized by negative DNA supercoiling. Two classes of cruciform DNA have been described; folded and unfolded. ;

G-quadruplex In molecular biology, G-quadruplex secondary structures (G4) are formed in nucleic acids by sequences that are rich in guanine. They are helical in shape and contain guanine tetrads that can form from one, two or four strands. The unimolecular ...

: ''G-quadruplex''

secondary structures Secondary may refer to: Science and nature * Secondary emission, of particles ** Secondary electrons, electrons generated as ionization products * The secondary winding, or the electrical or electronic circuit connected to the secondary winding i ...

(G4) are formed in nucleic acids by sequences that are rich in

guanine Guanine () ( symbol G or Gua) is one of the four main nucleobases found in the nucleic acids DNA and RNA, the others being adenine, cytosine, and thymine ( uracil in RNA). In DNA, guanine is paired with cytosine. The guanine nucleoside is ...

. They are helical in shape and contain guanine tetrads that can form from one, two or four strands. ; D-loop: A displacement loop or D-loop is a DNA structure where the two strands of a double-stranded DNA molecule are separated for a stretch and held apart by a third strand of DNA. An R-loop is similar to a D-loop, but in this case the third strand is RNA rather than DNA. The third strand has a base sequence which is complementary to one of the main strands and pairs with it, thus displacing the other complementary main strand in the region. Within that region the structure is thus a form of triple-stranded DNA. A diagram in the paper introducing the term illustrated the D-loop with a shape resembling a capital "D", where the displaced strand formed the loop of the "D".

In proteins

In proteins, a structural motif describes the connectivity between secondary structural elements. An individual motif usually consists of only a few elements, e.g., the 'helix-turn-helix' motif which has just three. Note that, while the ''spatial sequence'' of elements may be identical in all instances of a motif, they may be encoded in any order within the underlying

gene In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a b ...

. In addition to secondary structural elements, protein structural motifs often include loops of variable length and unspecified structure. Structural motifs may also appear as tandem repeats. ; Beta hairpin: Extremely common. Two antiparallel beta strands connected by a tight turn of a few amino acids between them. ; Greek key: Four beta strands, three connected by hairpins, the fourth folded over the top. ; Omega loop: A loop in which the residues that make up the beginning and end of the loop are very close together. ; Helix-loop-helix: Consists of alpha helices bound by a looping stretch of amino acids. This motif is seen in transcription factors. ; Zinc finger: Two beta strands with an alpha helix end folded over to bind a zinc ion. Important in DNA binding proteins. ; Helix-turn-helix: Two α helices joined by a short strand of amino acids and found in many proteins that regulate gene expression. ; Nest: Extremely common. Three consecutive amino acid residues form an anion-binding concavity. ;

Niche Niche may refer to: Science *Developmental niche, a concept for understanding the cultural context of child development * Ecological niche, a term describing the relational position of an organism's species *Niche differentiation, in ecology, the ...

: Extremely common. Three or four consecutive amino acid residues form a cation-binding feature.

References

* PROSITEbr>Database of protein families and domains
* SCOPbr>Structural classification of Proteins
*

CATH The CATH Protein Structure Classification database is a free, publicly available online resource that provides information on the evolutionary relationships of protein domains. It was created in the mid-1990s by Professor Christine Orengo and coll ...

br>Class Architecture Topology Homology
* FSSPbr>FSSP
* PASS2br>PASS2 - Protein Alignments as Structural Superfamilies
* SMoSbr>SMoS - Database of Structural Motifs of Superfamily
*S
S4: Server for Super-Secondary Structure Motif Mining

In nucleic acids

In proteins

See also

References

Further reading