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Protein

DNA-directed DNA polymerase

Gene

43

Organism
Escherichia virus RB43
Status
Unreviewed-Annotation score:

Annotation score:3 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>
-Protein inferred from homologyi <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

Replicates the viral genomic DNA. This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single-stranded DNA in the 3'- to 5'-direction for proofreading purpose.UniRule annotation

Caution

Lacks conserved residue(s) required for the propagation of feature annotation.UniRule annotation

<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>This subsection of the ‘Function’ section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

Mg2+UniRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Function’ section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the ‘Description’ field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi114Magnesium 1; catalytic; for 3'-5' exonuclease activityUniRule annotation1
Metal bindingi116Magnesium 1; catalytic; for 3'-5' exonuclease activityUniRule annotation1
Metal bindingi213Magnesium 2; catalytic; for 3'-5' exonuclease activityUniRule annotation1
Metal bindingi319Magnesium 1; catalytic; for 3'-5' exonuclease activityUniRule annotation1
Metal bindingi319Magnesium 2; catalytic; for 3'-5' exonuclease activityUniRule annotation1
Metal bindingi403Magnesium 3; catalytic; for polymerase activityUniRule annotation1
Metal bindingi403Magnesium 4; catalytic; for polymerase activityUniRule annotation1
Metal bindingi404Magnesium 4; catalytic; via carbonyl oxygen; for polymerase activityUniRule annotation1
<p>This subsection of the ‘Function’ section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei474SubstrateUniRule annotation1
Binding sitei554SubstrateUniRule annotation1
<p>This subsection describes interesting single amino acid sites on the sequence that are not defined in any other subsection. This subsection can be displayed in different sections (‘Function’, ‘PTM / Processing’, ‘Pathology and Biotech’) according to its content.<p><a href='/help/site' target='_top'>More...</a></p>Sitei615Optimization of metal coordination by the polymerase active siteUniRule annotation1
Metal bindingi617Magnesium 3; catalytic; for polymerase activityUniRule annotation1
Metal bindingi617Magnesium 4; catalytic; for polymerase activityUniRule annotation1
Sitei701Optimization of metal coordination by the polymerase active siteUniRule annotation1
Sitei709Essential for viral replicationUniRule annotation1

<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

GO - Biological processi

<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-bindingUniRule annotation, DNA-directed DNA polymeraseUniRule annotation, ExonucleaseUniRule annotation, Hydrolase, Multifunctional enzymeUniRule annotation, Nuclease, Nucleotidyltransferase, Transferase
Biological processDNA replication, Viral DNA replicationUniRule annotation
LigandMagnesiumUniRule annotation, Metal-bindingUniRule annotation

<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-directed DNA polymeraseUniRule annotation (EC:2.7.7.7UniRule annotation, EC:3.1.11.-UniRule annotation)
<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:43Imported
ORF Names:RB43ORF038cImported
<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 virus RB43Imported
<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 identifieri115991 [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 lineageiVirusesdsDNA viruses, no RNA stageCaudoviralesMyoviridaeTevenvirinaeKp15virusunclassified Kp15virus
<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
  • UP000001467 <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: Genome
  • UP000211060 Componenti: Genome
  • UP000211040 Componenti: Genome

<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

Part of the replicase complex that includes the DNA polymerase, the polymerase clamp, the clamp loader complex, the single-stranded DNA binding protein, and the primase/helicase. Interacts with the polymerase clamp; this interaction constitutes the polymerase holoenzyme.UniRule annotation

<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

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family_and_domains_section">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini104 – 285DNA_pol_B_exo1InterPro annotationAdd BLAST182
Domaini361 – 768DNA_pol_BInterPro annotationAdd BLAST408

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>Regioni372 – 901PolymeraseUniRule annotationAdd BLAST530
Regioni406 – 408Substrate bindingUniRule annotation3
Regioni700 – 703Binding of DNA in B-conformationUniRule annotation4
Regioni893 – 901Interaction with the polymerase clampUniRule annotation9

<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

The N-terminus contains the 3'-5' exonuclease activity. The C-terminus contains the polymerase activity and is involved in binding to the polymerase clamp protein. A beta hairpin structure is necessary for the proofreading function of the polymerase.UniRule annotation

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the DNA polymerase type-B family.UniRule annotation

Phylogenomic databases

KEGG Orthology (KO)

More...
KOi
K18942

Database of Orthologous Groups

More...
OrthoDBi
VOG0900001M

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.30.420.10, 1 hit

HAMAP database of protein families

More...
HAMAPi
MF_04100 DPOL_T4, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR006172 DNA-dir_DNA_pol_B
IPR017964 DNA-dir_DNA_pol_B_CS
IPR006133 DNA-dir_DNA_pol_B_exonuc
IPR006134 DNA-dir_DNA_pol_B_multi_dom
IPR034749 DPOL_T4
IPR012337 RNaseH-like_sf
IPR036397 RNaseH_sf

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF00136 DNA_pol_B, 1 hit
PF03104 DNA_pol_B_exo1, 1 hit

Protein Motif fingerprint database; a protein domain database

More...
PRINTSi
PR00106 DNAPOLB

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00486 POLBc, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF53098 SSF53098, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS00116 DNA_POLYMERASE_B, 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.

Q56C10-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MNEFYLSVEQ MGDHIYERFI DADGREQVRK TKYEPTLFQH AMAGTDSPYK
60 70 80 90 100
DIYGKTCIKK KFDCIKDAKN WMQRMKDVGM EALGMDDFRL AYISDTYRNE
110 120 130 140 150
IEYNRERIRI ASLDIEVTAP EFPDPREAKY AIDAITHYDS VEDKFFVYDL
160 170 180 190 200
VEGGLDEWVA SKVDTEKEIS EEDLKKIVYR AFQTEKSLMS AYIKDWKERT
210 220 230 240 250
PVIVTGWNSN KFDIAYIITR YLNIFGQNVV RHFSPFGKVT AKTTTDQYGN
260 270 280 290 300
EQLGYEIYGV SQMDGMDLYK KFSFTPQPSY SLGAIAEYET GKNKVDYEGS
310 320 330 340 350
LSELRQKDHQ TYITYNIVDV IRVLDIDGKR NFIELVLSVA YYAKINFPGV
360 370 380 390 400
MSPLKTWDAI IYNSLREDKI AIPENKRHTK TPYDGAYVKD PVVAPYKYIV
410 420 430 440 450
SFDLTSLYPS IIRQVNISPE TIANSFAVRP LDEYINKTAP RPSDEFSCSP
460 470 480 490 500
NGWMFRRDIK GVIPVEIKKV FDQRKMWKKR MMAGERNLEL IKHELEHLTD
510 520 530 540 550
AHNQMIDPDF DFYSDFSDES KAVLKTLTKQ MLKAVKKVCE KKIAQANTAQ
560 570 580 590 600
LNRKISINSL YGALGNEHFR YFDIRNASAI TMFGQLAIQW IERKVNEYLN
610 620 630 640 650
QLCNTTDYAY VRYCDTDSIY VCMDNVIEKV GGESKFRDNN HWVDFLDKFS
660 670 680 690 700
RERMEPIIDK GYRELCEYMN NVEHLMFMDR EIISGPPLGS KGLGSFWTAK
710 720 730 740 750
KRYAANVWDS EGTRYEKPKL KIMGMETQRS STPTAVKVFL KEAIRRILQE
760 770 780 790 800
GEESLHESFK VFEEEYKALD YREIAGVSSA NNITKYNDGT GHPIKGTPNH
810 820 830 840 850
IKGVLFFNRL TRGIQGITQI MEGEKVMVLP LRDKNPWQSD CIAWQSGSRL
860 870 880 890 900
PNEIESDILK WVDYNGLFEK HVISPLKNIT EACKIDYEKR ASLNTLFGDD

W
Length:901
Mass (Da):104,604
Last modified:May 10, 2005 - 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:iD62B88C4FE5E19EA
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
AY967407 Genomic DNA Translation: AAX78560.1
HE858210 Genomic DNA Translation: CCK73887.1
HE981739 Genomic DNA Translation: CCL97504.1

NCBI Reference Sequences

More...
RefSeqi
YP_239014.1, NC_007023.1

Genome annotation databases

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
3416336

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
vg:3416336

<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
AY967407 Genomic DNA Translation: AAX78560.1
HE858210 Genomic DNA Translation: CCK73887.1
HE981739 Genomic DNA Translation: CCL97504.1
RefSeqiYP_239014.1, NC_007023.1

3D structure databases

Database of comparative protein structure models

More...
ModBasei
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi3416336
KEGGivg:3416336

Phylogenomic databases

KOiK18942
OrthoDBiVOG0900001M

Family and domain databases

Gene3Di3.30.420.10, 1 hit
HAMAPiMF_04100 DPOL_T4, 1 hit
InterProiView protein in InterPro
IPR006172 DNA-dir_DNA_pol_B
IPR017964 DNA-dir_DNA_pol_B_CS
IPR006133 DNA-dir_DNA_pol_B_exonuc
IPR006134 DNA-dir_DNA_pol_B_multi_dom
IPR034749 DPOL_T4
IPR012337 RNaseH-like_sf
IPR036397 RNaseH_sf
PfamiView protein in Pfam
PF00136 DNA_pol_B, 1 hit
PF03104 DNA_pol_B_exo1, 1 hit
PRINTSiPR00106 DNAPOLB
SMARTiView protein in SMART
SM00486 POLBc, 1 hit
SUPFAMiSSF53098 SSF53098, 1 hit
PROSITEiView protein in PROSITE
PS00116 DNA_POLYMERASE_B, 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 nameiQ56C10_9CAUD
<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: Q56C10
<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/TrEMBL: May 10, 2005
Last sequence update: May 10, 2005
Last modified: December 5, 2018
This is version 93 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 statusiUnreviewed (UniProtKB/TrEMBL)

<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

Complete proteome, Reference proteomeImported
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