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UniProtKB - P28630 (HOLA_ECOLI)

Protein

DNA polymerase III subunit delta

Gene

holA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Part of the beta sliding clamp loading complex, which hydrolyzes ATP to load the beta clamp onto primed DNA to form the DNA replication pre-initiation complex (PubMed:2040637). DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3'-5' exonuclease activity. The delta subunit is the wrench that will open the beta subunit dimer, which has been modeled to leave a gap large enough for ssDNA to pass through (PubMed:11525728). The gamma complex (gamma3,delta,delta') is thought to load beta dimers onto DNA by binding ATP which alters the complex's conformation so it can bind beta sliding clamp dimers and open them at one interface. Primed DNA is recognized, ATP is hydrolyzed releasing the gamma complex and closing the beta sliding clamp ring around the primed DNA (PubMed:9927437).1 Publication2 Publications

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

View the complete GO annotation on QuickGO ...

GO - Biological processi

  • DNA-dependent DNA replication Source: EcoCyc
View the complete GO annotation on QuickGO ...

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

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

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		EcoCyc:EG11412-MONOMER
MetaCyc:EG11412-MONOMER

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
DNA polymerase III subunit delta (EC:2.7.7.7)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:holA
Ordered Locus Names:b0640, JW0635
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiEscherichia coli (strain K12)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri83333 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia ›
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000000318 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

Escherichia coli strain K12 genome database

More...EcoGenei		EG11412 holA

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

GO - Cellular componenti

View the complete GO annotation on QuickGO ...

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001055051 – 343DNA polymerase III subunit deltaAdd BLAST343

Proteomic databases

PaxDb, a database of protein abundance averages across all three domains of life

More...PaxDbi		P28630

PRoteomics IDEntifications database

More...PRIDEi		P28630

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

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 (PubMed:2040637). The polymerase is tethered to the template via the dimeric beta sliding clamp processivity factor. The clamp-loading complex (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-loading complex 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). The clamp loader hydrolyzes ATP to assemble the beta processivity factor onto the primed template (PubMed:2040637, PubMed:9927437) and plays a central role in the organization and communication at the replication fork; the minimal complex to load the beta sliding clamp on DNA is delta, delta', gamma (PubMed:9927437).5 Publications

<p>This subsection of the '<a href="http://www.uniprot.org/help/interaction_section%27">Interaction</a> section provides information about binary protein-protein interactions. The data presented in this section are a quality-filtered subset of binary interactions automatically derived from the <a href="http://www.ebi.ac.uk/intact/">IntAct database</a>. It is updated on a monthly basis. Each binary interaction is displayed on a separate line.<p><a href='/help/binary_interactions' target='_top'>More...</a></p>Binary interactionsi

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

More...BioGridi		4259908, 201 interactors

ComplexPortal: manually curated resource of macromolecular complexes

More...ComplexPortali		CPX-1926 DNA polymerase III clamp loader complex

Database of interacting proteins

More...DIPi		DIP-9931N

Protein interaction database and analysis system

More...IntActi		P28630, 49 interactors

STRING: functional protein association networks

More...STRINGi		316385.ECDH10B_0709

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1343
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase

More...ProteinModelPortali		P28630

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...SMRi		P28630

Database of comparative protein structure models

More...ModBasei		Search...

MobiDB: a database of protein disorder and mobility annotations

More...MobiDBi		Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...EvolutionaryTracei		P28630

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni1 – 140Domain 11 PublicationAdd BLAST140
Regioni141 – 210Domain 21 PublicationAdd BLAST70
Regioni211 – 343Domain 31 PublicationAdd BLAST133

<p>This subsection of the ‘Family and domains’ section provides general information on the biological role of a domain. The term ‘domain’ is intended here in its wide acceptation, it may be a structural domain, a transmembrane region or a functional domain. Several domains are described in this subsection.<p><a href='/help/domain_cc' target='_top'>More...</a></p>Domaini

Has three domains, each of which is closely related to a corresponding domain in the delta' stator, despite the 2 proteins having only 6-8% sequence identity. Interacts with the beta sliding clamp via domain 1 (residues 1-140, in particular residues 61-74), fitting into a cleft between domains 2 and 3 on the surface of the beta-clamp (PubMed:11525728). Residues 61-74 move about 45 degrees and 5.5 Angstroms in the beta-delta versus gamma-delta-delta' structure to contact respectively the beta or delta' (PubMed:11525728).1 Publication

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		ENOG4105DJF Bacteria
COG1466 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		HOG000256204

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		P28630

KEGG Orthology (KO)

More...KOi		K02340

Database for complete collections of gene phylogenies

More...PhylomeDBi		P28630

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR008921 DNA_pol3_clamp-load_cplx_C
IPR032780 DNA_pol3_delt_C
IPR010372 DNA_pol3_delta_N
IPR005790 DNA_polIII_delta
IPR027417 P-loop_NTPase

Pfam protein domain database

More...Pfami		View protein in Pfam
PF14840 DNA_pol3_delt_C, 1 hit
PF06144 DNA_pol3_delta, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF48019 SSF48019, 1 hit
SSF52540 SSF52540, 1 hit

TIGRFAMs; a protein family database

More...TIGRFAMsi		TIGR01128 holA, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>.<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

P28630-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MIRLYPEQLR AQLNEGLRAA YLLLGNDPLL LQESQDAVRQ VAAAQGFEEH 
        60         70         80         90        100
HTFSIDPNTD WNAIFSLCQA MSLFASRQTL LLLLPENGPN AAINEQLLTL 
       110        120        130        140        150
TGLLHDDLLL IVRGNKLSKA QENAAWFTAL ANRSVQVTCQ TPEQAQLPRW 
       160        170        180        190        200
VAARAKQLNL ELDDAANQVL CYCYEGNLLA LAQALERLSL LWPDGKLTLP 
       210        220        230        240        250
RVEQAVNDAA HFTPFHWVDA LLMGKSKRAL HILQQLRLEG SEPVILLRTL 
       260        270        280        290        300
QRELLLLVNL KRQSAHTPLR ALFDKHRVWQ NRRGMMGEAL NRLSQTQLRQ 
       310        320        330        340 
AVQLLTRTEL TLKQDYGQSV WAELEGLSLL LCHKPLADVF IDG
Length:343
Mass (Da):38,704
Last modified:December 1, 1992 - v1
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i87239A678FE16BE2
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...EMBLi

GenBank nucleotide sequence database

More...GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...DDBJi
Links Updated
L04576 Genomic DNA Translation: AAA23675.1
M94267 Genomic DNA Translation: AAB59047.1
U82598 Genomic DNA Translation: AAB40841.1
U00096 Genomic DNA Translation: AAC73741.1
AP009048 Genomic DNA Translation: BAA35287.1
M18277 Genomic DNA No translation available.

Protein sequence database of the Protein Information Resource

More...PIRi		A45251

NCBI Reference Sequences

More...RefSeqi		NP_415173.1, NC_000913.3
WP_000620535.1, NZ_LN832404.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		AAC73741; AAC73741; b0640
BAA35287; BAA35287; BAA35287

Database of genes from NCBI RefSeq genomes

More...GeneIDi		947573

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		ecj:JW0635
eco:b0640

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|1411691.4.peg.1628

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L04576 Genomic DNA Translation: AAA23675.1
M94267 Genomic DNA Translation: AAB59047.1
U82598 Genomic DNA Translation: AAB40841.1
U00096 Genomic DNA Translation: AAC73741.1
AP009048 Genomic DNA Translation: BAA35287.1
M18277 Genomic DNA No translation available.
PIRiA45251
RefSeqiNP_415173.1, NC_000913.3
WP_000620535.1, NZ_LN832404.1

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...PDBei

Protein Data Bank RCSB

More...RCSB PDBi

Protein Data Bank Japan

More...PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1JQJX-ray2.90C/D1-343[»]
1JQLX-ray2.50B1-140[»]
1JR3X-ray2.70D1-343[»]
1XXHX-ray3.45A/F1-343[»]
1XXIX-ray4.10A/F1-343[»]
3GLFX-ray3.39A/F1-343[»]
3GLGX-ray3.25A/F1-343[»]
3GLHX-ray3.89A/F/K1-343[»]
3GLIX-ray3.50A/F1-343[»]
ProteinModelPortaliP28630
SMRiP28630
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4259908, 201 interactors
ComplexPortaliCPX-1926 DNA polymerase III clamp loader complex
DIPiDIP-9931N
IntActiP28630, 49 interactors
STRINGi316385.ECDH10B_0709

Proteomic databases

PaxDbiP28630
PRIDEiP28630

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73741; AAC73741; b0640
BAA35287; BAA35287; BAA35287
GeneIDi947573
KEGGiecj:JW0635
eco:b0640
PATRICifig|1411691.4.peg.1628

Organism-specific databases

EchoBASE - an integrated post-genomic database for E. coli

More...EchoBASEi		EB1384
EcoGeneiEG11412 holA

Phylogenomic databases

eggNOGiENOG4105DJF Bacteria
COG1466 LUCA
HOGENOMiHOG000256204
InParanoidiP28630
KOiK02340
PhylomeDBiP28630

Enzyme and pathway databases

BioCyciEcoCyc:EG11412-MONOMER
MetaCyc:EG11412-MONOMER

Miscellaneous databases

EvolutionaryTraceiP28630

Protein Ontology

More...PROi		PR:P28630

Family and domain databases

InterProiView protein in InterPro
IPR008921 DNA_pol3_clamp-load_cplx_C
IPR032780 DNA_pol3_delt_C
IPR010372 DNA_pol3_delta_N
IPR005790 DNA_polIII_delta
IPR027417 P-loop_NTPase
PfamiView protein in Pfam
PF14840 DNA_pol3_delt_C, 1 hit
PF06144 DNA_pol3_delta, 1 hit
SUPFAMiSSF48019 SSF48019, 1 hit
SSF52540 SSF52540, 1 hit
TIGRFAMsiTIGR01128 holA, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...ProtoNeti		Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiHOLA_ECOLI
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P28630
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 1, 1992
Last sequence update: December 1, 1992
Last modified: December 5, 2018
This is version 156 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
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