In molecular biology the B-box-type zinc finger domain is a short
protein domain
In molecular biology, a protein domain is a region of a protein's polypeptide chain that is self-stabilizing and that folds independently from the rest. Each domain forms a compact folded three-dimensional structure. Many proteins consist o ...
of around 40 amino acid
residues
Residue may refer to:
Chemistry and biology
* An amino acid, within a peptide chain
* Crop residue, materials left after agricultural processes
* Pesticide residue, refers to the pesticides that may remain on or in food after they are appli ...
in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their
consensus sequence
In molecular biology and bioinformatics, the consensus sequence (or canonical sequence) is the calculated order of most frequent residues, either nucleotide or amino acid, found at each position in a sequence alignment. It serves as a simplified r ...
and in the spacing of the 7-8 zinc-binding residues. Several
proteins
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, respondi ...
contain both types 1 and 2 B-boxes, suggesting some level of
cooperativity
Cooperativity is a phenomenon displayed by systems involving identical or near-identical elements, which act dependently of each other, relative to a hypothetical standard non-interacting system in which the individual elements are acting indepen ...
between these two domains.
Occurrence
B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a
coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include
transcription factors,
ribonucleoprotein
Nucleoproteins are proteins conjugated with nucleic acids (either DNA or RNA). Typical nucleoproteins include ribosomes, nucleosomes and viral nucleocapsid proteins.
Structures
Nucleoproteins tend to be positively charged, facilitating inte ...
s and proto-oncoproteins; for example, MID1, MID2,
TRIM9
Tripartite motif-containing protein 9 is a protein that in humans is encoded by the ''TRIM9'' gene.
The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, ...
,
TNL,
TRIM36,
TRIM63
E3 ubiquitin-protein ligase TRIM63, also known as "MuRF1" (Muscle Ring-Finger Protein-1), is an enzyme that in humans is encoded by the ''TRIM63'' gene.
This gene encodes a member of the RING zinc finger protein family found in striated muscle a ...
, TRIFIC, NCL1 and CONSTANS-like proteins.
The microtubule-associated E3
ligase
In biochemistry, a ligase is an enzyme that can catalyze the joining ( ligation) of two large molecules by forming a new chemical bond. This is typically via hydrolysis of a small pendant chemical group on one of the larger molecules or the enz ...
MID1
EC contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in
turn
Turn may refer to:
Arts and entertainment
Dance and sports
* Turn (dance and gymnastics), rotation of the body
* Turn (swimming), reversing direction at the end of a pool
* Turn (professional wrestling), a transition between face and heel
* Turn, ...
recruits the
catalytic
Catalysis () is the process of increasing the rate of a chemical reaction by adding a substance known as a catalyst (). Catalysts are not consumed in the reaction and remain unchanged after it. If the reaction is rapid and the catalyst recycl ...
subunit of
phosphatase
In biochemistry, a phosphatase is an enzyme that uses water to cleave a phosphoric acid monoester into a phosphate ion and an alcohol. Because a phosphatase enzyme catalyzes the hydrolysis of its substrate, it is a subcategory of hydrolases. Ph ...
2A (PP2Ac). This
complex
Complex commonly refers to:
* Complexity, the behaviour of a system whose components interact in multiple ways so possible interactions are difficult to describe
** Complex system, a system composed of many components which may interact with each ...
is required for targeting of PP2Ac for
proteasome-mediated degradation
Proteasomes are protein complexes which degrade unneeded or damaged proteins by proteolysis, a chemical reaction that breaks peptide bonds. Enzymes that help such reactions are called proteases.
Proteasomes are part of a major mechanism by whi ...
. The MID1 B-box coordinates two 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 conven ...
s and adopts a beta/beta/alpha cross-brace
structure similar to that of ZZ, PHD, RING and FYVE zinc fingers.
Homologs
Prokaryotic homologs of the domain are present in several bacterial lineages and methanogenic archaea, and often show fusions to peptidase domains such as the rhomboid-like serine peptidase, and Zn-dependent
metallopeptidase. Other versions typically contain transmembrane helices and might also show fusions to domains such as DNAJ, FHA, SH3, WD40 and tetratricopeptide repeats. Together these associations suggest a role for the prokaryotic homologs of the B-box zinc finger domain in proteolytic processing, folding or stability of membrane-associated proteins. The domain architectural syntax is remarkably similar to that seen in prokaryotic homologs of the
AN1 zinc finger and
LIM domains.
References
External links
CO-like familyDBB familya
PlantTFDB: Plant Transcription Factor Database
See also
*
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 ...
{{InterPro content, IPR000315
Protein domains