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E7FHX6 (NDRZ_PYRFU) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 30. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Vitamin B12-dependent ribonucleoside-diphosphate reductase

Short name=B12-dependent RNR
EC=1.17.4.1
Alternative name(s):
Ribonucleotide reductase

Cleaved into the following 2 chains:

  1. Endonuclease PI-PfuI
    EC=3.1.-.-
    Alternative name(s):
    Pfu rnr-1 intein
  2. Pfu rnr-2 intein
    EC=3.1.-.-
Gene names
Name:rnr
Ordered Locus Names:PF0440
OrganismPyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) [Reference proteome] [HAMAP]
Taxonomic identifier186497 [NCBI]
Taxonomic lineageArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus

Protein attributes

Sequence length1740 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. Ref.1

Catalytic activity

2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H2O = ribonucleoside diphosphate + thioredoxin. Ref.1

Cofactor

5'-deoxyadenosylcobalamine (coenzyme B12). Ref.1

Pathway

Genetic information processing; DNA replication.

Post-translational modification

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

Sequence similarities

Belongs to the ribonucleoside diphosphate reductase class-2 family.

Contains 1 ATP-cone domain.

Contains 2 DOD-type homing endonuclease domains.

Biophysicochemical properties

Kinetic parameters:

KM=70 µM for CDP (at 80 degrees Celsius) Ref.1

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 301301Vitamin B12-dependent ribonucleoside-diphosphate reductase, 1st part Potential
PRO_0000428782
Chain302 – 755454Endonuclease PI-PfuI Potential
PRO_0000428783
Chain756 – 914159Vitamin B12-dependent ribonucleoside-diphosphate reductase, 2nd part Potential
PRO_0000428784
Chain915 – 1296382Pfu rnr-2 intein Potential
PRO_0000428785
Chain1297 – 1740444Vitamin B12-dependent ribonucleoside-diphosphate reductase, 3rd part Potential
PRO_0000428786

Regions

Domain4 – 9693ATP-cone By similarity
Domain443 – 582140DOD-type homing endonuclease 1
Domain1063 – 1194132DOD-type homing endonuclease 2
Region272 – 2732Substrate binding By similarity
Region913 – 9142Substrate binding By similarity
Region1297 – 12993Substrate binding By similarity
Region1471 – 14755Substrate binding By similarity

Sites

Active site9131Proton acceptor By similarity
Active site12971Cysteine radical intermediate By similarity
Active site12991Proton acceptor By similarity
Binding site2571Substrate By similarity
Binding site3011Substrate; via amide nitrogen By similarity

Amino acid modifications

Disulfide bond273 ↔ 1308Redox-active By similarity

Secondary structure

.................................................................................... 1740
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
E7FHX6 [UniParc].

Last modified March 8, 2011. Version 1.
Checksum: 49B27D2C17C3913B

FASTA1,740200,932
        10         20         30         40         50         60 
MAVEKVMKRD GRIVPFDESR IRWAVQRAMW EVGIRDEKKL DEVVKSIVQR INELYDGKIP 

        70         80         90        100        110        120 
HIENIQDIVE LELMRAGLFE VAKAYILYRK KKAEIREEKK RILNKKELDE IDKRFSINAL 

       130        140        150        160        170        180 
RVLASRYLKK DENGNIVESP RELFERVAIL AVIPDLLYDE RVFDKNGNYS QDLKRVEYYL 

       190        200        210        220        230        240 
EHFEEFDRKY SIGKYKLNKY HFERMVNLYK ELAEQGKMKV SIDEFLAMLE KGEFNEYEKE 

       250        260        270        280        290        300 
INEYFRLMTN QIFMPNTPAL INSGRPLGML SACFVVPIED DMESIMKAAH DVAMIQKMGG 

       310        320        330        340        350        360 
GCIDGKAKII FENEGEEHLT TMEEMYERYK HLGEFYDEEY NRWGIDVSNV PIYVKSFDPE 

       370        380        390        400        410        420 
SKRVVKGKVN VIWKYELGKD VTKYEIITNK GTKILTSPWH PFFVLTPDFK IVEKRADELK 

       430        440        450        460        470        480 
EGDILIGGMP DGEDYKFIFD YWLAGFIAGD GCFDKYHSHV KGHEYIYDRL RIYDYRIETF 

       490        500        510        520        530        540 
EIINDYLEKT FGRKYSIQKD RNIYYIDIKA RNITSHYLKL LEGIDNGIPP QILKEGKNAV 

       550        560        570        580        590        600 
LSFIAGLFDA EGHVSNKPGI ELGMVNKRLI EDVTHYLNAL GIKARIREKL RKDGIDYVLH 

       610        620        630        640        650        660 
VEEYSSLLRF YELIGKNLQN EEKREKLEKV LSNHKGGNFG LPLNFNAFKE WASEYGVEFK 

       670        680        690        700        710        720 
TNGSQTIAII NDERISLGQW HTRNRVSKAV LVKMLRKLYE ATKDEEVKRM LHLIEGLEVV 

       730        740        750        760        770        780 
RHITTTNEPR TFYDLTVENY QNYLAGENGM IFVHNTGLNF SKLRPEGDIV GTTTGAASGP 

       790        800        810        820        830        840 
VSFMHLIDAV SDVIKQGGVR RGANMGILEI WHPDIEKFIH AKEKNIGTNV LSNFNISVGI 

       850        860        870        880        890        900 
WEDFWEALKE GKKYPLINPR TGEVVKEVDP KTLFEELAYM AWAKADPGVI FFDVINRRNV 

       910        920        930        940        950        960 
LKKAKGGPIR ATNPCVVGDT RILTPEGYLK AEEIFSLAKE RGKKEAVAVE GIAEEGEPYA 

       970        980        990       1000       1010       1020 
YSVEILLPGE EKVEYETVHG KVLAVADPVA VPAYVWKVGR KKVARVKTKE GYEITATLDH 

      1030       1040       1050       1060       1070       1080 
KLMTPEGWKE VGKLKEGDKI LLPRFEVEEE FGSESIGEDL AFVLGWFIGD GYLNVNDKRA 

      1090       1100       1110       1120       1130       1140 
WFYFNAEKEE EIAVRIRDIL VKHFGIKAEL HRYGNQIKLG VRGEAYRWLE NIVKNNEKRI 

      1150       1160       1170       1180       1190       1200 
PEIVYRLKPR EIAAFLRGLF SADGYVDKDM AIRLTSKSRE LLREVQDLLL LFGILSKIYE 

      1210       1220       1230       1240       1250       1260 
KPYESEFHYT TKNGEERIYR SKGYYELVIT NYSRKLFAEK IGLEGYKMEK LSLKKTKVDQ 

      1270       1280       1290       1300       1310       1320 
PIVTVESVEV LGEEIVYDFT VPNYHMYISN GFMSHNCGEE PLYEYESCNL ASINLAKFVK 

      1330       1340       1350       1360       1370       1380 
YDENGKPYFD WDEYAYVIQK VAKYLDNSID VNKFPLPEID YNTKLTRRIG VGMMGLADAL 

      1390       1400       1410       1420       1430       1440 
FKLGIPYNSE EGFKFMRKVT EYLTFYAYKY SVEAAKKRGT FPLYDKTEYP EGKLPVEGFY 

      1450       1460       1470       1480       1490       1500 
HPEIWNLPWD KLVEEIKKYG LRNAMVTTCP PTGSVSMIAD TSSGIEPVYA LVYKKSVTVG 

      1510       1520       1530       1540       1550       1560 
EFYYVDPVFE EELKKRGLYS EELLKKISDN YGSVQGLEEI PEDMQRVFVT ALDIHWLDHI 

      1570       1580       1590       1600       1610       1620 
IAQASIQMWL TDSASKTINM INEATVEDVK AAYLIARFLG CKGVTVYRDG SLSVQVYSVE 

      1630       1640       1650       1660       1670       1680 
GEKKKRRFKP KPSEYAKKIL LEIVEKEPWI KNFINVDEIL NGKKEQLLFS LRPANESKLK 

      1690       1700       1710       1720       1730       1740 
VPGREEEVRP GNIPEEKIRE LLGVVYCPVC YEKEGKLVEL KMESGCATCP VCGWSKCVIS 

« Hide

References

« Hide 'large scale' references
[1]"Ribonucleotide reductase in the archaeon Pyrococcus furiosus: a critical enzyme in the evolution of DNA genomes?"
Riera J., Robb F.T., Weiss R., Fontecave M.
Proc. Natl. Acad. Sci. U.S.A. 94:475-478(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-15, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES.
Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1.
[2]"Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P. horikoshii inferred from complete genomic sequences."
Maeder D.L., Weiss R.B., Dunn D.M., Cherry J.L., Gonzalez J.M., DiRuggiero J., Robb F.T.
Genetics 152:1299-1305(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1.
[3]"Crystal structure of an archaeal intein-encoded homing endonuclease PI-PfuI."
Ichiyanagi K., Ishino Y., Ariyoshi M., Komori K., Morikawa K.
J. Mol. Biol. 300:889-901(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) OF 302-755.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U78098 Genomic DNA. Translation: AAB36947.1.
AE009950 Genomic DNA. Translation: AAL80564.1.
PIRT43215.
RefSeqNP_578169.1. NC_003413.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1DQ3X-ray2.10A302-755[»]
ProteinModelPortalE7FHX6.
SMRE7FHX6. Positions 302-755.
ModBaseSearch...
MobiDBSearch...

Proteomic databases

PRIDEE7FHX6.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAL80564; AAL80564; PF0440.
GeneID1468281.
KEGGpfu:PF0440.

Phylogenomic databases

HOGENOMHOG000229277.
KOK00525.
OMAISNGFMS.

Enzyme and pathway databases

BioCycMetaCyc:MONOMER-15780.
UniPathwayUPA00326.

Family and domain databases

Gene3D2.170.16.10. 5 hits.
3.10.28.10. 3 hits.
3.30.160.90. 1 hit.
InterProIPR005144. ATP-cone.
IPR028992. Hedgehog/Intein_dom.
IPR003586. Hint_dom_C.
IPR003587. Hint_dom_N.
IPR027434. Homing_endonucl.
IPR006142. INTEIN.
IPR004042. Intein_endonuc.
IPR006141. Intein_splice_site.
IPR015147. PI-PfuI_intein_endonucl_subdom.
IPR000788. RNR_lg_C.
IPR013509. RNR_lsu_N.
IPR013344. RNR_NrdJ/NrdZ.
IPR008926. RNR_R1-su_N.
IPR015146. RNR_stirrup.
[Graphical view]
PfamPF03477. ATP-cone. 1 hit.
PF09062. Endonuc_subdom. 1 hit.
PF14528. LAGLIDADG_3. 2 hits.
PF02867. Ribonuc_red_lgC. 3 hits.
PF00317. Ribonuc_red_lgN. 1 hit.
PF09061. Stirrup. 1 hit.
[Graphical view]
PRINTSPR00379. INTEIN.
SMARTSM00305. HintC. 2 hits.
SM00306. HintN. 2 hits.
[Graphical view]
SUPFAMSSF48168. SSF48168. 1 hit.
SSF51294. SSF51294. 4 hits.
SSF54786. SSF54786. 1 hit.
SSF55608. SSF55608. 4 hits.
TIGRFAMsTIGR01443. intein_Cterm. 2 hits.
TIGR01445. intein_Nterm. 2 hits.
TIGR02504. NrdJ_Z. 1 hit.
PROSITEPS51161. ATP_CONE. 1 hit.
PS50818. INTEIN_C_TER. 2 hits.
PS50819. INTEIN_ENDONUCLEASE. 2 hits.
PS50817. INTEIN_N_TER. 2 hits.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceE7FHX6.

Entry information

Entry nameNDRZ_PYRFU
AccessionPrimary (citable) accession number: E7FHX6
Secondary accession number(s): P95484, Q7LX09
Entry history
Integrated into UniProtKB/Swiss-Prot: April 16, 2014
Last sequence update: March 8, 2011
Last modified: June 11, 2014
This is version 30 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

Intein-containing proteins

List of intein-containing protein entries