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Protein

Beta sliding clamp

Gene

dnaN

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

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).1 Publication14 Publications

Miscellaneous

The temperature- and UV-sensitive allele dnaN159 does not grow at temperatures higher than 37 degrees Celsius. The global SOS response is chronically induced. The UV-sensitivity of dnaN159 is dependent upon Pol IV (dinB), it has an enhanced Pol V-dependent mutation rate (umuC, umuD), and is absolutely dependent on the polymerase activity of Pol I (polA) for viability.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei24DNA1 Publication1
Binding sitei73DNA1 Publication1
Binding sitei149DNA1 Publication1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi153 – 154DNA1 Publication2

GO - Molecular functioni

GO - Biological processi

  • cellular response to DNA damage stimulus Source: EcoliWiki
  • DNA strand elongation involved in DNA replication Source: EcoCyc

Keywordsi

Molecular functionDNA-binding, DNA-directed DNA polymerase, Nucleotidyltransferase, Transferase
Biological processDNA replication

Enzyme and pathway databases

BioCyciEcoCyc:EG10242-MONOMER
MetaCyc:EG10242-MONOMER

Names & Taxonomyi

Protein namesi
Recommended name:
Beta sliding clamp1 Publication
Short name:
Beta clamp
Short name:
Sliding clamp
Alternative name(s):
Beta-clamp processivity factor
DNA polymerase III beta sliding clamp subunit
Gene namesi
Name:dnaN
Ordered Locus Names:b3701, JW3678
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10242 dnaN

Subcellular locationi

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Biotechnological usei

Small molecules can bind to the hydrophobic cleft and inhibit binding of various protein factors, suggesting this may make and attractive antibiotic target (PubMed:18678908).1 Publication

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi24R → A: Mild defect in DNA replication, impaired loading of clamp on DNA, polymerase speed is wild-type. More severe replication defect and very poor clamp loading; when associated with A-149. 1 Publication1
Mutagenesisi66G → E in dnaN159; a temperature- and UV-sensitive mutation, displays altered DNA polymerase usage, chronically induced SOS response; when associated with A-174. 1 Publication1
Mutagenesisi133A → T: Reduction of synthesis of beta*, probably due to mutation of its promoter. 1 Publication1
Mutagenesisi135M → L: 3-fold reduction of synthesis of beta*, probably due to loss of its start codon. 1 Publication1
Mutagenesisi146M → L: No effect on synthesis of beta*. 1 Publication1
Mutagenesisi149Q → A: Mild defect in DNA replication, impaired loading of clamp on DNA, polymerase speed is wild-type. More severe replication defect and very poor clamp loading; when associated with A-24. 1 Publication1
Mutagenesisi153 – 154YY → SS: Very poor loading of clamp on DNA, polymerase speed is wild-type. 1 Publication2
Mutagenesisi174G → A in dnaN159; a temperature- and UV-sensitive mutation, displays altered DNA polymerase usage, chronically induced SOS response; when associated with A-66. 1 Publication1
Mutagenesisi272 – 273IL → AA: Monomeric in solution, binds very tightly to subunit delta (holA). The monomer binds tightly to linear and circular DNA. Cannot bind both Pol III and IV simultaneously. 3 Publications2

Chemistry databases

ChEMBLiCHEMBL3562169

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001054341 – 366Beta sliding clampAdd BLAST366

Proteomic databases

PaxDbiP0A988
PRIDEiP0A988

Expressioni

Inductioni

Induced 1.5-fold by hydroxyurea (PubMed:20005847). A shorter isoform, beta* is induced by UV treatment and also at low levels in late logarithmic/early stationary phase growth (at protein level) (PubMed:8576210). Beta* transcription induced by naldixic acid (PubMed:8576211).3 Publications

Interactioni

Subunit structurei

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).24 Publications

Binary interactionsi

GO - Molecular functioni

Protein-protein interaction databases

BioGridi4259535, 183 interactors
ComplexPortaliCPX-1927 DNA polymerase III, beta sliding clamp processivity factor complex
CPX-1954 Hda-beta clamp complex
DIPiDIP-36038N
IntActiP0A988, 39 interactors
MINTiP0A988
STRINGi316385.ECDH10B_3887

Chemistry databases

BindingDBiP0A988

Structurei

Secondary structure

1366
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliP0A988
SMRiP0A988
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A988

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 1201CuratedAdd BLAST120
Regioni129 – 2432CuratedAdd BLAST115
Regioni245 – 3653CuratedAdd BLAST121

Sequence similaritiesi

Belongs to the beta sliding clamp family.Curated

Phylogenomic databases

eggNOGiENOG4105CZ8 Bacteria
COG0592 LUCA
HOGENOMiHOG000071791
InParanoidiP0A988
KOiK02338
PhylomeDBiP0A988

Family and domain databases

CDDicd00140 beta_clamp, 1 hit
InterProiView protein in InterPro
IPR001001 DNA_polIII_beta
IPR022635 DNA_polIII_beta_C
IPR022637 DNA_polIII_beta_cen
IPR022634 DNA_polIII_beta_N
PANTHERiPTHR30478 PTHR30478, 1 hit
PfamiView protein in Pfam
PF00712 DNA_pol3_beta, 1 hit
PF02767 DNA_pol3_beta_2, 1 hit
PF02768 DNA_pol3_beta_3, 1 hit
PIRSFiPIRSF000804 DNA_pol_III_b, 1 hit
SMARTiView protein in SMART
SM00480 POL3Bc, 1 hit
TIGRFAMsiTIGR00663 dnan, 1 hit

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative promoter usage. AlignAdd to basket
Isoform Beta1 Publication (identifier: P0A988-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide
        10         20         30         40         50
MKFTVEREHL LKPLQQVSGP LGGRPTLPIL GNLLLQVADG TLSLTGTDLE
60 70 80 90 100
MEMVARVALV QPHEPGATTV PARKFFDICR GLPEGAEIAV QLEGERMLVR
110 120 130 140 150
SGRSRFSLST LPAADFPNLD DWQSEVEFTL PQATMKRLIE ATQFSMAHQD
160 170 180 190 200
VRYYLNGMLF ETEGEELRTV ATDGHRLAVC SMPIGQSLPS HSVIVPRKGV
210 220 230 240 250
IELMRMLDGG DNPLRVQIGS NNIRAHVGDF IFTSKLVDGR FPDYRRVLPK
260 270 280 290 300
NPDKHLEAGC DLLKQAFARA AILSNEKFRG VRLYVSENQL KITANNPEQE
310 320 330 340 350
EAEEILDVTY SGAEMEIGFN VSYVLDVLNA LKCENVRMML TDSVSSVQIE
360
DAASQSAAYV VMPMRL
Length:366
Mass (Da):40,587
Last modified:April 1, 1988 - v1
Checksum:i7A45646F61255B5A
GO
Isoform Beta*1 Publication (identifier: P0A988-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-134: Missing.

Note: Beta* protein is expressed in late logarithmic/early stationary phase and induced by UV treatment (PubMed:8576210). Mutations in the Shine-Dalgarno region of beta* (some silent at the amino acid level) decrease production of beta* (PubMed:8576211).2 Publications
Show »
Length:232
Mass (Da):25,968
Checksum:iD70A75A4CC15CB43
GO

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0590301 – 134Missing in isoform Beta*. 1 PublicationAdd BLAST134

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J01602 Genomic DNA Translation: AAB59150.1
L10328 Genomic DNA Translation: AAA62052.1
U00096 Genomic DNA Translation: AAC76724.1
AP009048 Genomic DNA Translation: BAE77593.1
M19876 Genomic DNA Translation: AAA23695.1
M13822 Genomic DNA Translation: AAA24512.1
K02179 Genomic DNA Translation: AAA24510.1
X04341 Genomic DNA Translation: CAA27869.1
PIRiA91510 DJEC3B
RefSeqiNP_418156.1, NC_000913.3
WP_000673464.1, NZ_LN832404.1

Genome annotation databases

EnsemblBacteriaiAAC76724; AAC76724; b3701
BAE77593; BAE77593; BAE77593
GeneIDi948218
KEGGiecj:JW3678
eco:b3701
PATRICifig|1411691.4.peg.3002

Keywords - Coding sequence diversityi

Alternative promoter usage

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J01602 Genomic DNA Translation: AAB59150.1
L10328 Genomic DNA Translation: AAA62052.1
U00096 Genomic DNA Translation: AAC76724.1
AP009048 Genomic DNA Translation: BAE77593.1
M19876 Genomic DNA Translation: AAA23695.1
M13822 Genomic DNA Translation: AAA24512.1
K02179 Genomic DNA Translation: AAA24510.1
X04341 Genomic DNA Translation: CAA27869.1
PIRiA91510 DJEC3B
RefSeqiNP_418156.1, NC_000913.3
WP_000673464.1, NZ_LN832404.1

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1JQJX-ray2.90A/B1-366[»]
1JQLX-ray2.50A1-366[»]
1MMIX-ray1.85A/B1-366[»]
1OK7X-ray1.65A/B1-366[»]
1UNNX-ray1.90A/B1-366[»]
1WAImodel-A/B1-366[»]
2POLX-ray2.50A/B1-366[»]
2XURX-ray1.90A/B1-366[»]
3BEPX-ray1.92A/B1-366[»]
3D1EX-ray1.90A/B1-366[»]
3D1FX-ray2.00A/B1-366[»]
3D1GX-ray1.64A/B1-366[»]
3F1VX-ray1.77A/B1-366[»]
3PWEX-ray2.20A/B1-366[»]
3Q4JX-ray2.30A/B/C/D/E/F1-366[»]
3Q4KX-ray2.60A/B1-366[»]
3Q4LX-ray1.95A/B1-366[»]
3QSBX-ray1.90A/B1-366[»]
4K3KX-ray1.85A/B1-366[»]
4K3LX-ray1.50A/B1-366[»]
4K3MX-ray1.85A/B1-366[»]
4K3OX-ray2.00A/B1-366[»]
4K3PX-ray2.15A/B1-366[»]
4K3QX-ray1.85A/B1-366[»]
4K3RX-ray1.86A/B1-366[»]
4K3SX-ray1.75A/B1-366[»]
4MJPX-ray1.86A/B1-366[»]
4MJQX-ray1.73A/B1-366[»]
4MJRX-ray1.62A/B1-366[»]
4N94X-ray1.73A/B1-366[»]
4N95X-ray1.80A/B1-366[»]
4N96X-ray1.70A/B1-366[»]
4N97X-ray1.97A/B1-366[»]
4N98X-ray1.70A/B1-366[»]
4N99X-ray2.30A/B1-366[»]
4N9AX-ray1.90A/B1-366[»]
5FKUelectron microscopy8.34B/C1-366[»]
5FKVelectron microscopy8.00B/C1-366[»]
5FKWelectron microscopy7.30B/C1-366[»]
5M1Selectron microscopy6.70B/C1-366[»]
ProteinModelPortaliP0A988
SMRiP0A988
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4259535, 183 interactors
ComplexPortaliCPX-1927 DNA polymerase III, beta sliding clamp processivity factor complex
CPX-1954 Hda-beta clamp complex
DIPiDIP-36038N
IntActiP0A988, 39 interactors
MINTiP0A988
STRINGi316385.ECDH10B_3887

Chemistry databases

BindingDBiP0A988
ChEMBLiCHEMBL3562169

Proteomic databases

PaxDbiP0A988
PRIDEiP0A988

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76724; AAC76724; b3701
BAE77593; BAE77593; BAE77593
GeneIDi948218
KEGGiecj:JW3678
eco:b3701
PATRICifig|1411691.4.peg.3002

Organism-specific databases

EchoBASEiEB0238
EcoGeneiEG10242 dnaN

Phylogenomic databases

eggNOGiENOG4105CZ8 Bacteria
COG0592 LUCA
HOGENOMiHOG000071791
InParanoidiP0A988
KOiK02338
PhylomeDBiP0A988

Enzyme and pathway databases

BioCyciEcoCyc:EG10242-MONOMER
MetaCyc:EG10242-MONOMER

Miscellaneous databases

EvolutionaryTraceiP0A988
PROiPR:P0A988

Family and domain databases

CDDicd00140 beta_clamp, 1 hit
InterProiView protein in InterPro
IPR001001 DNA_polIII_beta
IPR022635 DNA_polIII_beta_C
IPR022637 DNA_polIII_beta_cen
IPR022634 DNA_polIII_beta_N
PANTHERiPTHR30478 PTHR30478, 1 hit
PfamiView protein in Pfam
PF00712 DNA_pol3_beta, 1 hit
PF02767 DNA_pol3_beta_2, 1 hit
PF02768 DNA_pol3_beta_3, 1 hit
PIRSFiPIRSF000804 DNA_pol_III_b, 1 hit
SMARTiView protein in SMART
SM00480 POL3Bc, 1 hit
TIGRFAMsiTIGR00663 dnan, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiDPO3B_ECOLI
AccessioniPrimary (citable) accession number: P0A988
Secondary accession number(s): P00583, Q2M813
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: April 1, 1988
Last modified: November 7, 2018
This is version 122 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
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