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 bioch ...

, 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, respo ...

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 cl ...

, 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 ''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 when ...

: 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, or an alternative DNA structure. The formation of cruciform DNA requires the presence of palindromes called inverted repeat sequences. These inverted repeats contain a sequence of DNA in one strand that is rep ...

: 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 biomolecules wi ...

sequence of

inverted repeats An inverted repeat (or IR) is a single stranded sequence of nucleotides followed downstream by its reverse complement. The intervening sequence of nucleotides between the initial sequence and the reverse complement can be any length including zero. ...

to form a structure consisting of a stem, branch point and loop in the shape of a cruciform, stabilized by negative

DNA supercoiling DNA supercoiling refers to the amount of twist in a particular DNA strand, which determines the amount of strain on it. A given strand may be "positively supercoiled" or "negatively supercoiled" (more or less tightly wound). The amount of a st ...

. Two classes of cruciform DNA have been described; folded and unfolded. ;

G-quadruplex In molecular biology, G-quadruplex Nucleic acid secondary structure, 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 o ...

: ''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 ...

(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 called ...

. They are helical in shape and contain guanine tetrads that can form from one, two or four strands. ;

D-loop In molecular biology, 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 cas ...

: 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 An R-loop is a three-stranded nucleic acid structure, composed of a DNA:RNA hybrid and the associated non-template single-stranded DNA. R-loops may be formed in a variety of circumstances, and may be tolerated or cleared by cellular components. T ...

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 A complement is something that completes something else. Complement may refer specifically to: The arts * Complement (music), an interval that, when added to another, spans an octave ** Aggregate complementation, the separation of pitch-class ...

to one of the main strands and

pairs Concentration, also known as Memory, Shinkei-suijaku (Japanese meaning "nervous breakdown"), Matching Pairs, Match Match, Match Up, Pelmanism, Pexeso or simply Pairs, is a card game in which all of the cards are laid face down on a surface and tw ...

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 Triple-stranded DNA (also known as H-DNA or Triplex-DNA) is a DNA structure in which three oligonucleotides wind around each other and form a triple helix. In triple-stranded DNA, the third strand binds to a B-form DNA (via Watson–Crick bas ...

. 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 ba ...

. 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 Tandem repeats occur in DNA when a pattern of one or more nucleotides is repeated and the repetitions are directly adjacent to each other. Several protein domains also form tandem repeats within their amino acid primary structure, such as armadil ...

. ;

Beta hairpin The beta hairpin (sometimes also called beta-ribbon or beta-beta unit) is a simple protein structural motif involving two beta strands that look like a hairpin. The motif consists of two strands that are adjacent in primary structure, oriented in ...

: 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 The omega loop is a non-regular protein structural motif, consisting of a loop of six or more amino acid residues and any amino acid sequence. The defining characteristic is that residues that make up the beginning and end of the loop are close tog ...

: 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 The alpha helix (α-helix) is a common motif in the secondary structure of proteins and is a right hand-helix conformation in which every backbone N−H group hydrogen bonds to the backbone C=O group of the amino acid located four residues ear ...

bound by a looping stretch of amino acids. This motif is seen in transcription factors. ;

Zinc finger A zinc finger is a small protein structural motif that is characterized by the coordination of one or more zinc ions (Zn2+) in order to stabilize the fold. It was originally coined to describe the finger-like appearance of a hypothesized struct ...

: Two beta strands with an alpha helix end folded over to bind a zinc

ion An ion () is an atom or molecule with a net electrical charge. The charge of an electron is considered to be negative by convention and this charge is equal and opposite to the charge of a proton, which is considered to be positive by conve ...

. Important in DNA binding proteins. ;

Helix-turn-helix Helix-turn-helix is a DNA-binding protein (DBP). The helix-turn-helix (HTH) is a major structural motif capable of binding DNA. Each monomer incorporates two α helices, joined by a short strand of amino acids, that bind to the major groove of D ...

: Two α helices joined by a short strand of amino acids and found in many proteins that regulate gene expression. ;

Nest A nest is a structure built for certain animals to hold eggs or young. Although nests are most closely associated with birds, members of all classes of vertebrates and some invertebrates construct nests. They may be composed of organic materia ...

: 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

PROSITE PROSITE is a protein database. It consists of entries describing the protein families, domains and functional sites as well as amino acid patterns and profiles in them. These are manually curated by a team of the Swiss Institute of Bioinformati ...

br>Database of protein families and domains
*

SCOP A ( or ) was a poet as represented in Old English poetry. The scop is the Old English counterpart of the Old Norse ', with the important difference that "skald" was applied to historical persons, and scop is used, for the most part, to designa ...

br>Structural classification of Proteins
* CATHbr>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