SubmitCancel

Skip Header

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

E7FHX6

- NDRZ_PYRFU

UniProt

E7FHX6 - NDRZ_PYRFU

(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
Vitamin B12-dependent ribonucleoside-diphosphate reductase
Gene
rnr, PF0440
Organism
Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
Status
Reviewed - Annotation score: 4 out of 5 - Experimental evidence at protein leveli

Functioni

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

Catalytic activityi

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

Cofactori

5'-deoxyadenosylcobalamine (coenzyme B12).1 Publication

Kineticsi

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

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei257 – 2571Substrate By similarity
Binding sitei301 – 3011Substrate; via amide nitrogen By similarity
Active sitei913 – 9131Proton acceptor By similarity
Active sitei1297 – 12971Cysteine radical intermediate By similarity
Active sitei1299 – 12991Proton acceptor By similarity

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. cobalamin binding Source: UniProtKB-KW
  3. endonuclease activity Source: InterPro
  4. ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor Source: UniProtKB-EC

GO - Biological processi

  1. DNA replication Source: UniProtKB-UniPathway
  2. intein-mediated protein splicing Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

DNA replication

Keywords - Ligandi

ATP-binding, Cobalamin, Cobalt, Nucleotide-binding

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-15780.
UniPathwayiUPA00326.

Names & Taxonomyi

Protein namesi
Recommended name:
Vitamin B12-dependent ribonucleoside-diphosphate reductase (EC:1.17.4.1)
Short name:
B12-dependent RNR
Alternative name(s):
Ribonucleotide reductase
Cleaved into the following 2 chains:
Alternative name(s):
Pfu rnr-1 intein
Gene namesi
Name:rnr
Ordered Locus Names:PF0440
OrganismiPyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
Taxonomic identifieri186497 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
ProteomesiUP000001013: Chromosome

Subcellular locationi

GO - Cellular componenti

  1. ribonucleoside-diphosphate reductase complex Source: InterPro
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 301301Vitamin B12-dependent ribonucleoside-diphosphate reductase, 1st part Reviewed prediction
PRO_0000428782Add
BLAST
Chaini302 – 755454Endonuclease PI-PfuI Reviewed prediction
PRO_0000428783Add
BLAST
Chaini756 – 914159Vitamin B12-dependent ribonucleoside-diphosphate reductase, 2nd part Reviewed prediction
PRO_0000428784Add
BLAST
Chaini915 – 1296382Pfu rnr-2 intein Reviewed prediction
PRO_0000428785Add
BLAST
Chaini1297 – 1740444Vitamin B12-dependent ribonucleoside-diphosphate reductase, 3rd part Reviewed prediction
PRO_0000428786Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi273 ↔ 1308Redox-active By similarity

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 Reviewed prediction.

Keywords - PTMi

Autocatalytic cleavage, Disulfide bond, Protein splicing

Proteomic databases

PRIDEiE7FHX6.

Interactioni

Protein-protein interaction databases

IntActiE7FHX6. 1 interaction.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi308 – 3158
Beta strandi317 – 3215
Helixi322 – 3298
Helixi330 – 3323
Beta strandi335 – 3373
Turni338 – 3414
Beta strandi342 – 3465
Beta strandi353 – 3586
Turni359 – 3624
Beta strandi363 – 37715
Beta strandi383 – 3886
Beta strandi393 – 3964
Beta strandi401 – 4055
Beta strandi411 – 4155
Turni416 – 4183
Helixi439 – 45012
Beta strandi451 – 4577
Beta strandi466 – 47510
Helixi477 – 49115
Beta strandi498 – 5025
Beta strandi504 – 5085
Helixi511 – 52111
Helixi524 – 5263
Helixi530 – 5334
Helixi537 – 55115
Beta strandi553 – 5553
Turni556 – 5583
Beta strandi559 – 5657
Helixi567 – 57812
Turni579 – 5813
Beta strandi585 – 5906
Beta strandi592 – 60110
Helixi604 – 61310
Helixi615 – 6173
Helixi621 – 63212
Helixi645 – 6539
Turni654 – 6563
Beta strandi658 – 6625
Beta strandi665 – 6706
Beta strandi673 – 6764
Helixi680 – 6834
Helixi688 – 70215
Helixi705 – 71612
Beta strandi718 – 7269
Beta strandi730 – 7378
Turni738 – 7403
Beta strandi742 – 7498
Beta strandi751 – 7544

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1DQ3X-ray2.10A302-755[»]
ProteinModelPortaliE7FHX6.
SMRiE7FHX6. Positions 302-755.

Miscellaneous databases

EvolutionaryTraceiE7FHX6.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini4 – 9693ATP-cone By similarity
Add
BLAST
Domaini443 – 582140DOD-type homing endonuclease 1
Add
BLAST
Domaini1063 – 1194132DOD-type homing endonuclease 2
Add
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni272 – 2732Substrate binding By similarity
Regioni913 – 9142Substrate binding By similarity
Regioni1297 – 12993Substrate binding By similarity
Regioni1471 – 14755Substrate binding By similarity

Sequence similaritiesi

Contains 1 ATP-cone domain.

Keywords - Domaini

Repeat

Phylogenomic databases

HOGENOMiHOG000229277.
KOiK00525.
OMAiISNGFMS.

Family and domain databases

Gene3Di2.170.16.10. 5 hits.
3.10.28.10. 3 hits.
3.30.160.90. 1 hit.
InterProiIPR005144. 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]
PfamiPF03477. 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]
PRINTSiPR00379. INTEIN.
SMARTiSM00305. HintC. 2 hits.
SM00306. HintN. 2 hits.
[Graphical view]
SUPFAMiSSF48168. SSF48168. 1 hit.
SSF51294. SSF51294. 4 hits.
SSF54786. SSF54786. 1 hit.
SSF55608. SSF55608. 4 hits.
TIGRFAMsiTIGR01443. intein_Cterm. 2 hits.
TIGR01445. intein_Nterm. 2 hits.
TIGR02504. NrdJ_Z. 1 hit.
PROSITEiPS51161. ATP_CONE. 1 hit.
PS50818. INTEIN_C_TER. 2 hits.
PS50819. INTEIN_ENDONUCLEASE. 2 hits.
PS50817. INTEIN_N_TER. 2 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

E7FHX6-1 [UniParc]FASTAAdd to Basket

« Hide

MAVEKVMKRD GRIVPFDESR IRWAVQRAMW EVGIRDEKKL DEVVKSIVQR     50
INELYDGKIP HIENIQDIVE LELMRAGLFE VAKAYILYRK KKAEIREEKK 100
RILNKKELDE IDKRFSINAL RVLASRYLKK DENGNIVESP RELFERVAIL 150
AVIPDLLYDE RVFDKNGNYS QDLKRVEYYL EHFEEFDRKY SIGKYKLNKY 200
HFERMVNLYK ELAEQGKMKV SIDEFLAMLE KGEFNEYEKE INEYFRLMTN 250
QIFMPNTPAL INSGRPLGML SACFVVPIED DMESIMKAAH DVAMIQKMGG 300
GCIDGKAKII FENEGEEHLT TMEEMYERYK HLGEFYDEEY NRWGIDVSNV 350
PIYVKSFDPE SKRVVKGKVN VIWKYELGKD VTKYEIITNK GTKILTSPWH 400
PFFVLTPDFK IVEKRADELK EGDILIGGMP DGEDYKFIFD YWLAGFIAGD 450
GCFDKYHSHV KGHEYIYDRL RIYDYRIETF EIINDYLEKT FGRKYSIQKD 500
RNIYYIDIKA RNITSHYLKL LEGIDNGIPP QILKEGKNAV LSFIAGLFDA 550
EGHVSNKPGI ELGMVNKRLI EDVTHYLNAL GIKARIREKL RKDGIDYVLH 600
VEEYSSLLRF YELIGKNLQN EEKREKLEKV LSNHKGGNFG LPLNFNAFKE 650
WASEYGVEFK TNGSQTIAII NDERISLGQW HTRNRVSKAV LVKMLRKLYE 700
ATKDEEVKRM LHLIEGLEVV RHITTTNEPR TFYDLTVENY QNYLAGENGM 750
IFVHNTGLNF SKLRPEGDIV GTTTGAASGP VSFMHLIDAV SDVIKQGGVR 800
RGANMGILEI WHPDIEKFIH AKEKNIGTNV LSNFNISVGI WEDFWEALKE 850
GKKYPLINPR TGEVVKEVDP KTLFEELAYM AWAKADPGVI FFDVINRRNV 900
LKKAKGGPIR ATNPCVVGDT RILTPEGYLK AEEIFSLAKE RGKKEAVAVE 950
GIAEEGEPYA YSVEILLPGE EKVEYETVHG KVLAVADPVA VPAYVWKVGR 1000
KKVARVKTKE GYEITATLDH KLMTPEGWKE VGKLKEGDKI LLPRFEVEEE 1050
FGSESIGEDL AFVLGWFIGD GYLNVNDKRA WFYFNAEKEE EIAVRIRDIL 1100
VKHFGIKAEL HRYGNQIKLG VRGEAYRWLE NIVKNNEKRI PEIVYRLKPR 1150
EIAAFLRGLF SADGYVDKDM AIRLTSKSRE LLREVQDLLL LFGILSKIYE 1200
KPYESEFHYT TKNGEERIYR SKGYYELVIT NYSRKLFAEK IGLEGYKMEK 1250
LSLKKTKVDQ PIVTVESVEV LGEEIVYDFT VPNYHMYISN GFMSHNCGEE 1300
PLYEYESCNL ASINLAKFVK YDENGKPYFD WDEYAYVIQK VAKYLDNSID 1350
VNKFPLPEID YNTKLTRRIG VGMMGLADAL FKLGIPYNSE EGFKFMRKVT 1400
EYLTFYAYKY SVEAAKKRGT FPLYDKTEYP EGKLPVEGFY HPEIWNLPWD 1450
KLVEEIKKYG LRNAMVTTCP PTGSVSMIAD TSSGIEPVYA LVYKKSVTVG 1500
EFYYVDPVFE EELKKRGLYS EELLKKISDN YGSVQGLEEI PEDMQRVFVT 1550
ALDIHWLDHI IAQASIQMWL TDSASKTINM INEATVEDVK AAYLIARFLG 1600
CKGVTVYRDG SLSVQVYSVE GEKKKRRFKP KPSEYAKKIL LEIVEKEPWI 1650
KNFINVDEIL NGKKEQLLFS LRPANESKLK VPGREEEVRP GNIPEEKIRE 1700
LLGVVYCPVC YEKEGKLVEL KMESGCATCP VCGWSKCVIS 1740
Length:1,740
Mass (Da):200,932
Last modified:March 8, 2011 - v1
Checksum:i49B27D2C17C3913B
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U78098 Genomic DNA. Translation: AAB36947.1.
AE009950 Genomic DNA. Translation: AAL80564.1.
PIRiT43215.
RefSeqiNP_578169.1. NC_003413.1.

Genome annotation databases

EnsemblBacteriaiAAL80564; AAL80564; PF0440.
GeneIDi1468281.
KEGGipfu:PF0440.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U78098 Genomic DNA. Translation: AAB36947.1 .
AE009950 Genomic DNA. Translation: AAL80564.1 .
PIRi T43215.
RefSeqi NP_578169.1. NC_003413.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1DQ3 X-ray 2.10 A 302-755 [» ]
ProteinModelPortali E7FHX6.
SMRi E7FHX6. Positions 302-755.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

IntActi E7FHX6. 1 interaction.

Proteomic databases

PRIDEi E7FHX6.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAL80564 ; AAL80564 ; PF0440 .
GeneIDi 1468281.
KEGGi pfu:PF0440.

Phylogenomic databases

HOGENOMi HOG000229277.
KOi K00525.
OMAi ISNGFMS.

Enzyme and pathway databases

UniPathwayi UPA00326 .
BioCyci MetaCyc:MONOMER-15780.

Miscellaneous databases

EvolutionaryTracei E7FHX6.

Family and domain databases

Gene3Di 2.170.16.10. 5 hits.
3.10.28.10. 3 hits.
3.30.160.90. 1 hit.
InterProi IPR005144. 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 ]
Pfami PF03477. 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 ]
PRINTSi PR00379. INTEIN.
SMARTi SM00305. HintC. 2 hits.
SM00306. HintN. 2 hits.
[Graphical view ]
SUPFAMi SSF48168. SSF48168. 1 hit.
SSF51294. SSF51294. 4 hits.
SSF54786. SSF54786. 1 hit.
SSF55608. SSF55608. 4 hits.
TIGRFAMsi TIGR01443. intein_Cterm. 2 hits.
TIGR01445. intein_Nterm. 2 hits.
TIGR02504. NrdJ_Z. 1 hit.
PROSITEi PS51161. ATP_CONE. 1 hit.
PS50818. INTEIN_C_TER. 2 hits.
PS50819. INTEIN_ENDONUCLEASE. 2 hits.
PS50817. INTEIN_N_TER. 2 hits.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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.

Entry informationi

Entry nameiNDRZ_PYRFU
AccessioniPrimary (citable) accession number: E7FHX6
Secondary accession number(s): P95484, Q7LX09
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 16, 2014
Last sequence update: March 8, 2011
Last modified: September 3, 2014
This is version 31 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

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Intein-containing proteins
    List of intein-containing protein entries
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi