DNA clamp

The DNA clamp is an α+β protein that assembles into a multimeric, six-domain ring structure that completely encircles the DNA double helix as the polymerase adds nucleotides to the growing strand.{{cite journal | vauthors = Bruck I, O'Donnell M | title = The ring-type polymerase sliding clamp family | journal = Genome Biology | volume = 2 | issue = 1 | pages = REVIEWS3001 | year = 2001 | pmid = 11178284 | pmc = 150441 | doi = 10.1186/gb-2001-2-1-reviews3001 | doi-access = free }} Each domain is in turn made of two β-α-β-β-β structural repeats.{{cite journal | vauthors = Neuwald AF, Poleksic A | title = PSI-BLAST searches using hidden markov models of structural repeats: prediction of an unusual sliding DNA clamp and of beta-propellers in UV-damaged DNA-binding protein | journal = Nucleic Acids Research | volume = 28 | issue = 18 | pages = 3570–3580 | date = September 2000 | pmid = 10982878 | doi = 10.1093/nar/28.18.3570 | pmc = 110734 | doi-access = free }} The DNA clamp assembles on the DNA at the replication fork and "slides" along the DNA with the advancing polymerase, aided by a layer of water molecules in the central pore of the clamp between the DNA and the protein surface. Because of the toroidal shape of the assembled multimer, the clamp cannot dissociate from the template strand without also dissociating into monomers.

The DNA clamp fold is found in bacteria, archaea, eukaryotes and some viruses. In bacteria, the sliding clamp is a homodimer composed of two identical beta subunits of DNA polymerase III and hence is referred to as the beta clamp. In archaea{{cite journal | vauthors = Matsumiya S, Ishino Y, Morikawa K | title = Crystal structure of an archaeal DNA sliding clamp: proliferating cell nuclear antigen from Pyrococcus furiosus | journal = Protein Science | volume = 10 | issue = 1 | pages = 17–23 | date = January 2001 | pmid = 11266590 | pmc = 2249843 | doi = 10.1110/ps.36401 }} and eukaryotes, it is a trimer composed of three molecules of PCNA. The T4 bacteriophage also uses a sliding clamp, called gp45 that is a trimer similar in structure to PCNA but lacks sequence homology to either PCNA or the bacterial beta clamp.

=== Bacterial ===

{{Infobox nonhuman protein

| Name = DNA polymerase III subunit beta

| image = E_coli_beta_clamp_1MMI.png

| width =

| caption = Crystallographic structure of the dimeric DNA polymerase beta subunit from E. coli.{{PDB|1MMI}}; {{cite journal | vauthors = Oakley AJ, Prosselkov P, Wijffels G, Beck JL, Wilce MC, Dixon NE | title = Flexibility revealed by the 1.85 A crystal structure of the beta sliding-clamp subunit of Escherichia coli DNA polymerase III | journal = Acta Crystallographica. Section D, Biological Crystallography | volume = 59 | issue = Pt 7 | pages = 1192–1199 | date = July 2003 | pmid = 12832762 | doi = 10.1107/S0907444903009958 | bibcode = 2003AcCrD..59.1192O | url = https://espace.library.uq.edu.au/view/UQ:39327/UQ39327_OA.pdf }}

| Symbol = dnaN

| AltSymbols =

| Organism = Escherichia coli

| TaxID = 879462

| CAS_number =

| CAS_supplemental =

| EntrezGene = 948218

| PDB = 1MMI

| RefSeqmRNA =

| RefSeqProtein = NP_418156

| UniProt = P0A988

| ECnumber = 2.7.7.7

| Chromosome = MG1655

| EntrezChromosome = NC_000913

| GenLoc_start = 3879078

| GenLoc_end = 3880508

}}

The beta clamp is a specific DNA clamp and a subunit of the DNA polymerase III holoenzyme found in bacteria. Two beta subunits are assembled around the DNA by the gamma subunit and ATP hydrolysis; this assembly is called the pre-initiation complex. After assembly around the DNA, the beta subunits' affinity for the gamma subunit is replaced by an affinity for the alpha and epsilon subunits, which together create the complete holoenzyme.{{cite book | vauthors = Lewin B | title = Genes VI | publisher = Oxford University Press | location = Oxford [Oxfordshire] | year = 1997 | pages = 484–7 | isbn = 978-0-19-857779-9 }}{{cite book | vauthors = Lehninger AL | title = Biochemistry: The Molecular Basis of Cell Structure and Function | publisher = Worth Publishers | location = New York | year = 1975 | pages = [https://archive.org/details/biochemistrymole00lehn_0/page/894 894] | isbn = 978-0-87901-047-8 | url = https://archive.org/details/biochemistrymole00lehn_0/page/894 }}{{cite journal | vauthors = Stukenberg PT, Studwell-Vaughan PS, O'Donnell M | title = Mechanism of the sliding beta-clamp of DNA polymerase III holoenzyme | journal = The Journal of Biological Chemistry | volume = 266 | issue = 17 | pages = 11328–11334 | date = June 1991 | pmid = 2040637 | doi = 10.1016/S0021-9258(18)99166-0 | doi-access = free }} 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 beta subunits in turn bind the αε polymerase complex. The α subunit possesses DNA polymerase activity and the ε subunit is a 3’-5’ exonuclease.

The beta chain of bacterial DNA polymerase III is composed of three topologically equivalent domains (N-terminal, central, and C-terminal). Two beta chain molecules are tightly associated to form a closed ring encircling duplex DNA.

{{Clear}}

Certain NSAIDs (carprofen, bromfenac, and vedaprofen) exhibit some suppression of bacterial DNA replication by inhibiting bacterial DNA clamp.{{cite journal | vauthors = Yin Z, Wang Y, Whittell LR, Jergic S, Liu M, Harry E, Dixon NE, Kelso MJ, Beck JL, Oakley AJ | display-authors = 6 | title = DNA replication is the target for the antibacterial effects of nonsteroidal anti-inflammatory drugs | journal = Chemistry & Biology | volume = 21 | issue = 4 | pages = 481–487 | date = April 2014 | pmid = 24631121 | doi = 10.1016/j.chembiol.2014.02.009 | doi-access = free }}

{{Infobox protein

| Name = proliferating cell nuclear antigen

| caption = The assembled human DNA clamp, a trimer of the human protein PCNA.{{PDB|1AXC}}; {{cite journal | vauthors = Gulbis JM, Kelman Z, Hurwitz J, O'Donnell M, Kuriyan J | title = Structure of the C-terminal region of p21(WAF1/CIP1) complexed with human PCNA | journal = Cell | volume = 87 | issue = 2 | pages = 297–306 | date = October 1996 | pmid = 8861913 | doi = 10.1016/S0092-8674(00)81347-1 | s2cid = 17461501 | doi-access = free }}

| image = 1axc tricolor.png

| width =

| HGNCid = 8729

| Symbol = PCNA

| AltSymbols =

| EntrezGene = 5111

| OMIM = 176740

| RefSeq = NM_002592

| UniProt = P12004

| PDB = 1axc

| ECnumber = 2.7.7.7

| Chromosome = 20

| Arm = p

| Band = ter

| LocusSupplementaryData = -p12

}}

The sliding clamp in eukaryotes is assembled from a specific subunit of DNA polymerase delta called the proliferating cell nuclear antigen (PCNA). The N-terminal and C-terminal domains of PCNA are topologically identical. Three PCNA molecules are tightly associated to form a closed ring encircling duplex DNA.

The sequence of PCNA is well conserved between plants, animals and fungi, indicating a strong selective pressure for structure conservation, and suggesting that this type of DNA replication mechanism is conserved throughout eukaryotes.{{cite journal | vauthors = Suzuka I, Hata S, Matsuoka M, Kosugi S, Hashimoto J | title = Highly conserved structure of proliferating cell nuclear antigen (DNA polymerase delta auxiliary protein) gene in plants | journal = European Journal of Biochemistry | volume = 195 | issue = 2 | pages = 571–575 | date = January 1991 | pmid = 1671766 | doi = 10.1111/j.1432-1033.1991.tb15739.x | doi-access = free }}{{cite journal | vauthors = Marshall AC, Kroker AJ, Murray LA, Gronthos K, Rajapaksha H, Wegener KL, Bruning JB | title = Structure of the sliding clamp from the fungal pathogen Aspergillus fumigatus (AfumPCNA) and interactions with Human p21 | journal = The FEBS Journal | volume = 284 | issue = 6 | pages = 985–1002 | date = March 2017 | pmid = 28165677 | doi = 10.1111/febs.14035 | doi-access = free }} In eukaryotes, a homologous, heterotrimeric "9-1-1 clamp" made up of RAD9-RAD1-HUS1 (911) is responsible for DNA damage checkpoint control.{{cite journal | vauthors = Majka J, Burgers PM | title = The PCNA-RFC families of DNA clamps and clamp loaders | journal = Progress in Nucleic Acid Research and Molecular Biology | volume = 78 | pages = 227–260 | date = 2004 | pmid = 15210332 | doi = 10.1016/S0079-6603(04)78006-X | isbn = 9780125400787 }} This 9-1-1 clamp mounts onto DNA in the opposite direction.{{cite journal | vauthors = Zheng F, Georgescu RE, Yao NY, O'Donnell ME, Li H | title = DNA is loaded through the 9-1-1 DNA checkpoint clamp in the opposite direction of the PCNA clamp | journal = Nature Structural & Molecular Biology | volume = 29 | issue = 4 | pages = 376–385 | date = April 2022 | pmid = 35314830 | doi = 10.1038/s41594-022-00742-6 | pmc = 9010301 | doi-access = free }}

Archaea, probable evolutionary precursor of eukaryotes, also universally have at least one PCNA gene. This PCNA ring works with PolD, the single eukaryotic-like DNA polymerase in archaea responsible for multiple functions from replication to repair. Some unusual species have two or even three PCNA genes, forming heterotrimers or distinct specialized homotrimers.{{cite journal | vauthors = Pan M, Kelman LM, Kelman Z | title = The archaeal PCNA proteins | journal = Biochemical Society Transactions | volume = 39 | issue = 1 | pages = 20–24 | date = January 2011 | pmid = 21265741 | doi = 10.1042/bst0390020 }} Archaeons also share with eukaryotes the PIP (PCNA-interacting protein) motif, but a wider variety of such proteins performing different functions are found.{{cite journal | vauthors = MacNeill SA | title = PCNA-binding proteins in the archaea: novel functionality beyond the conserved core | journal = Current Genetics | volume = 62 | issue = 3 | pages = 527–532 | date = August 2016 | pmid = 26886233 | pmc = 4929162 | doi = 10.1007/s00294-016-0577-3 }}

PCNA is also appropriated by some viruses. The giant virus genus Chlorovirus, with PBCV-1 as a representative, carries in its genome two PCNA genes ({{UniProt|Q84513}}, {{UniProt|O41056}}) and a eukaryotic-type DNA polymerase.{{cite journal | vauthors = Van Etten JL, Agarkova IV, Dunigan DD | title = Chloroviruses | journal = Viruses | volume = 12 | issue = 1 | date = December 2019 | page = 20 | pmid = 31878033 | doi = 10.3390/v12010020 | pmc = 7019647 | doi-access = free }} Members of Baculoviridae also encode a PCNA homolog ({{UniProt|P11038}}).{{cite journal | vauthors = Fu Y, Wang R, Liang A | title = Function analysis of Ac-PCNA and Sf-PCNA during the Autographa californica multiple nucleopolyhedrovirus infection process | journal = Molecular and Cellular Biochemistry | volume = 443 | issue = 1–2 | pages = 57–68 | date = June 2018 | pmid = 29075988 | doi = 10.1007/s11010-017-3210-y | s2cid = 9507736 }}

{{Clear}}

{{Infobox nonhuman protein

| Name = DNA polymerase accessory protein 45

| image = 1CZD.png

| width =

| caption = Crystallographic structure of the trimeric gp45 sliding clamp from bacteriophage T4.{{PDB|1CZD}}; {{cite journal | vauthors = Moarefi I, Jeruzalmi D, Turner J, O'Donnell M, Kuriyan J | title = Crystal structure of the DNA polymerase processivity factor of T4 bacteriophage | journal = Journal of Molecular Biology | volume = 296 | issue = 5 | pages = 1215–1223 | date = March 2000 | pmid = 10698628 | doi = 10.1006/jmbi.1999.3511 }}

| Symbol = gp45

| AltSymbols =

| Organism = Enterobacteria phage T4

| TaxID = 10665

| CAS_number =

| CAS_supplemental =

| EntrezGene = 1258821

| PDB = 1CZD

| RefSeqmRNA =

| RefSeqProtein = NP_049666

| UniProt = P04525

| ECnumber = 2.7.7.7

| Chromosome = 1

| EntrezChromosome = NC_000866

| GenLoc_start = 31813

| GenLoc_end = 32705

}}

The viral gp45 sliding clamp subunit protein contains two domains. Each domain consists of two alpha helices and two beta sheets – the fold is duplicated and has internal pseudo two-fold symmetry.{{cite journal | vauthors = Shamoo Y, Steitz TA | title = Building a replisome from interacting pieces: sliding clamp complexed to a peptide from DNA polymerase and a polymerase editing complex | journal = Cell | volume = 99 | issue = 2 | pages = 155–166 | date = October 1999 | pmid = 10535734 | doi = 10.1016/S0092-8674(00)81647-5 | s2cid = 18103622 | doi-access = free }} Three gp45 molecules are tightly associated to form a closed ring encircling duplex DNA.

{{Clear}}

Some members of Herpesviridae encode a protein that has a DNA clamp fold but does not associate into a ring clamp. The two-domain protein does, however, associate with the viral DNA polymerase and also acts to increase processivity.{{cite journal | vauthors = Zuccola HJ, Filman DJ, Coen DM, Hogle JM | title = The crystal structure of an unusual processivity factor, herpes simplex virus UL42, bound to the C terminus of its cognate polymerase | journal = Molecular Cell | volume = 5 | issue = 2 | pages = 267–278 | date = February 2000 | pmid = 10882068 | doi = 10.1016/S1097-2765(00)80422-0 | doi-access = free }} As it does not form a ring, it does not need a clamp loader to be attached to DNA.{{cite journal | vauthors = Neuwald AF, Poleksic A | title = PSI-BLAST searches using hidden markov models of structural repeats: prediction of an unusual sliding DNA clamp and of beta-propellers in UV-damaged DNA-binding protein | journal = Nucleic Acids Research | volume = 28 | issue = 18 | pages = 3570–3580 | date = September 2000 | pmid = 10982878 | pmc = 110734 | doi = 10.1093/nar/28.18.3570 }}

{{Clear}}

Sliding clamps are loaded onto their associated DNA template strands by specialized proteins known as "sliding clamp loaders", which also disassemble the clamps after replication has completed. The binding sites for these initiator proteins overlap with the binding sites for the DNA polymerase, so the clamp cannot simultaneously associate with a clamp loader and with a polymerase. Thus the clamp will not be actively disassembled while the polymerase remains bound. DNA clamps also associate with other factors involved in DNA and genome homeostasis, such as nucleosome assembly factors, Okazaki fragment ligases, and DNA repair proteins. All of these proteins also share a binding site on the DNA clamp that overlaps with the clamp loader site, ensuring that the clamp will not be removed while any enzyme is still working on the DNA. The activity of the clamp loader requires ATP hydrolysis to "close" the clamp around the DNA.

{{Reflist}}

• [http://www.pdbe.org/quips?story=BetaClamp Clamping down on pathogenic bacteria]– how to shut down a key DNA polymerase complex. Quips at PDBe {{Webarchive|url=https://archive.today/20130802040403/http://www.pdbe.org/quips?story=BetaClamp |date=2013-08-02 }}
• {{cite book | vauthors = Watson JD, Baker TA, Bell SP, Gann A, Levine M, Losick R | title = Molecular Biology of the Gene | publisher = Pearson/Benjamin Cummings | location = San Francisco | year = 2004 | isbn = 978-0-8053-4635-0 }}

{{Commonscat|DNA clamps}}

• [https://web.archive.org/web/20110516101151/http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.e.bjj.A.html SCOP DNA clamp fold]
• [https://web.archive.org/web/20070312210431/http://www.cathdb.info/cgi-bin/cath/GotoCath.pl?cath=3.70 CATH box architecture]
• {{MeshName|clamp+protein+DnaN,+E+coli}}

{{DNA replication}}

{{Protein tertiary structure}}

Category:Biotechnology

Category:Protein folds

Category:DNA replication