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 of s ...

of around 40 amino acid residues 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, respo ...

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 A coiled coil is a structural motif in proteins in which 2–7 alpha helix, alpha-helices are coiled together like the strands of a rope. (Protein dimer, Dimers and Protein trimer, trimers are the most common types.) Many coiled coil-type protei ...

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 Transcription refers to the process of converting sounds (voice, music etc.) into letters or musical notes, or producing a copy of something in another medium, including: Genetics * Transcription (biology), the copying of DNA into RNA, the fir ...

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 in ...

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, a ...

, 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 enzym ...

MID1
EC
contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in 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 recyc ...

subunit of

phosphatase In biochemistry, a phosphatase is an enzyme that uses water to cleave a phosphoric acid Ester, monoester into a phosphate ion and an Alcohol (chemistry), alcohol. Because a phosphatase enzyme catalysis, catalyzes the hydrolysis of its Substrate ...

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 conve ...

s and adopts a beta/beta/alpha cross-brace

structure A structure is an arrangement and organization of interrelated elements in a material object or system, or the object or system so organized. Material structures include man-made objects such as buildings and machines and natural objects such as ...

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 A metalloproteinase, or metalloprotease, is any protease enzyme whose catalytic mechanism involves a metal. An example is ADAM12 which plays a significant role in the fusion of muscle cells during embryo development, in a process known as myogen ...

. 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 In molecular biology, the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of ANSWISSPROT a ubiquitin-like protein in ''Xenopus laevis''. The AN1-ty ...

and LIM domains.

References

External links

CO-like familyDBB family
a
PlantTFDB: Plant Transcription Factor Database

Occurrence

Homologs

References

External links

See also