UniProtKB - P28903 (NRDD_ECOLI)
Protein
Anaerobic ribonucleoside-triphosphate reductase
Gene
nrdD
Organism
Escherichia coli (strain K12)
Status
Functioni
Catalyzes the conversion of ribonucleotides into deoxyribonucleotides, which are required for DNA synthesis and repair.5 Publications
Miscellaneous
The glycyl radical is involved in generation of a transient thiyl (sulfanyl) radical on a cysteine residue, which attacks the substrate, forming a ribonucleotide 3'-radical, followed by water loss to form a ketyl (alpha-oxoalkyl) radical. The ketyl radical gains an electron from a cysteine residue and a proton from formic acid, forming 3'-keto-deoxyribonucleotide and generating a thiosulfuranyl radical bridge between methionine and cysteine residues. Oxidation of formate by the thiosulfuranyl radical results in the release of CO2 and regeneration of the thiyl radical.1 Publication
Caution
Was originally thought to contain an iron sulfur cluster (PubMed:8381402). It was shown later that only NrdG contains an iron sulfur center (PubMed:8621608).1 Publication1 Publication
Catalytic activityi
- a ribonucleoside 5'-triphosphate + formate + H+ = a 2'-deoxyribonucleoside 5'-triphosphate + CO2 + H2O5 PublicationsEC:1.1.98.65 Publications
Activity regulationi
Activated under anaerobic conditions by NrdG, a tightly associated activase (PubMed:1460049, PubMed:7852304, PubMed:9305874). Activation involves the formation of a glycyl radical at Gly-681 (PubMed:7852304, PubMed:8636106, PubMed:9305874). Exposure of the activated reductase to oxygen leads to C-terminal truncation and inactivation of the protein, by cleavage at the N-terminal side of Gly-681 (PubMed:8421692, PubMed:7826394). The presence of zinc protects the protein from proteolysis and prevents the formation of disulfide bridges within it (PubMed:19381696).7 Publications
Kineticsi
- KM=0.35 mM for CTP1 Publication
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Metal bindingi | 644 | Zinc2 Publications | 1 | |
Metal bindingi | 647 | Zinc2 Publications | 1 | |
Metal bindingi | 662 | Zinc2 Publications | 1 | |
Metal bindingi | 665 | Zinc2 Publications | 1 |
GO - Molecular functioni
- ATP binding Source: EcoCyc
- CTP reductase activity Source: EcoCyc
- dATP binding Source: EcoCyc
- dGTP binding Source: EcoCyc
- pyrimidine deoxyribonucleotide binding Source: EcoCyc
- ribonucleoside-triphosphate reductase activity Source: EcoCyc
- zinc ion binding Source: EcoCyc
GO - Biological processi
- 2'-deoxyribonucleotide biosynthetic process Source: EcoCyc
- DNA replication Source: InterPro
- nucleobase-containing small molecule interconversion Source: EcoliWiki
Keywordsi
Molecular function | Oxidoreductase |
Ligand | ATP-binding, Metal-binding, Nucleotide-binding, Zinc |
Enzyme and pathway databases
BioCyci | EcoCyc:RIBONUCLEOSIDE-TRIP-REDUCT-MONOMER MetaCyc:RIBONUCLEOSIDE-TRIP-REDUCT-MONOMER |
SABIO-RKi | P28903 |
Names & Taxonomyi
Protein namesi | Recommended name: Anaerobic ribonucleoside-triphosphate reductaseCurated (EC:1.1.98.65 Publications)Alternative name(s): Class III ribonucleoside-triphosphate reductaseCurated |
Gene namesi | Name:nrdD1 Publication Ordered Locus Names:b4238, JW4197 |
Organismi | Escherichia coli (strain K12) |
Taxonomic identifieri | 83333 [NCBI] |
Taxonomic lineagei | Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia › |
Proteomesi |
|
Subcellular locationi
GO - Cellular componenti
- anaerobic ribonucleoside-triphosphate reductase complex Source: EcoCyc
Pathology & Biotechi
Mutagenesis
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 644 | C → A: Loss of activity. 1 Publication | 1 | |
Mutagenesisi | 647 | C → A: Almost loss of activity. 1 Publication | 1 | |
Mutagenesisi | 662 | C → A: Loss of activity. 1 Publication | 1 | |
Mutagenesisi | 665 | C → A: Loss of activity. 1 Publication | 1 | |
Mutagenesisi | 680 | C → S: Still retains some radical and some enzyme activity. 1 Publication | 1 | |
Mutagenesisi | 681 | G → A: Lacks both radical and enzyme activity. 1 Publication | 1 | |
Mutagenesisi | 682 | Y → F: Still retains some radical and some enzyme activity. 1 Publication | 1 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000166683 | 1 – 712 | Anaerobic ribonucleoside-triphosphate reductaseAdd BLAST | 712 |
Amino acid modifications
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Modified residuei | 681 | Glycine radicalPROSITE-ProRule annotation2 Publications | 1 |
Keywords - PTMi
Organic radicalProteomic databases
jPOSTi | P28903 |
PaxDbi | P28903 |
PRIDEi | P28903 |
Expressioni
Inductioni
Induced 2-fold by hydroxyurea.1 Publication
Interactioni
Subunit structurei
Binary interactionsi
P28903
With | #Exp. | IntAct |
---|---|---|
nrdG [P0A9N8] | 3 | EBI-370011,EBI-1135026 |
Protein-protein interaction databases
BioGRIDi | 4259318, 27 interactors 853044, 4 interactors |
ComplexPortali | CPX-3821, nrdDG class III anaerobic ribonucleotide reductase activation complex CPX-3822, nrdD class III anaerobic ribonucleotide reductase complex |
DIPi | DIP-10358N |
IntActi | P28903, 9 interactors |
STRINGi | 511145.b4238 |
Family & Domainsi
Domains and Repeats
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Domaini | 3 – 92 | ATP-conePROSITE-ProRule annotationAdd BLAST | 90 | |
Domaini | 583 – 708 | Glycine radicalPROSITE-ProRule annotationAdd BLAST | 126 |
Sequence similaritiesi
Belongs to the anaerobic ribonucleoside-triphosphate reductase family.Curated
Phylogenomic databases
eggNOGi | COG1328, Bacteria |
HOGENOMi | CLU_002707_2_0_6 |
InParanoidi | P28903 |
PhylomeDBi | P28903 |
Family and domain databases
CDDi | cd01675, RNR_III, 1 hit |
InterProi | View protein in InterPro IPR005144, ATP-cone_dom IPR019777, Form_AcTrfase_GR_CS IPR001150, Gly_radical IPR012833, NrdD |
Pfami | View protein in Pfam PF03477, ATP-cone, 1 hit PF13597, NRDD, 1 hit |
TIGRFAMsi | TIGR02487, NrdD, 1 hit |
PROSITEi | View protein in PROSITE PS51161, ATP_CONE, 1 hit PS00850, GLY_RADICAL_1, 1 hit PS51149, GLY_RADICAL_2, 1 hit |
i Sequence
Sequence statusi: Complete.
P28903-1 [UniParc]FASTAAdd to basket
10 20 30 40 50
MTPHVMKRDG CKVPFKSERI KEAILRAAKA AEVDDADYCA TVAAVVSEQM
60 70 80 90 100
QGRNQVDINE IQTAVENQLM SGPYKQLARA YIEYRHDRDI EREKRGRLNQ
110 120 130 140 150
EIRGLVEQTN ASLLNENANK DSKVIPTQRD LLAGIVAKHY ARQHLLPRDV
160 170 180 190 200
VQAHERGDIH YHDLDYSPFF PMFNCMLIDL KGMLTQGFKM GNAEIEPPKS
210 220 230 240 250
ISTATAVTAQ IIAQVASHIY GGTTINRIDE VLAPFVTASY NKHRKTAEEW
260 270 280 290 300
NIPDAEGYAN SRTIKECYDA FQSLEYEVNT LHTANGQTPF VTFGFGLGTS
310 320 330 340 350
WESRLIQESI LRNRIAGLGK NRKTAVFPKL VFAIRDGLNH KKGDPNYDIK
360 370 380 390 400
QLALECASKR MYPDILNYDQ VVKVTGSFKT PMGCRSFLGV WENENGEQIH
410 420 430 440 450
DGRNNLGVIS LNLPRIALEA KGDEATFWKL LDERLVLARK ALMTRIARLE
460 470 480 490 500
GVKARVAPIL YMEGACGVRL NADDDVSEIF KNGRASISLG YIGIHETINA
510 520 530 540 550
LFGGEHVYDN EQLRAKGIAI VERLRQAVDQ WKEETGYGFS LYSTPSENLC
560 570 580 590 600
DRFCRLDTAE FGVVPGVTDK GYYTNSFHLD VEKKVNPYDK IDFEAPYPPL
610 620 630 640 650
ANGGFICYGE YPNIQHNLKA LEDVWDYSYQ HVPYYGTNTP IDECYECGFT
660 670 680 690 700
GEFECTSKGF TCPKCGNHDA SRVSVTRRVC GYLGSPDARP FNAGKQEEVK
710
RRVKHLGNGQ IG
Experimental Info
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sequence conflicti | 257 | G → R in AAA24226 (PubMed:8421692).Curated | 1 | |
Sequence conflicti | 420 | A → P in AAA24226 (PubMed:8421692).Curated | 1 |
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | L06097 Genomic DNA Translation: AAA24226.1 U14003 Genomic DNA Translation: AAA97135.1 U00096 Genomic DNA Translation: AAC77195.1 AP009048 Genomic DNA Translation: BAE78237.1 U06195 Genomic DNA Translation: AAC43383.1 Z46865 Genomic DNA Translation: CAA86938.1 |
PIRi | A47331 |
RefSeqi | NP_418659.1, NC_000913.3 WP_000187778.1, NZ_LN832404.1 |
Genome annotation databases
EnsemblBacteriai | AAC77195; AAC77195; b4238 BAE78237; BAE78237; BAE78237 |
GeneIDi | 948755 |
KEGGi | ecj:JW4197 eco:b4238 |
PATRICi | fig|1411691.4.peg.2464 |
Similar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | L06097 Genomic DNA Translation: AAA24226.1 U14003 Genomic DNA Translation: AAA97135.1 U00096 Genomic DNA Translation: AAC77195.1 AP009048 Genomic DNA Translation: BAE78237.1 U06195 Genomic DNA Translation: AAC43383.1 Z46865 Genomic DNA Translation: CAA86938.1 |
PIRi | A47331 |
RefSeqi | NP_418659.1, NC_000913.3 WP_000187778.1, NZ_LN832404.1 |
3D structure databases
SMRi | P28903 |
ModBasei | Search... |
Protein-protein interaction databases
BioGRIDi | 4259318, 27 interactors 853044, 4 interactors |
ComplexPortali | CPX-3821, nrdDG class III anaerobic ribonucleotide reductase activation complex CPX-3822, nrdD class III anaerobic ribonucleotide reductase complex |
DIPi | DIP-10358N |
IntActi | P28903, 9 interactors |
STRINGi | 511145.b4238 |
Proteomic databases
jPOSTi | P28903 |
PaxDbi | P28903 |
PRIDEi | P28903 |
Genome annotation databases
EnsemblBacteriai | AAC77195; AAC77195; b4238 BAE78237; BAE78237; BAE78237 |
GeneIDi | 948755 |
KEGGi | ecj:JW4197 eco:b4238 |
PATRICi | fig|1411691.4.peg.2464 |
Organism-specific databases
EchoBASEi | EB1388 |
Phylogenomic databases
eggNOGi | COG1328, Bacteria |
HOGENOMi | CLU_002707_2_0_6 |
InParanoidi | P28903 |
PhylomeDBi | P28903 |
Enzyme and pathway databases
BioCyci | EcoCyc:RIBONUCLEOSIDE-TRIP-REDUCT-MONOMER MetaCyc:RIBONUCLEOSIDE-TRIP-REDUCT-MONOMER |
SABIO-RKi | P28903 |
Miscellaneous databases
PROi | PR:P28903 |
Family and domain databases
CDDi | cd01675, RNR_III, 1 hit |
InterProi | View protein in InterPro IPR005144, ATP-cone_dom IPR019777, Form_AcTrfase_GR_CS IPR001150, Gly_radical IPR012833, NrdD |
Pfami | View protein in Pfam PF03477, ATP-cone, 1 hit PF13597, NRDD, 1 hit |
TIGRFAMsi | TIGR02487, NrdD, 1 hit |
PROSITEi | View protein in PROSITE PS51161, ATP_CONE, 1 hit PS00850, GLY_RADICAL_1, 1 hit PS51149, GLY_RADICAL_2, 1 hit |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | NRDD_ECOLI | |
Accessioni | P28903Primary (citable) accession number: P28903 Secondary accession number(s): Q2M669 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | December 1, 1992 |
Last sequence update: | August 29, 2003 | |
Last modified: | December 2, 2020 | |
This is version 163 of the entry and version 2 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Prokaryotic Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
Direct protein sequencing, Reference proteomeDocuments
- SIMILARITY comments
Index of protein domains and families