Beta sliding clamp - P0A988 (DPO3B_ECOLI)

 

Protein Feature View of PDB entries mapped to a UniProtKB sequence  

  • Number of PDB entries for P0A988: 41
 
Function
Confers DNA tethering and processivity to DNA polymerases and other proteins. Acts as a clamp, forming a ring around DNA (a reaction catalyzed by the clamp-loading complex) which diffuses in an ATP-independent manner freely and bidirectionally along dsDNA (PubMed:2040637). DNA bound in the ring is bent 22 degrees, in solution primed DNA is bound more tightly than dsDNA, suggesting the clamp binds both ss- and dsDNA (PubMed:18191219). In a complex of DNA with this protein, alpha, epsilon and tau subunits however the DNA is only slightly bent (PubMed:26499492). Coordinates protein traffic at the replication fork, where it interacts with multiple DNA polymerases, repair factors and other proteins (PubMed:15466025, PubMed:16168375, PubMed:22716942, PubMed:14592985, PubMed:14729336, PubMed:26499492, PubMed:15952889). Initially characterized for its ability to contact the alpha subunit (dnaE) of DNA polymerase III (Pol III), tethering it to the DNA and conferring very high processivity (PubMed:2040637). Pol III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria; it also exhibits 3'-5' exonuclease proofreading activity. The beta chain is required for initiation of replication as well as for processivity of DNA replication (PubMed:3519609, PubMed:2040637). A single clamp can bind both Pol III and IV, allowing the repair Pol IV to access DNA when it is damaged and needs to be fixed, a process the replicative polymerase cannot perform; when DNA is repaired Pol III takes over again (PubMed:16168375). Serves as a processivity factor for DNA polymerases II (PubMed:1999435, PubMed:1534562), IV (PubMed:10801133) and V (PubMed:10801133). A shorter protein beta* may be important for increasing survival after UV irradiation, and stimulates DNA synthesis with increased processivity in the presence of core Pol III plus the clamp loader complex (PubMed:8576210, PubMed:8576212). UniProt
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Subunit Structure
Forms a ring-shaped head-to-tail homodimer (PubMed:2040637, PubMed:9927437, PubMed:1349852, PubMed:12832762, PubMed:14592985, PubMed:14729336, PubMed:18191219, PubMed:18678908) around DNA (PubMed:18191219), which can be opened by the delta subunit (PubMed:9927437, PubMed:11525728). Binds interacting factors in a hydrophobic surface cleft between domains 2 and 3, each monomer is able to bind different proteins simultaneously (PubMed:16168375, PubMed:11525728, PubMed:14592985, PubMed:14729336, PubMed:26499492). The beta* isoform probably forms homotrimers which probably load onto DNA (PubMed:8576212). The DNA polymerase III holoenzyme complex contains at least 10 different subunits organized into 3 functionally essential subassemblies: the Pol III core, the beta sliding clamp processivity factor and the clamp-loading complex. The Pol III core (subunits alpha, epsilon and theta) contains the polymerase and the 3'-5' exonuclease proofreading activities. The polymerase is tethered to the template via the dimeric beta sliding clamp processivity factor (this entry) (PubMed:15466025). The clamp loader (also called gamma complex) assembles the beta sliding clamp onto the primed template and plays a central role in the organization and communication at the replication fork. The clamp loader contains delta, delta', psi and chi, and 3 copies of either or both of two different DnaX proteins, gamma and tau. The DNA replisome complex has a single clamp loader (3 tau and 1 each of delta, delta', psi and chi subunits) which binds 3 Pol III cores (1 core on the leading strand and 2 on the lagging strand) each with a beta sliding clamp dimer. Additional proteins in the replisome are other copies of gamma, psi and chi, Ssb, DNA helicase and RNA primase (PubMed:20413500, PubMed:22157955, PubMed:26499492). The beta sliding clamp can also be part of the RIDA complex (regulatory inactivation of DnaA), consisting of ATP-DnaA, ADP-Hda and DNA-loaded beta clamp (PubMed:15150238, PubMed:18977760, PubMed:22716942). Also interacts with a number of other DNA machines such as DNA polymerases I (PubMed:11459978), II (PubMed:1999435, PubMed:1534562), IV (PubMed:14729336) and V, DNA mismatch repair enzyme MutS (PubMed:11459978, PubMed:11573000) and DNA ligase (PubMed:11459978). Binds to CrfC homooligomers at the midcell position during DNA replication (PubMed:23994470). Many proteins that bind the beta sliding clamp have the consensus sequence Gln-Leu[Ser/Asp]Leu-Phe (PubMed:15134440). UniProt
  • Isoforms: 2 , currently showing only the 'canonical' sequence.
  • Other Gene names: dnaN, b3701, JW3678
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Data in green originates from UniProtKB  
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Data in yellow originates from Pfam  , by interacting with the HMMER3 web site  
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Data in orange originates from the SCOP   (version 1.75) and SCOPe   (version 2.04) classifications.
Data in grey has been calculated using BioJava  . Protein disorder predictions are based on JRONN (Troshin, P. and Barton, G. J. unpublished), a Java implementation of RONN  
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Data in blue originates from PDB
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The PDB to UniProt mapping is based on the data provided by the EBI SIFTS project. See also Velankar et al., Nucleic Acids Research 33, D262-265 (2005).
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