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P07071

- NRDD_BPT4

UniProt

P07071 - NRDD_BPT4

Protein

Anaerobic ribonucleoside-triphosphate reductase

Gene

NRDD

Organism
Enterobacteria phage T4 (Bacteriophage T4)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 104 (01 Oct 2014)
      Sequence version 4 (23 Jan 2002)
      Previous versions | rss
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    Functioni

    Catalytic activityi

    2'-deoxyribonucleoside triphosphate + thioredoxin disulfide + H2O = ribonucleoside triphosphate + thioredoxin.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi543 – 5431Zinc
    Metal bindingi546 – 5461Zinc
    Metal bindingi561 – 5611Zinc
    Metal bindingi564 – 5641Zinc

    GO - Molecular functioni

    1. metal ion binding Source: UniProtKB-KW
    2. ribonucleoside-triphosphate reductase activity Source: UniProtKB-EC

    GO - Biological processi

    1. DNA replication Source: InterPro

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Ligandi

    Metal-binding, Zinc

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Anaerobic ribonucleoside-triphosphate reductase (EC:1.17.4.2)
    Gene namesi
    Name:NRDD
    Synonyms:49.1, 55.11/55.13, SUNY
    OrganismiEnterobacteria phage T4 (Bacteriophage T4)
    Taxonomic identifieri10665 [NCBI]
    Taxonomic lineageiVirusesdsDNA viruses, no RNA stageCaudoviralesMyoviridaeTevenvirinaeT4likevirus
    Virus hostiEscherichia coli [TaxID: 562]
    ProteomesiUP000009087: Genome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 605605Anaerobic ribonucleoside-triphosphate reductasePRO_0000166686Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei580 – 5801Glycine radical

    Keywords - PTMi

    Organic radical

    Expressioni

    Inductioni

    Probably by activating enzyme under anaerobic conditions by generation of an organic free radical. Exposure of this activated protein to oxygen may result in cleavage at the glycine residue harboring its organic radical with loss of the 25 C-terminal AA.

    Interactioni

    Subunit structurei

    Tetramer consisting of 2 alpha (NrdD) and 2 beta (NrdG) subunits.

    Structurei

    Secondary structure

    1
    605
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi30 – 4718
    Helixi52 – 598
    Beta strandi62 – 654
    Turni66 – 738
    Helixi84 – 896
    Beta strandi92 – 943
    Beta strandi97 – 993
    Helixi105 – 12016
    Beta strandi123 – 1253
    Beta strandi127 – 1293
    Helixi132 – 14817
    Turni149 – 1557
    Helixi159 – 18426
    Turni185 – 1884
    Beta strandi195 – 1995
    Helixi205 – 22016
    Turni223 – 2264
    Beta strandi232 – 2387
    Turni240 – 2434
    Helixi251 – 26414
    Beta strandi268 – 2714
    Helixi272 – 2798
    Turni289 – 2913
    Beta strandi310 – 3189
    Helixi319 – 3246
    Helixi334 – 35825
    Turni359 – 3613
    Helixi364 – 3663
    Helixi368 – 3714
    Beta strandi384 – 3863
    Helixi387 – 3904
    Turni391 – 3944
    Beta strandi395 – 4028
    Helixi404 – 4118
    Helixi416 – 43419
    Beta strandi437 – 4415
    Helixi448 – 46013
    Turni464 – 4674
    Beta strandi468 – 4714
    Beta strandi480 – 4823
    Helixi486 – 4938
    Helixi494 – 4985
    Beta strandi506 – 5094
    Helixi517 – 53014
    Beta strandi532 – 5376
    Beta strandi540 – 5423
    Turni544 – 5463
    Beta strandi553 – 5553
    Beta strandi556 – 5605
    Beta strandi562 – 5643
    Helixi569 – 5713
    Beta strandi573 – 5764
    Beta strandi578 – 5814

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    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. Positions 27-589.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP07071.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini482 – 605124Glycine radicalPROSITE-ProRule annotationAdd
    BLAST

    Sequence similaritiesi

    Contains 1 glycine radical domain.PROSITE-ProRule annotation

    Family and domain databases

    InterProiIPR019777. Form_AcTrfase_GR_CS.
    IPR001150. Gly_radical.
    IPR012833. NrdD.
    [Graphical view]
    TIGRFAMsiTIGR02487. NrdD. 1 hit.
    PROSITEiPS00850. GLY_RADICAL_1. 1 hit.
    PS51149. GLY_RADICAL_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P07071-1 [UniParc]FASTAAdd to Basket

    « Hide

    MTIEKEIEGL IHKTNKDLLN ENANKDSRVF PTQRDLMAGI VSKHIAKNMV    50
    PSFIMKAHES GIIHVHDIDY SPALPFTNCC LVDLKGMLEN GFKLGNAQIE 100
    TPKSIGVATA IMAQITAQVA SHQYGGTTFA NVDKVLSPYV KRTYAKHIED 150
    AEKWQIADAL NYAQSKTEKD VYDAFQAYEY EVNTLFSSNG QTPFVTITFG 200
    TGTDWTERMI QKAILKNRIK GLGRDGITPI FPKLVMFVEE GVNLYKDDPN 250
    YDIKQLALEC ASKRMYPDII SAKNNKAITG SSVPVSPMGC RSFLSVWKDS 300
    TGNEILDGRN NLGVVTLNLP RIALDSYIGT QFNEQKFVEL FNERMDLCFE 350
    ALMCRISSLK GVKATVAPIL YQEGAFGVRL KPDDDIIELF KNGRSSVSLG 400
    YIGIHELNIL VGRDIGREIL TKMNAHLKQW TERTGFAFSL YSTPAENLCY 450
    RFCKLDTEKY GSVKDVTDKG WYTNSFHVSV EENITPFEKI SREAPYHFIA 500
    TGGHISYVEL PDMKNNLKGL EAVWDYAAQH LDYFGVNMPV DKCFTCGSTH 550
    EMTPTENGFV CSICGETDPK KMNTIRRTCG YLGNPNERGF NLGKNKEIMH 600
    RVKHQ 605
    Length:605
    Mass (Da):67,957
    Last modified:January 23, 2002 - v4
    Checksum:iC5F29CE03126800B
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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.

    Genome annotation databases

    GeneIDi1258655.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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 .
    PIRi E29284. Z6BPT9.
    S01907. Z4BPT9.
    RefSeqi NP_049690.1. NC_000866.4.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1H78 X-ray 2.50 A 1-605 [» ]
    1H79 X-ray 2.90 A 1-605 [» ]
    1H7A X-ray 2.75 A 1-605 [» ]
    1H7B X-ray 2.45 A 1-605 [» ]
    1HK8 X-ray 2.45 A 1-605 [» ]
    ProteinModelPortali P07071.
    SMRi P07071. Positions 27-589.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    GeneIDi 1258655.

    Miscellaneous databases

    EvolutionaryTracei P07071.

    Family and domain databases

    InterProi IPR019777. Form_AcTrfase_GR_CS.
    IPR001150. Gly_radical.
    IPR012833. NrdD.
    [Graphical view ]
    TIGRFAMsi TIGR02487. NrdD. 1 hit.
    PROSITEi PS00850. GLY_RADICAL_1. 1 hit.
    PS51149. GLY_RADICAL_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Nucleotide sequence and primary structures of gene products coded for by the T4 genome between map positions 48.266 kb and 39.166 kb."
      Tomaschewski J., Rueger W.
      Nucleic Acids Res. 15:3632-3633(1987) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: C.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    3. "Regulation of two nested proteins from gene 49 (recombination endonuclease VII) and of a lambda RexA-like protein of bacteriophage T4."
      Barth K.A., Powell D., Trupin M., Mosig G.
      Genetics 120:329-343(1988) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-181.
    4. "The product of the split sunY gene of bacteriophage T4 is a processed protein."
      Zeh A., Shub D.A.
      J. Bacteriol. 173:6980-6985(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION.
    5. "A possible glycine radical in anaerobic ribonucleotide reductase from Escherichia coli: nucleotide sequence of the cloned nrdD gene."
      Sun X., Harder J., Krook M., Joernvall H., Sjoeberg B.-M., Reichard P.
      Proc. Natl. Acad. Sci. U.S.A. 90:577-581(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: POSSIBLE FUNCTION.
    6. "Intron-containing T4 bacteriophage gene sunY encodes an anaerobic ribonucleotide reductase."
      Young P., Oehman M., Xu M.Q., Shub D.A., Sjoeberg B.-M.
      J. Biol. Chem. 269:20229-20232(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION.
    7. "Bacteriophage T4 anaerobic ribonucleotide reductase contains a stable glycyl radical at position 580."
      Young P., Andersson J., Sahlin M., Sjoeberg B.-M.
      J. Biol. Chem. 271:20770-20775(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION.
    8. "A glycyl radical site in the crystal structure of a class III ribonucleotide reductase."
      Logan D.T., Andersson J., Sjoeberg B.-M., Nordlund P.
      Science 283:1499-1504(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.75 ANGSTROMS).
    9. "A metal-binding site in the catalytic subunit of anaerobic ribonucleotide reductase."
      Logan D.T., Mulliez E., Larsson K.-M., Bodevin S., Atta M., Garnaud P.E., Sjoeberg B.-M., Fontecave M.
      Proc. Natl. Acad. Sci. U.S.A. 100:3826-3831(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.45 ANGSTROMS).

    Entry informationi

    Entry nameiNRDD_BPT4
    AccessioniPrimary (citable) accession number: P07071
    Secondary accession number(s): P07073, Q38428, Q9T0V5
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 1, 1988
    Last sequence update: January 23, 2002
    Last modified: October 1, 2014
    This is version 104 of the entry and version 4 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programViral Protein Annotation Program

    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

    External Data

    Dasty 3