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UniProtKB - P07071 (NRDD_BPT4)

Protein

Anaerobic ribonucleoside-triphosphate reductase

Gene

nrdD

Organism
Enterobacteria phage T4 (Bacteriophage T4)
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

Catalyzes the conversion of ribonucleotides into deoxyribonucleotides, which are required for DNA synthesis and repair.2 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>This subsection of the ‘Function’ section describes regulatory mechanisms for enzymes, transporters or microbial transcription factors, and reports the components which regulate (by activation or inhibition) the reaction.<p><a href='/help/activity_regulation' target='_top'>More...</a></p>Activity regulationi

Activated under anaerobic conditions by NrdG, a tightly associated activase. Activation involves the formation of a glycyl radical at Gly-580.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<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 sitei114Substrate 21 Publication1
Binding sitei146Substrate 22 Publications1
<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 bindingi543Zinc1 Publication1 Publication1
Metal bindingi546Zinc1 Publication1 Publication1
Metal bindingi561Zinc1 Publication1 Publication1
Metal bindingi564Zinc1 Publication1 Publication1

<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

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 functionOxidoreductase
LigandMetal-binding, Zinc

<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:
Anaerobic ribonucleoside-triphosphate reductaseCurated (EC:1.1.98.61 Publication)
Alternative name(s):
Class III ribonucleoside-triphosphate reductaseCurated
<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:nrdD1 Publication
Synonyms:49.1, 55.11/55.13, SUNY
<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>OrganismiEnterobacteria phage T4 (Bacteriophage T4)
<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 identifieri10665 [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 lineageiViruses › dsDNA viruses, no RNA stage › Caudovirales › Myoviridae › Tevenvirinae › T4virus
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section only exists in viral entries and indicates the host(s) either as a specific organism or taxonomic group of organisms that are susceptible to be infected by a virus.<p><a href='/help/virus_host' target='_top'>More...</a></p>Virus hostiEscherichia coli [TaxID: 562]
<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
  • UP000009087 <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

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology_and_biotech_section">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi580G → A: Lacks both glycyl radical and activity. Does not affect interaction with NrdG. 1 Publication1

Chemistry databases

Drug and drug target database

More...DrugBanki		DB03222 2'-Deoxyadenosine 5'-Triphosphate
DB03258 2'-Deoxycytidine-5'-Triphosphate
DB02181 2'-Deoxyguanosine-5'-Triphosphate
DB02452 Thymidine-5'-Triphosphate

<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_00001666861 – 605Anaerobic ribonucleoside-triphosphate reductaseAdd BLAST605

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section specifies the position and type of each modified residue excluding <a href="http://www.uniprot.org/manual/lipid">lipids</a>, <a href="http://www.uniprot.org/manual/carbohyd">glycans</a> and <a href="http://www.uniprot.org/manual/crosslnk">protein cross-links</a>.<p><a href='/help/mod_res' target='_top'>More...</a></p>Modified residuei580Glycine radical1 Publication1

Keywords - PTMi

Organic radical

<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

Homodimer. Forms a tetramer composed of two NrdD and two NrdG subunits.1 Publication

<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

1605
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		P07071

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

More...SMRi		P07071

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		P07071

<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>Domaini482 – 605Glycine radicalPROSITE-ProRule annotationAdd BLAST124

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>Regioni64 – 66Substrate 1 binding2 Publications3
Regioni100 – 103Substrate 2 binding2 Publications4
Regioni444 – 448Substrate 1 binding2 Publications5

<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 anaerobic ribonucleoside-triphosphate reductase family.Curated

Phylogenomic databases

Database of Orthologous Groups

More...OrthoDBi		VOG0900003Y

Family and domain databases

Conserved Domains Database

More...CDDi		cd01675 RNR_III, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR019777 Form_AcTrfase_GR_CS
IPR001150 Gly_radical
IPR012833 NrdD

Pfam protein domain database

More...Pfami		View protein in Pfam
PF13597 NRDD, 1 hit

TIGRFAMs; a protein family database

More...TIGRFAMsi		TIGR02487 NrdD, 1 hit

PROSITE; a protein domain and family database

More...PROSITEi		View protein in PROSITE
PS00850 GLY_RADICAL_1, 1 hit
PS51149 GLY_RADICAL_2, 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.

P07071-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MTIEKEIEGL IHKTNKDLLN ENANKDSRVF PTQRDLMAGI VSKHIAKNMV 
        60         70         80         90        100
PSFIMKAHES GIIHVHDIDY SPALPFTNCC LVDLKGMLEN GFKLGNAQIE 
       110        120        130        140        150
TPKSIGVATA IMAQITAQVA SHQYGGTTFA NVDKVLSPYV KRTYAKHIED 
       160        170        180        190        200
AEKWQIADAL NYAQSKTEKD VYDAFQAYEY EVNTLFSSNG QTPFVTITFG 
       210        220        230        240        250
TGTDWTERMI QKAILKNRIK GLGRDGITPI FPKLVMFVEE GVNLYKDDPN 
       260        270        280        290        300
YDIKQLALEC ASKRMYPDII SAKNNKAITG SSVPVSPMGC RSFLSVWKDS 
       310        320        330        340        350
TGNEILDGRN NLGVVTLNLP RIALDSYIGT QFNEQKFVEL FNERMDLCFE 
       360        370        380        390        400
ALMCRISSLK GVKATVAPIL YQEGAFGVRL KPDDDIIELF KNGRSSVSLG 
       410        420        430        440        450
YIGIHELNIL VGRDIGREIL TKMNAHLKQW TERTGFAFSL YSTPAENLCY 
       460        470        480        490        500
RFCKLDTEKY GSVKDVTDKG WYTNSFHVSV EENITPFEKI SREAPYHFIA 
       510        520        530        540        550
TGGHISYVEL PDMKNNLKGL EAVWDYAAQH LDYFGVNMPV DKCFTCGSTH 
       560        570        580        590        600
EMTPTENGFV CSICGETDPK KMNTIRRTCG YLGNPNERGF NLGKNKEIMH 

RVKHQ
Length:605
Mass (Da):67,957
Last modified:January 23, 2002 - v4
<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:iC5F29CE03126800B
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
Y00122 Genomic DNA Translation: CAA68308.1
Y00122 Genomic DNA Translation: CAA68310.1 Sequence problems.
AF158101 Genomic DNA Translation: AAD42633.1
X12629 Genomic DNA Translation: CAA31150.1

Protein sequence database of the Protein Information Resource

More...PIRi		E29284 Z6BPT9
S01907 Z4BPT9

NCBI Reference Sequences

More...RefSeqi		NP_049690.1, NC_000866.4

Genome annotation databases

Database of genes from NCBI RefSeq genomes

More...GeneIDi		1258655

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		vg:1258655

<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
Y00122 Genomic DNA Translation: CAA68308.1
Y00122 Genomic DNA Translation: CAA68310.1 Sequence problems.
AF158101 Genomic DNA Translation: AAD42633.1
X12629 Genomic DNA Translation: CAA31150.1
PIRiE29284 Z6BPT9
S01907 Z4BPT9
RefSeqiNP_049690.1, NC_000866.4

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
1H78X-ray2.50A1-605[»]
1H79X-ray2.90A1-605[»]
1H7AX-ray2.75A1-605[»]
1H7BX-ray2.45A1-605[»]
1HK8X-ray2.45A1-605[»]
ProteinModelPortaliP07071
SMRiP07071
ModBaseiSearch...
MobiDBiSearch...

Chemistry databases

DrugBankiDB03222 2'-Deoxyadenosine 5'-Triphosphate
DB03258 2'-Deoxycytidine-5'-Triphosphate
DB02181 2'-Deoxyguanosine-5'-Triphosphate
DB02452 Thymidine-5'-Triphosphate

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi1258655
KEGGivg:1258655

Phylogenomic databases

OrthoDBiVOG0900003Y

Miscellaneous databases

EvolutionaryTraceiP07071

Protein Ontology

More...PROi		PR:P07071

Family and domain databases

CDDicd01675 RNR_III, 1 hit
InterProiView protein in InterPro
IPR019777 Form_AcTrfase_GR_CS
IPR001150 Gly_radical
IPR012833 NrdD
PfamiView protein in Pfam
PF13597 NRDD, 1 hit
TIGRFAMsiTIGR02487 NrdD, 1 hit
PROSITEiView protein in PROSITE
PS00850 GLY_RADICAL_1, 1 hit
PS51149 GLY_RADICAL_2, 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 nameiNRDD_BPT4
<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: P07071
Secondary accession number(s): P07073, Q38428, Q9T0V5
<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: April 1, 1988
Last sequence update: January 23, 2002
Last modified: December 5, 2018
This is version 125 of the entry and version 4 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 programViral 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, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
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