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P07071

- NRDD_BPT4

UniProt

P07071 - NRDD_BPT4

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Protein
Anaerobic ribonucleoside-triphosphate reductase
Gene
NRDD, 49.1, 55.11/55.13, SUNY
Organism
Enterobacteria phage T4 (Bacteriophage T4)
Status
Reviewed - Annotation score: 4 out of 5 - Experimental evidence at protein leveli

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
Complete GO annotation...

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 reductase
PRO_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

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.

Miscellaneous databases

EvolutionaryTraceiP07071.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini482 – 605124Glycine radical
Add
BLAST

Sequence similaritiesi

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

« Hide 'large scale' publications
  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: May 14, 2014
This is version 103 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

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