Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.

P07071

- NRDD_BPT4

UniProt

P07071 - NRDD_BPT4

(max 400 entries)x

Your basket is currently empty.

Select item(s) and click on "Add to basket" to create your own collection here
(400 entries max)

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

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

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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

        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
Checksum:iC5F29CE03126800B
GO

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.

Genome annotation databases

GeneIDi1258655.

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 .
PIRi E29284. Z6BPT9.
S01907. Z4BPT9.
RefSeqi NP_049690.1. NC_000866.4.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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: November 26, 2014
This is version 105 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