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The gamma complex of DNA polymerase III (composed of γδδ'χψ subunits) catalyzes [[ATP]] to chaperone two beta subunits to bind to DNA. Once bound to DNA, the beta subunits can freely slide along double stranded DNA. The complex between the dimeric beta protein and DNA is known as the [[pre-initiation complex]]. The beta subunits in turn bind the αε polymerase complex (where the α subunit possesses [[DNA polymerase]] activity and the ε subunit is a 3‘-5’ [[exonuclease]]).<ref name="Stukenberg_1991"/>
The gamma complex of DNA polymerase III (composed of γδδ'χψ subunits) catalyzes [[ATP]] to chaperone two beta subunits to bind to DNA. Once bound to DNA, the beta subunits can freely slide along double stranded DNA. The complex between the dimeric beta protein and DNA is known as the [[pre-initiation complex]]. The beta subunits in turn bind the αε polymerase complex (where the α subunit possesses [[DNA polymerase]] activity and the ε subunit is a 3‘-5’ [[exonuclease]]).<ref name="Stukenberg_1991"/>


⚫
A [[spliceosome]] is sized at over a million k[[atomic mass unit|D]]. Also based in the [[cell nucleus]] are multitudes of massive biomolecular constructs - [[replicase]]s, [[isomerase]]s, [[Rna]] [[polymerase]]s - all massive constructs. In perspective, a [[DNA]] double strand is only 20 atoms across.
The beta clamp a biological construct that mimics the purpose of the couplings that affix the fuel lines to the fuel injectors in an engine .


⚫
One DNA molecule (times 23 pairs ) is at the constant beck-and-call of the dozens of types (not [[copy number]]s) of these highly variant, space and raw materials requiring giants and requires an intermediary that binds the DNA and then proffers its other active [[binding site]] that will then be approached by and utilized as a point of attachment to the 'factoryase'. That intermediary is the beta clamp - two parts in [[prokaryote]]s, three parts in [[eukaryote]]s.
In this auto analogy, fuel shall represent information stored in the 2' Dna ; the fuel line itself represents all of the Dna unpacking bio-hardware eg. Helicase and DnaB (unwinding).


⚫
Being composed of subunits, the beta clamp is naturally itself a subunit - a component of a construct that, when fully assembled, is called a holoenzyme. For illustration, the replicase DNA polymerase III is a factoryase that is concerned with the replication ( copying via duplication ) of double stranded (ds) DNA. Its capabilities include being able to replicate both strands, in opposite directions, simultaneously.<ref>see [[semi-discontinuous replication]]</ref>
The fuel injectors shall be likened to transcription factors, that enable and direct the expression of Dna as allowed by their unique conformations.


⚫
It comprises nine types ( molecular species ) of subunits : the alpha - DNA synthesis (130 kD), epsilon - proof reading (25 kD) and theta - assembly? (10 kD) make up a catalytic core. Tau (71 kD) causes two of these cores to assemble and bind, i.e. dimerise, forming Pol III* . Addition of gamma (55 kD), { which itself has several subunits } , forms Pol III' (750 kD). Gamma and delta (32 kD) together bind to the DNA template at a control sequence. A pair of beta subunits form the Beta Dimer that along with two other subunits complete the holoenzyme ( 900 kD ).
Then, the combustion chambers must be the nucleus and the nucleolus : 'where it all happens' - this is to say that both the quantity of functional units involved and the diversity of the properties of control factors are really quite very immense.


Next, parallel the engine's [[crankshaft]] with [[messenger Rna]]. Potential motive power is produced and sent on its way to the transmission / [[ribosome]]s.


⚫
DNA Pol III subunit inventory , as fully assembled :
⚫
A [[spliceosome]] is sized at over a million kD.<ref>one dalton is the mass of a proton : see [[Atomic Weights]]</ref> Also based in the [[cell nucleus]] are multitudes of massive biomolecular constructs - [[replicase]]s, [[isomerase]]s, [[Rna]] [[polymerase]]s - all massive constructs. In perspective, a [[Dna]] double strand is only 20 atoms across.

⚫
One Dna molecule (times 23 pairs ) is at the constant beck-and-call of the dozens of types (not [[copy number]]s) of these highly variant, space and raw materials requiring giants and requires an intermediary that binds the Dna and then proffers its other active [[binding site]] that will then be approached by and utilized as a point of attachment to the 'factoryase'. That intermediary is the beta clamp - two parts in [[prokaryote]]s, three parts in [[eukaryote]]s.

⚫
Being composed of subunits, the beta clamp is naturally itself a subunit - a component of a construct that, when fully assembled, is called a holoenzyme. For illustration, the replicase Dna polymerase III is a factoryase that is concerned with the replication ( copying via duplication ) of double stranded (ds) Dna. Its capabilities include being able to replicate both strands, in opposite directions, simultaneously.<ref>see [[semi-discontinuous replication]]</ref>

⚫
It comprises nine types ( molecular species ) of subunits : the alpha - Dna synthesis (130 kD), epsilon - proof reading (25 kD) and theta - assembly? (10 kD) make up a catalytic core. Tau (71 kD) causes two of these cores to assemble and bind, i.e. dimerise, forming Pol III* . Addition of gamma (55 kD), { which itself has several subunits } , forms Pol III' (750 kD). Gamma and delta (32 kD) together bind to the Dna template at a control sequence. A pair of beta subunits form the Beta Dimer that along with two other subunits complete the holoenzyme ( 900 kD ).


⚫
Dna Pol III subunit inventory , as fully assembled :


First core = 2 beta, 2 delta, 1 gamma, 1 alpha, 1 epsilon, 1 theta, 1 psi and 1 chi ;
First core = 2 beta, 2 delta, 1 gamma, 1 alpha, 1 epsilon, 1 theta, 1 psi and 1 chi ;
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The structure of Dna Pol III is convoked in three stages. 1) Assembly begins with the coalescence of the five-subunit 'clamp loader' ( 2 delta, 1 gamma, 1 psi and 1 chi ). This 'gamma complex' conjoins with a beta dimer forming a pre-initiation complex. Involved in locating and priming the dsDna control sequence for reception, this complex cleaves ATP to complete the encirclement of the Dna duplex molecule. Hence, the term 'loader' refers in part to the energy used to drive the attachment to Dna.
The structure of DNA Pol III is convoked in three stages. 1) Assembly begins with the coalescence of the five-subunit 'clamp loader' ( 2 delta, 1 gamma, 1 psi and 1 chi ). This 'gamma complex' conjoins with a beta dimer forming a pre-initiation complex. Involved in locating and priming the dsDNA control sequence for reception, this complex cleaves ATP to complete the encirclement of the DNA duplex molecule. Hence, the term 'loader' refers in part to the energy used to drive the attachment to DNA.


2) As always, intermolecular binding results in conformational changes. For example : the Kinase class of factoryases uses the docking and undocking of just one phosphate moiety to alter the shape of it's bulk to switch between active and inactive forms.
2) As always, intermolecular binding results in conformational changes. For example : the Kinase class of factoryases uses the docking and undocking of just one phosphate moiety to alter the shape of it's bulk to switch between active and inactive forms.


When the beta dimer clamps the Dna, its affinity for the gamma complex is replaced by an attraction for the core-polymerase, which brings the core to Dna.
When the beta dimer clamps the DNA, its affinity for the gamma complex is replaced by an attraction for the core-polymerase, which brings the core to DNA.


3) A pair of Tau(s) dimerize and bind to the first core; the second Tau captures the second core along with its beta clamp.
3) A pair of Tau(s) dimerize and bind to the first core; the second Tau captures the second core along with its beta clamp.


The clamp loader, without possessing any catalytic activity in itself, remains bound throughout the replication process, as it is needed to unload the gamma complex from Dna (more ATP used ?).
The clamp loader, without possessing any catalytic activity in itself, remains bound throughout the replication process, as it is needed to unload the gamma complex from DNA (more ATP used ?).


Crystal structure studies of beta show that it forms a ring shaped di/trimer, the Beta Ring. This beta ring clamp empowers the holoenzyme with very fast procession speeds.
Crystal structure studies of beta show that it forms a ring shaped di/trimer, the Beta Ring. This beta ring clamp empowers the holoenzyme with very fast procession speeds.


Beta strongly circumferences Dna, yet can easily slide along a Dna duplex.
Beta strongly circumferences DNA, yet can easily slide along a DNA duplex.

⚫
Honoring B. Lewin's contribution, here is an unparaphrasable passage : {{quote|The dimer surrounds the duplex, providing the "sliding clamp" that allows the holoenzyme to slide along DNA. The structure explains the high processivity - there is no way for the enzyme to fall off !}}


Honoring B. Lewin's contribution, here is an unparaphrasable passage:{{fact}}
Closing with another auto analogy : Dna possesses the information, factoryases extract and develop the information, the beta ring clamp is what conjoins the two ; truly ( in terms of the biological expression of information ) the beta clamp is ' where the rubber hits the road' .


⚫
{{quote|The dimer surrounds the duplex, providing the "sliding clamp" that allows the holoenzyme to slide along DNA. The structure explains the high processivity - there is no way for the enzyme to fall off !}}
{ An image would be instructive. }


== References ==
== References ==

Revision as of 12:12, 31 January 2010

DNA polymerase III subunit beta
Crystallographic structure of the dimeric DNA polymerase beta subunit from E. coli.[1]
Identifiers
SymboldnaN
NCBI gene948218
PDB1MMI
UniProtP0A988
Other data
EC number2.7.7.7
Search for
StructuresSwiss-model
DomainsInterPro

The beta clamp is the dimeric beta subunit of DNA polymerase III which act as sliding DNA clamps to keep the polymerase bound to the DNA.[2] DNA polymerase III is the primary enzyme complex involved in prokaryotic DNA replication.

The gamma complex of DNA polymerase III (composed of γδδ'χψ subunits) catalyzes ATP to chaperone two beta subunits to bind to DNA. Once bound to DNA, the beta subunits can freely slide along double stranded DNA. The complex between the dimeric beta protein and DNA is known as the pre-initiation complex. The beta subunits in turn bind the αε polymerase complex (where the α subunit possesses DNA polymerase activity and the ε subunit is a 3‘-5’ exonuclease).[2]

A spliceosome is sized at over a million kD. Also based in the cell nucleus are multitudes of massive biomolecular constructs - replicases, isomerases, Rna polymerases - all massive constructs. In perspective, a DNA double strand is only 20 atoms across.

One DNA molecule (times 23 pairs ) is at the constant beck-and-call of the dozens of types (not copy numbers) of these highly variant, space and raw materials requiring giants and requires an intermediary that binds the DNA and then proffers its other active binding site that will then be approached by and utilized as a point of attachment to the 'factoryase'. That intermediary is the beta clamp - two parts in prokaryotes, three parts in eukaryotes.

Being composed of subunits, the beta clamp is naturally itself a subunit - a component of a construct that, when fully assembled, is called a holoenzyme. For illustration, the replicase DNA polymerase III is a factoryase that is concerned with the replication ( copying via duplication ) of double stranded (ds) DNA. Its capabilities include being able to replicate both strands, in opposite directions, simultaneously.[3]

It comprises nine types ( molecular species ) of subunits : the alpha - DNA synthesis (130 kD), epsilon - proof reading (25 kD) and theta - assembly? (10 kD) make up a catalytic core. Tau (71 kD) causes two of these cores to assemble and bind, i.e. dimerise, forming Pol III* . Addition of gamma (55 kD), { which itself has several subunits } , forms Pol III' (750 kD). Gamma and delta (32 kD) together bind to the DNA template at a control sequence. A pair of beta subunits form the Beta Dimer that along with two other subunits complete the holoenzyme ( 900 kD ).


DNA Pol III subunit inventory , as fully assembled :

First core = 2 beta, 2 delta, 1 gamma, 1 alpha, 1 epsilon, 1 theta, 1 psi and 1 chi ; Second core = 2 beta, 2 tau (to hold the two alphas together), 1 alpha, 1 epsilon, and 1 theta .

Holoenzyme total = 2 alpha, 4 beta, 1 gamma, 2 delta, 2 epsilon, 2 theta, 2 tau, 1 psi and 1 chi totals 17 subunits .


The structure of DNA Pol III is convoked in three stages. 1) Assembly begins with the coalescence of the five-subunit 'clamp loader' ( 2 delta, 1 gamma, 1 psi and 1 chi ). This 'gamma complex' conjoins with a beta dimer forming a pre-initiation complex. Involved in locating and priming the dsDNA control sequence for reception, this complex cleaves ATP to complete the encirclement of the DNA duplex molecule. Hence, the term 'loader' refers in part to the energy used to drive the attachment to DNA.

2) As always, intermolecular binding results in conformational changes. For example : the Kinase class of factoryases uses the docking and undocking of just one phosphate moiety to alter the shape of it's bulk to switch between active and inactive forms.

When the beta dimer clamps the DNA, its affinity for the gamma complex is replaced by an attraction for the core-polymerase, which brings the core to DNA.

3) A pair of Tau(s) dimerize and bind to the first core; the second Tau captures the second core along with its beta clamp.

The clamp loader, without possessing any catalytic activity in itself, remains bound throughout the replication process, as it is needed to unload the gamma complex from DNA (more ATP used ?).

Crystal structure studies of beta show that it forms a ring shaped di/trimer, the Beta Ring. This beta ring clamp empowers the holoenzyme with very fast procession speeds.

Beta strongly circumferences DNA, yet can easily slide along a DNA duplex.

Honoring B. Lewin's contribution, here is an unparaphrasable passage:[citation needed]

The dimer surrounds the duplex, providing the "sliding clamp" that allows the holoenzyme to slide along DNA. The structure explains the high processivity - there is no way for the enzyme to fall off !

References

  1. ^ PDB: 1MMI​; Oakley AJ, Prosselkov P, Wijffels G, Beck JL, Wilce MC, Dixon NE (2003). "Flexibility revealed by the 1.85 Å crystal structure of the beta sliding-clamp subunit of Escherichia coli DNA polymerase III". Acta Crystallogr. D Biol. Crystallogr. 59 (Pt 7): 1192–9. PMID 12832762. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  2. ^ a b Stukenberg PT, Studwell-Vaughan PS, O'Donnell M (1991). "Mechanism of the sliding beta-clamp of DNA polymerase III holoenzyme". J. Biol. Chem. 266 (17): 11328–34. PMID 2040637. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  3. ^ see semi-discontinuous replication

Further reading

  • Lehninger, Albert L (1975). Biochemistry: The Molecular Basis of Cell Structure and Function. New York: Worth Publishers. p. 894. ISBN 0-87901-047-9.
  • Lewin, Benjamin (1997). Genes VI. Oxford [Oxfordshire]: Oxford University Press. pp. 484–7. ISBN 0-19-857779-6.
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