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Protein

Ribonucleoside-diphosphate reductase subunit beta

Gene

nrdB

Organism
Aquifex aeolicus (strain VF5)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Protein inferred from homologyi

Functioni

Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity).By similarity

Catalytic activityi

2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H2O = ribonucleoside diphosphate + thioredoxin.PROSITE-ProRule annotation

Cofactori

Fe cationBy similarityNote: Binds 2 iron ions per subunit.By similarity

Pathwayi: DNA replication

This protein is involved in the pathway DNA replication, which is part of Genetic information processing.
View all proteins of this organism that are known to be involved in the pathway DNA replication and in Genetic information processing.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi97Iron 1PROSITE-ProRule annotation1
Metal bindingi127Iron 1PROSITE-ProRule annotation1
Metal bindingi127Iron 2By similarity1
Metal bindingi130Iron 1PROSITE-ProRule annotation1
Active sitei134PROSITE-ProRule annotation1
Metal bindingi194Iron 2By similarity1
Metal bindingi228Iron 2By similarity1
Metal bindingi577Iron 2By similarity1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease, Oxidoreductase

Keywords - Biological processi

DNA replication, Intron homing

Keywords - Ligandi

Iron, Metal-binding

Enzyme and pathway databases

UniPathwayiUPA00326.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribonucleoside-diphosphate reductase subunit beta (EC:1.17.4.1)
Alternative name(s):
Ribonucleotide reductase small subunit
Cleaved into the following chain:
Alternative name(s):
Aae RIR2 intein
Gene namesi
Name:nrdB
Ordered Locus Names:aq_1505
OrganismiAquifex aeolicus (strain VF5)
Taxonomic identifieri224324 [NCBI]
Taxonomic lineageiBacteriaAquificaeAquificalesAquificaceaeAquifex
Proteomesi
  • UP000000798 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000305981 – 229Ribonucleoside-diphosphate reductase subunit beta, 1st partSequence analysisAdd BLAST229
ChainiPRO_0000030599230 – 575Aae NrdB inteinSequence analysisAdd BLAST346
ChainiPRO_0000030600576 – 696Ribonucleoside-diphosphate reductase subunit beta, 2nd partSequence analysisAdd BLAST121

Post-translational modificationi

This protein undergoes a protein self splicing that involves a post-translational excision of the intervening region (intein) followed by peptide ligation.Curated

Keywords - PTMi

Autocatalytic cleavage, Protein splicing

Interactioni

Subunit structurei

Tetramer of two alpha and two beta subunits.By similarity

Protein-protein interaction databases

STRINGi224324.aq_1505.

Structurei

3D structure databases

ProteinModelPortaliO67475.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini377 – 507DOD-type homing endonucleasePROSITE-ProRule annotationAdd BLAST131

Sequence similaritiesi

Contains 1 DOD-type homing endonuclease domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiENOG4105E05. Bacteria.
COG0208. LUCA.
COG1372. LUCA.
InParanoidiO67475.
KOiK00526.
OrthoDBiPOG091H05VC.

Family and domain databases

CDDicd01049. RNRR2. 1 hit.
Gene3Di1.10.620.20. 4 hits.
2.170.16.10. 1 hit.
3.10.28.10. 1 hit.
InterProiIPR009078. Ferritin-like_SF.
IPR028992. Hedgehog/Intein_dom.
IPR003587. Hint_dom_N.
IPR027434. Homing_endonucl.
IPR030934. Intein_C.
IPR004042. Intein_endonuc.
IPR006141. Intein_N.
IPR012348. RNR-rel.
IPR033909. RNR_small.
IPR030475. RNR_small_AS.
IPR000358. RNR_small_fam.
[Graphical view]
PANTHERiPTHR23409. PTHR23409. 2 hits.
PfamiPF00268. Ribonuc_red_sm. 2 hits.
[Graphical view]
SMARTiSM00306. HintN. 1 hit.
[Graphical view]
SUPFAMiSSF47240. SSF47240. 2 hits.
SSF51294. SSF51294. 2 hits.
TIGRFAMsiTIGR01443. intein_Cterm. 1 hit.
TIGR01445. intein_Nterm. 1 hit.
PROSITEiPS50818. INTEIN_C_TER. 1 hit.
PS50819. INTEIN_ENDONUCLEASE. 1 hit.
PS50817. INTEIN_N_TER. 1 hit.
PS00368. RIBORED_SMALL. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

O67475-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEKTEKNELV RKLIFNPQGD REASKRKIIK GNPTNIFELN EIKYSWAFDL
60 70 80 90 100
YKLMGFTNFW IPEEIQMLED RKQYETVLSD YEKRAYELVL SFLIALDSFQ
110 120 130 140 150
VDMLKEFGRM ITAPEVEMAI TAQEFQESVH AYSYQFILES VVDPVKADEI
160 170 180 190 200
YNYWREDERL LERNKVIAEL YNEFIRKPNE ENFIKATIGN YILESLYFYS
210 220 230 240 250
GFAFFYTLGR QGKMRNTVQQ IKYINRDELC FIEGTEVLTK RGFVDFRELR
260 270 280 290 300
EDDLVAQYDI ETGEISWTKP YAYVERDYEG SMYRLKHPKS NWEVVATEGH
310 320 330 340 350
EFIVRNLKTG KERKEPIEKV KLHPYSAIPV AGRYTGEVEE YDLWELVSGK
360 370 380 390 400
GITLKTRSAV KNKLTPIEKL LIVLQADGTI DSKRNGKFTG FQQLKFFFSK
410 420 430 440 450
YRKINEFEKI LNECAPYGIK WKKYERQDGI AYTVYYPNDL PIKPTKFFDE
460 470 480 490 500
WVRLDEITEE WIREFVEELV KWDGHIPKDR NKKKVYYYST KEKRNKDFVQ
510 520 530 540 550
ALCALGGMRT VVSRERNPKA KNPVYRIWIY LEDDYINTQT MVKEEFYYKG
560 570 580 590 600
KVYCVSVPKG NIVVRYKDSV CIAGNCHVTL FRNIINTLRK ENPELFTPEI
610 620 630 640 650
EKWIVEYFKY AVNEEIKWGQ YVTQNQILGI NDVLIERYIK YLGNLRITQI
660 670 680 690
GFDPIYPEVT ENPLKWIDEF RKINNTKTDF FQAKPQTYSK ANELKW
Length:696
Mass (Da):82,931
Last modified:August 1, 1998 - v1
Checksum:iE5929D55C455A5EB
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000657 Genomic DNA. Translation: AAC07431.1.
PIRiA70431.
RefSeqiNP_214040.1. NC_000918.1.
WP_010880978.1. NC_000918.1.

Genome annotation databases

EnsemblBacteriaiAAC07431; AAC07431; aq_1505.
GeneIDi1193098.
KEGGiaae:aq_1505.
PATRICi20960124. VBIAquAeo85532_1175.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000657 Genomic DNA. Translation: AAC07431.1.
PIRiA70431.
RefSeqiNP_214040.1. NC_000918.1.
WP_010880978.1. NC_000918.1.

3D structure databases

ProteinModelPortaliO67475.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224324.aq_1505.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC07431; AAC07431; aq_1505.
GeneIDi1193098.
KEGGiaae:aq_1505.
PATRICi20960124. VBIAquAeo85532_1175.

Phylogenomic databases

eggNOGiENOG4105E05. Bacteria.
COG0208. LUCA.
COG1372. LUCA.
InParanoidiO67475.
KOiK00526.
OrthoDBiPOG091H05VC.

Enzyme and pathway databases

UniPathwayiUPA00326.

Family and domain databases

CDDicd01049. RNRR2. 1 hit.
Gene3Di1.10.620.20. 4 hits.
2.170.16.10. 1 hit.
3.10.28.10. 1 hit.
InterProiIPR009078. Ferritin-like_SF.
IPR028992. Hedgehog/Intein_dom.
IPR003587. Hint_dom_N.
IPR027434. Homing_endonucl.
IPR030934. Intein_C.
IPR004042. Intein_endonuc.
IPR006141. Intein_N.
IPR012348. RNR-rel.
IPR033909. RNR_small.
IPR030475. RNR_small_AS.
IPR000358. RNR_small_fam.
[Graphical view]
PANTHERiPTHR23409. PTHR23409. 2 hits.
PfamiPF00268. Ribonuc_red_sm. 2 hits.
[Graphical view]
SMARTiSM00306. HintN. 1 hit.
[Graphical view]
SUPFAMiSSF47240. SSF47240. 2 hits.
SSF51294. SSF51294. 2 hits.
TIGRFAMsiTIGR01443. intein_Cterm. 1 hit.
TIGR01445. intein_Nterm. 1 hit.
PROSITEiPS50818. INTEIN_C_TER. 1 hit.
PS50819. INTEIN_ENDONUCLEASE. 1 hit.
PS50817. INTEIN_N_TER. 1 hit.
PS00368. RIBORED_SMALL. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRIR2_AQUAE
AccessioniPrimary (citable) accession number: O67475
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 26, 2001
Last sequence update: August 1, 1998
Last modified: November 30, 2016
This is version 120 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Intein-containing proteins
    List of intein-containing protein entries
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.