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UniProtKB - P28905 (HOLC_ECOLI)

Entry version 150 (17 Jun 2020)
Sequence version 1 (01 Dec 1992)
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Protein

DNA polymerase III subunit chi

Gene

holC

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

Annotation score:4 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' to 5' exonuclease activity.1 Publication

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">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

Complete GO annotation on QuickGO ...

GO - Biological processi

  • DNA replication Source: UniProtKB-KW
  • positive regulation of DNA-dependent DNA replication initiation Source: EcoliWiki
  • response to radiation Source: EcoCyc
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:EG11413-MONOMER
ECOL316407:JW4216-MONOMER
MetaCyc:EG11413-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%5Fand%5Ftaxonomy%5Fsection">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 chi (EC:2.7.7.7)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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:holC
Ordered Locus Names:b4259, JW4216
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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%5Fand%5Ftaxonomy%5Fsection">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%5Fand%5Ftaxonomy%5Fsection">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%5Fand%5Ftaxonomy%5Fsection">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%5Fmanual">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

<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

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 or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001055171 – 147DNA polymerase III subunit chiAdd BLAST147

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

More...jPOSTi		P28905

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

More...PaxDbi		P28905

PRoteomics IDEntifications database

More...PRIDEi		P28905

<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%5Fsection">'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%5Fsection">'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) and plays a central role in the organization and communication at the replication fork.

3 Publications

<p>This subsection of the '<a href="http://www.uniprot.org/help/interaction%5Fsection%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="https://www.ebi.ac.uk/intact/">IntAct database</a>. It is updated at every <a href="http://www.uniprot.org/help/synchronization">UniProt release</a>.<p><a href='/help/binary_interactions' target='_top'>More...</a></p>Binary interactionsi

Hide details

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGRID)

More...BioGRIDi		4262725, 159 interactors
853072, 5 interactors

ComplexPortal: manually curated resource of macromolecular complexes

More...ComplexPortali		CPX-1926 DNA polymerase III clamp loader complex
CPX-1964 DNA polymerase III clamp loader chi-psi subcomplex

Database of interacting proteins

More...DIPi		DIP-9933N

Protein interaction database and analysis system

More...IntActi		P28905, 41 interactors

Molecular INTeraction database

More...MINTi		P28905

STRING: functional protein association networks

More...STRINGi		511145.b4259

<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

1147
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

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

More...SMRi		P28905

Database of comparative protein structure models

More...ModBasei		Search...

Protein Data Bank in Europe - Knowledge Base

More...PDBe-KBi		Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...EvolutionaryTracei		P28905

<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

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		ENOG4105MYG Bacteria
COG2927 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		CLU_131584_0_0_6

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		P28905

KEGG Orthology (KO)

More...KOi		K02339

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...Gene3Di		3.40.50.10110, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR007459 DNA_pol3_chi
IPR036768 PolIII_chi_sf

The PANTHER Classification System

More...PANTHERi		PTHR38767 PTHR38767, 1 hit

Pfam protein domain database

More...Pfami		View protein in Pfam
PF04364 DNA_pol3_chi, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF102400 SSF102400, 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%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<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%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">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.

P28905-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MKNATFYLLD NDTTVDGLSA VEQLVCEIAA ERWRSGKRVL IACEDEKQAY 
        60         70         80         90        100
RLDEALWARP AESFVPHNLA GEGPRGGAPV EIAWPQKRSS SRRDILISLR 
       110        120        130        140 
TSFADFATAF TEVVDFVPYE DSLKQLARER YKAYRVAGFN LNTATWK
Length:147
Mass (Da):16,633
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:i7FEFFC359B28AA88
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
L04574 Genomic DNA Translation: AAA70368.1
Z14155 Genomic DNA Translation: CAA78524.1
U14003 Genomic DNA Translation: AAA97156.1
U00096 Genomic DNA Translation: AAC77216.1
AP009048 Genomic DNA Translation: BAE78256.1
X15130 Genomic DNA Translation: CAA33226.1

Protein sequence database of the Protein Information Resource

More...PIRi		A46739

NCBI Reference Sequences

More...RefSeqi		NP_418680.1, NC_000913.3
WP_000786400.1, NZ_LN832404.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		AAC77216; AAC77216; b4259
BAE78256; BAE78256; BAE78256

Database of genes from NCBI RefSeq genomes

More...GeneIDi		948787

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		ecj:JW4216
eco:b4259

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|1411691.4.peg.2445

<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
L04574 Genomic DNA Translation: AAA70368.1
Z14155 Genomic DNA Translation: CAA78524.1
U14003 Genomic DNA Translation: AAA97156.1
U00096 Genomic DNA Translation: AAC77216.1
AP009048 Genomic DNA Translation: BAE78256.1
X15130 Genomic DNA Translation: CAA33226.1
PIRiA46739
RefSeqiNP_418680.1, NC_000913.3
WP_000786400.1, 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
1EM8X-ray2.10A/C1-147[»]
3SXUX-ray1.85A1-147[»]
SMRiP28905
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

BioGRIDi4262725, 159 interactors
853072, 5 interactors
ComplexPortaliCPX-1926 DNA polymerase III clamp loader complex
CPX-1964 DNA polymerase III clamp loader chi-psi subcomplex
DIPiDIP-9933N
IntActiP28905, 41 interactors
MINTiP28905
STRINGi511145.b4259

Proteomic databases

jPOSTiP28905
PaxDbiP28905
PRIDEiP28905

Genome annotation databases

EnsemblBacteriaiAAC77216; AAC77216; b4259
BAE78256; BAE78256; BAE78256
GeneIDi948787
KEGGiecj:JW4216
eco:b4259
PATRICifig|1411691.4.peg.2445

Organism-specific databases

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

More...EchoBASEi		EB1385

Phylogenomic databases

eggNOGiENOG4105MYG Bacteria
COG2927 LUCA
HOGENOMiCLU_131584_0_0_6
InParanoidiP28905
KOiK02339

Enzyme and pathway databases

BioCyciEcoCyc:EG11413-MONOMER
ECOL316407:JW4216-MONOMER
MetaCyc:EG11413-MONOMER

Miscellaneous databases

EvolutionaryTraceiP28905

Protein Ontology

More...PROi		PR:P28905

Family and domain databases

Gene3Di3.40.50.10110, 1 hit
InterProiView protein in InterPro
IPR007459 DNA_pol3_chi
IPR036768 PolIII_chi_sf
PANTHERiPTHR38767 PTHR38767, 1 hit
PfamiView protein in Pfam
PF04364 DNA_pol3_chi, 1 hit
SUPFAMiSSF102400 SSF102400, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...ProtoNeti		Search...

MobiDB: a database of protein disorder and mobility annotations

More...MobiDBi		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 nameiHOLC_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: P28905
Secondary accession number(s): P11649, Q2M650
<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%5Fand%5Fisoforms">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: June 17, 2020
This is version 150 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, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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