HolA

Last updated

DNA polymerase III, delta subunit
Identifiers
Organism Escherichia coli
(str. K-12 substr. MG1655)
Symbol holA
Entrez 947573
RefSeq (Prot) NP_415173.1
UniProt P28630
Other data
EC number 2.7.7.7
Chromosome genome: 0.67 - 0.67 Mb
DNA polymerase III, delta subunit

PDB 1xxh EBI.jpg

atpgs bound e. coli clamp loader complex
Identifiers
Symbol DNA_pol3_delta
Pfam PF06144
Pfam clan CL0023
InterPro IPR010372
SCOP 1jql
SUPERFAMILY 1jql

In molecular biology, holA is a gene that encodes the δ (delta) subunit of DNA polymerase III in E. coli and other bacteria. Along with the γ, δ', χ, and ψ subunits that make up the core polymerase, and the β accessory proteins, the δ subunit is responsible for the high speed and processivity of polIII. [1] [2]

Molecular biology branch of biology that deals with the molecular basis of biological activity

Molecular biology is a branch of biology that concerns the molecular basis of biological activity between biomolecules in the various systems of a cell, including the interactions between DNA, RNA, proteins and their biosynthesis, as well as the regulation of these interactions. Writing in Nature in 1961, William Astbury described molecular biology as:

...not so much a technique as an approach, an approach from the viewpoint of the so-called basic sciences with the leading idea of searching below the large-scale manifestations of classical biology for the corresponding molecular plan. It is concerned particularly with the forms of biological molecules and [...] is predominantly three-dimensional and structural – which does not mean, however, that it is merely a refinement of morphology. It must at the same time inquire into genesis and function.

Gene basic physical and functional unit of heredity

In biology, a gene is a sequence of nucleotides in DNA or RNA that codes for a molecule that has a function. During gene expression, the DNA is first copied into RNA. The RNA can be directly functional or be the intermediate template for a protein that performs a function. The transmission of genes to an organism's offspring is the basis of the inheritance of phenotypic trait. These genes make up different DNA sequences called genotypes. Genotypes along with environmental and developmental factors determine what the phenotypes will be. Most biological traits are under the influence of polygenes as well as gene–environment interactions. Some genetic traits are instantly visible, such as eye color or number of limbs, and some are not, such as blood type, risk for specific diseases, or the thousands of basic biochemical processes that constitute life.

Bacteria A domain of prokaryotes – single celled organisms without a nucleus

Bacteria are a type of biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a number of shapes, ranging from spheres to rods and spirals. Bacteria were among the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit soil, water, acidic hot springs, radioactive waste, and the deep portions of Earth's crust. Bacteria also live in symbiotic and parasitic relationships with plants and animals. Most bacteria have not been characterised, and only about half of the bacterial phyla have species that can be grown in the laboratory. The study of bacteria is known as bacteriology, a branch of microbiology.

Related Research Articles

RNA polymerase, both abbreviated RNAP or RNApol, official name DNA-directed RNA polymerase, is an enzyme that synthesizes RNA from a DNA template. RNAP locally opens the double-stranded DNA so that one strand of the exposed nucleotides can be used as a template for the synthesis of RNA, a process called transcription. A transcription factor and its associated transcription mediator complex must be attached to a DNA binding site called a promoter region before RNAP can initiate the DNA unwinding at that position. RNAP not only initiates RNA transcription, it also guides the nucleotides into position, facilitates attachment and elongation, has intrinsic proofreading and replacement capabilities, and termination recognition capability. In eukaryotes, RNAP can build chains as long as 2.4 million nucleotides.

DNA polymerase Enzyme that synthesizes DNA from a DNA template

DNA polymerase is an enzyme that synthesizes DNA molecules from deoxyribonucleotides, the building blocks of DNA. These enzymes are essential for DNA replication and usually work in pairs to create two identical DNA strands from a single original DNA molecule. During this process, DNA polymerase "reads" the existing DNA strands to create two new strands that match the existing ones.

DNA polymerase III holoenzyme DNA Replication Enzyme

DNA polymerase III holoenzyme is the primary enzyme complex involved in prokaryotic DNA replication. It was discovered by Thomas Kornberg and Malcolm Gefter in 1970. The complex has high processivity and, specifically referring to the replication of the E.coli genome, works in conjunction with four other DNA polymerases. Being the primary holoenzyme involved in replication activity, the DNA Pol III holoenzyme also has proofreading capabilities that corrects replication mistakes by means of exonuclease activity working 3'→5'. DNA Pol III is a component of the replisome, which is located at the replication fork.

dnaQ is the gene encoding the ε subunit of DNA polymerase III in Escherichia coli. The ε subunit is one of three core proteins in the DNA polymerase complex. It functions as a 3’→5’ DNA directed proofreading exonuclease that removes incorrectly incorporated bases during replication. dnaQ may also be referred to as mutD.

RNA polymerase II type of protein

RNA polymerase II is a multiprotein complex. It is one of the three RNAP enzymes found in the nucleus of eukaryotic cells. It catalyzes the transcription of DNA to synthesize precursors of mRNA and most snRNA and microRNA. A 550 kDa complex of 12 subunits, RNAP II is the most studied type of RNA polymerase. A wide range of transcription factors are required for it to bind to upstream gene promoters and begin transcription.

DNA polymerase II

DNA polymerase II is a prokaryotic DNA-Dependent DNA polymerase encoded by the PolB gene.

UvrABC endonuclease is a multienzyme complex in Escherichia coli involved in DNA repair by nucleotide excision repair, and it is, therefore, sometimes called an excinuclease. This UvrABC repair process, sometimes called the short-patch process, involves the removal of twelve nucleotides where a genetic mutation has occurred followed by a DNA polymerase, replacing these aberrant nucleotides with the correct nucleotides and completing the DNA repair. The subunits for this enzyme are encoded in the uvrA, uvrB, and uvrC genes. This enzyme complex is able to repair many different types of damage, including cyclobutyl dimer formation.

DNA clamp

A DNA clamp, also known as a sliding clamp or β-clamp, is a protein fold that serves as a processivity-promoting factor in DNA replication. As a critical component of the DNA polymerase III holoenzyme, the clamp protein binds DNA polymerase and prevents this enzyme from dissociating from the template DNA strand. The clamp-polymerase protein–protein interactions are stronger and more specific than the direct interactions between the polymerase and the template DNA strand; because one of the rate-limiting steps in the DNA synthesis reaction is the association of the polymerase with the DNA template, the presence of the sliding clamp dramatically increases the number of nucleotides that the polymerase can add to the growing strand per association event. The presence of the DNA clamp can increase the rate of DNA synthesis up to 1,000-fold compared with a nonprocessive polymerase.

Transcription factor II Human is an important protein complex, having roles in transcription of various protein-coding genes and DNA nucleotide excision repair (NER) pathways. TFIIH first came to light in 1989 when general transcription factor-δ or basic transcription factor 2 was characterized as an indispensable transcription factor in vitro. This factor was also isolated from yeast and finally named as TFIIH in 1992.

POLG protein-coding gene in the species Homo sapiens

DNA polymerase subunit gamma is an enzyme that in humans is encoded by the POLG gene. Mitochondrial DNA polymerase is heterotrimeric, consisting of a homodimer of accessory subunits plus a catalytic subunit. The protein encoded by this gene is the catalytic subunit of mitochondrial DNA polymerase. Defects in this gene are a cause of progressive external ophthalmoplegia with mitochondrial DNA deletions 1 (PEOA1), sensory ataxic neuropathy dysarthria and ophthalmoparesis (SANDO), Alpers-Huttenlocher syndrome (AHS), and mitochondrial neurogastrointestinal encephalopathy syndrome (MNGIE).

POLD1 protein-coding gene in the species Homo sapiens

The gene polymerase delta 1 (POLD1) encodes the large, POLD1/p125, catalytic subunit of the DNA polymerase delta (Polδ) complex. The Polδ enzyme is responsible for synthesizing the lagging strand of DNA, and has also been implicated in some activities at the leading strand. The POLD1/p125 subunit encodes both DNA polymerizing and exonuclease domains, which provide the protein an important second function in proofreading to ensure replication accuracy during DNA synthesis, and in a number of types of replication-linked DNA repair following DNA damage. Germline mutations impairing activity of POLD1 have been implicated in several types of hereditary cancer, in some sporadic cancers, and in a developmental syndrome of premature aging, Mandibular hypoplasia, Deafness, and Progeroid features and Lipodystrophy. Studies of POLD1 emphasize the importance of maintaining genomic stability to limit tumorigenesis. It is currently unclear whether the enhanced tumorigenesis associated with POLD1 defects is the result of increased base substitutions or due to fork collapse and production of DNA double strand breaks (DSBs). Recent reviews have addressed important functions of POLD1 and Polδ.

POLG2 protein-coding gene in the species Homo sapiens

DNA polymerase subunit gamma-2, mitochondrial is a protein that in humans is encoded by the POLG2 gene. The POLG2 gene encodes a 55 kDa accessory subunit protein that imparts high processivity and salt tolerance to the catalytic subunit of DNA polymerase gamma, encoded by the POLG gene. Mutations in this gene result in autosomal dominant progressive external ophthalmoplegia with mitochondrial DNA deletions.

POLD2 protein-coding gene in the species Homo sapiens

DNA polymerase delta subunit 2 is an enzyme that in humans is encoded by the POLD2 gene. It is a component of the DNA polymerase delta complex.

POLD3 protein-coding gene in the species Homo sapiens

DNA polymerase delta subunit 3 is an enzyme that in humans is encoded by the POLD3 gene. It is a component of the DNA polymerase delta complex.

DNA polymerase delta(DNA Pol δ) is an enzyme complex found in eukaryotes that is involved in DNA replication and repair. The DNA polymerase delta complex consists of 4 subunits: POLD1, POLD2, POLD3, and POLD4. DNA Pol δ is an enzyme used for both leading and lagging strand synthesis. It exhibits increased processivity when interacting with the proliferating cell nuclear antigen (PCNA). As well, the multisubunit protein replication factor C, through its role as the clamp loader for PCNA is important for DNA Pol δ function.

Bacterial DNA binding protein

In molecular biology, bacterial DNA binding proteins are a family of small, usually basic proteins of about 90 residues that bind DNA and are known as histone-like proteins. Since bacterial binding proteins have a diversity of functions, it has been difficult to develop a common function for all of them. They are commonly referred to as histone-like and have many similar traits with the eukaryotic histone proteins. Eukaryotic histones package DNA to help it to fit in the nucleus, and they are known to be the most conserved proteins in nature. Examples include the HU protein in Escherichia coli, a dimer of closely related alpha and beta chains and in other bacteria can be a dimer of identical chains. HU-type proteins have been found in a variety of eubacteria and archaebacteria, and are also encoded in the chloroplast genome of some algae. The integration host factor (IHF), a dimer of closely related chains which is suggested to function in genetic recombination as well as in translational and transcriptional control is found in Enterobacteria and viral proteins including the African swine fever virus protein A104R.

In E. coli and other bacteria, holB is a gene that encodes the delta prime subunit of DNA polymerase III.

holC

In E. coli and other bacteria, holC is a gene that encodes the chi subunit of DNA polymerase III.

In E. coli and other bacteria, holD is a gene that encodes the psi subunit of DNA polymerase III.

holE

In E. coli and other bacteria, holE is a gene that encodes the theta subunit of DNA polymerase III.

References

  1. Dong Z, Onrust R, Skangalis M, O'Donnell M (June 1993). "DNA polymerase III accessory proteins. I. holA and holB encoding delta and delta'" (PDF). The Journal of Biological Chemistry. 268 (16): 11758–65. PMID   8505303.
  2. Carter JR, Franden MA, Aebersold R, McHenry CS (1992). "Molecular cloning, sequencing, and overexpression of the structural gene encoding the delta subunit of Escherichia coli DNA polymerase III holoenzyme" (PDF). Journal of Bacteriology. 174 (21): 7013–25. PMC   207382 Lock-green.svg. PMID   1400251.