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Protein

Anaerobic ribonucleoside-triphosphate reductase

Gene

nrdD

Organism
Enterobacteria phage T4 (Bacteriophage T4)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the conversion of ribonucleotides into deoxyribonucleotides, which are required for DNA synthesis and repair.2 Publications

Catalytic activityi

Ribonucleoside 5'-triphosphate + formate = 2'-deoxyribonucleoside 5'-triphosphate + CO2 + H2O.1 Publication

Enzyme 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
Binding sitei114Substrate 21 Publication1
Binding sitei146Substrate 22 Publications1
Metal bindingi543Zinc1 Publication1 Publication1
Metal bindingi546Zinc1 Publication1 Publication1
Metal bindingi561Zinc1 Publication1 Publication1
Metal bindingi564Zinc1 Publication1 Publication1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionOxidoreductase
LigandMetal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Anaerobic ribonucleoside-triphosphate reductaseCurated (EC:1.1.98.61 Publication)
Alternative name(s):
Class III ribonucleoside-triphosphate reductaseCurated
Gene namesi
Name:nrdD1 Publication
Synonyms:49.1, 55.11/55.13, SUNY
OrganismiEnterobacteria phage T4 (Bacteriophage T4)
Taxonomic identifieri10665 [NCBI]
Taxonomic lineageiVirusesdsDNA viruses, no RNA stageCaudoviralesMyoviridaeTevenvirinaeT4virus
Virus hostiEscherichia coli [TaxID: 562]
Proteomesi
  • UP000009087 Componenti: Genome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi580G → A: Lacks both glycyl radical and activity. Does not affect interaction with NrdG. 1 Publication1

Chemistry databases

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

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001666861 – 605Anaerobic ribonucleoside-triphosphate reductaseAdd BLAST605

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei580Glycine radical1 Publication1

Keywords - PTMi

Organic radical

Interactioni

Subunit structurei

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

Structurei

Secondary structure

1605
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi30 – 47Combined sources18
Helixi52 – 59Combined sources8
Beta strandi62 – 65Combined sources4
Turni66 – 73Combined sources8
Helixi84 – 89Combined sources6
Beta strandi92 – 94Combined sources3
Beta strandi97 – 99Combined sources3
Helixi105 – 120Combined sources16
Beta strandi123 – 125Combined sources3
Beta strandi127 – 129Combined sources3
Helixi132 – 148Combined sources17
Turni149 – 155Combined sources7
Helixi159 – 184Combined sources26
Turni185 – 188Combined sources4
Beta strandi195 – 199Combined sources5
Helixi205 – 220Combined sources16
Turni223 – 226Combined sources4
Beta strandi232 – 238Combined sources7
Turni240 – 243Combined sources4
Helixi251 – 264Combined sources14
Beta strandi268 – 271Combined sources4
Helixi272 – 279Combined sources8
Turni289 – 291Combined sources3
Beta strandi310 – 318Combined sources9
Helixi319 – 324Combined sources6
Helixi334 – 358Combined sources25
Turni359 – 361Combined sources3
Helixi364 – 366Combined sources3
Helixi368 – 371Combined sources4
Beta strandi384 – 386Combined sources3
Helixi387 – 390Combined sources4
Turni391 – 394Combined sources4
Beta strandi395 – 402Combined sources8
Helixi404 – 411Combined sources8
Helixi416 – 434Combined sources19
Beta strandi437 – 441Combined sources5
Helixi448 – 460Combined sources13
Turni464 – 467Combined sources4
Beta strandi468 – 471Combined sources4
Beta strandi480 – 482Combined sources3
Helixi486 – 493Combined sources8
Helixi494 – 498Combined sources5
Beta strandi506 – 509Combined sources4
Helixi517 – 530Combined sources14
Beta strandi532 – 537Combined sources6
Beta strandi540 – 542Combined sources3
Turni544 – 546Combined sources3
Beta strandi553 – 555Combined sources3
Beta strandi558 – 560Combined sources3
Helixi562 – 564Combined sources3
Helixi569 – 571Combined sources3
Beta strandi573 – 576Combined sources4
Beta strandi578 – 581Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
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...

Miscellaneous databases

EvolutionaryTraceiP07071.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini482 – 605Glycine radicalPROSITE-ProRule annotationAdd BLAST124

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni64 – 66Substrate 1 binding2 Publications3
Regioni100 – 103Substrate 2 binding2 Publications4
Regioni444 – 448Substrate 1 binding2 Publications5

Sequence similaritiesi

Phylogenomic databases

KOiK00527.
OrthoDBiVOG0900003Y.

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.

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.
KEGGivg:1258655.

Similar proteinsi

Entry informationi

Entry nameiNRDD_BPT4
AccessioniPrimary (citable) accession number: P07071
Secondary accession number(s): P07073, Q38428, Q9T0V5
Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 1, 1988
Last sequence update: January 23, 2002
Last modified: August 30, 2017
This is version 121 of the entry and version 4 of the sequence. See 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