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E7FHX6

- NDRZ_PYRFU

UniProt

E7FHX6 - NDRZ_PYRFU

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Protein

Vitamin B12-dependent ribonucleoside-diphosphate reductase

Gene

rnr

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 – 2571SubstrateBy similarity
Binding sitei301 – 3011Substrate; via amide nitrogenBy similarity
Active sitei913 – 9131Proton acceptorBy similarity
Active sitei1297 – 12971Cysteine radical intermediateBy similarity
Active sitei1299 – 12991Proton acceptorBy 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

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 301301Vitamin B12-dependent ribonucleoside-diphosphate reductase, 1st partSequence AnalysisPRO_0000428782Add
BLAST
Chaini302 – 755454Endonuclease PI-PfuISequence AnalysisPRO_0000428783Add
BLAST
Chaini756 – 914159Vitamin B12-dependent ribonucleoside-diphosphate reductase, 2nd partSequence AnalysisPRO_0000428784Add
BLAST
Chaini915 – 1296382Pfu rnr-2 inteinSequence AnalysisPRO_0000428785Add
BLAST
Chaini1297 – 1740444Vitamin B12-dependent ribonucleoside-diphosphate reductase, 3rd partSequence AnalysisPRO_0000428786Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi273 ↔ 1308Redox-activeBy 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.Curated

Keywords - PTMi

Autocatalytic cleavage, Disulfide bond, Protein splicing

Proteomic databases

PRIDEiE7FHX6.

Interactioni

Protein-protein interaction databases

IntActiE7FHX6. 1 interaction.

Structurei

Secondary structure

1
1740
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi308 – 3158Combined sources
Beta strandi317 – 3215Combined sources
Helixi322 – 3298Combined sources
Helixi330 – 3323Combined sources
Beta strandi335 – 3373Combined sources
Turni338 – 3414Combined sources
Beta strandi342 – 3465Combined sources
Beta strandi353 – 3586Combined sources
Turni359 – 3624Combined sources
Beta strandi363 – 37715Combined sources
Beta strandi383 – 3886Combined sources
Beta strandi393 – 3964Combined sources
Beta strandi401 – 4055Combined sources
Beta strandi411 – 4155Combined sources
Turni416 – 4183Combined sources
Helixi439 – 45012Combined sources
Beta strandi451 – 4577Combined sources
Beta strandi466 – 47510Combined sources
Helixi477 – 49115Combined sources
Beta strandi498 – 5025Combined sources
Beta strandi504 – 5085Combined sources
Helixi511 – 52111Combined sources
Helixi524 – 5263Combined sources
Helixi530 – 5334Combined sources
Helixi537 – 55115Combined sources
Beta strandi553 – 5553Combined sources
Turni556 – 5583Combined sources
Beta strandi559 – 5657Combined sources
Helixi567 – 57812Combined sources
Turni579 – 5813Combined sources
Beta strandi585 – 5906Combined sources
Beta strandi592 – 60110Combined sources
Helixi604 – 61310Combined sources
Helixi615 – 6173Combined sources
Helixi621 – 63212Combined sources
Helixi645 – 6539Combined sources
Turni654 – 6563Combined sources
Beta strandi658 – 6625Combined sources
Beta strandi665 – 6706Combined sources
Beta strandi673 – 6764Combined sources
Helixi680 – 6834Combined sources
Helixi688 – 70215Combined sources
Helixi705 – 71612Combined sources
Beta strandi718 – 7269Combined sources
Beta strandi730 – 7378Combined sources
Turni738 – 7403Combined sources
Beta strandi742 – 7498Combined sources
Beta strandi751 – 7544Combined sources

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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiE7FHX6.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini4 – 9693ATP-conePROSITE-ProRule annotationAdd
BLAST
Domaini443 – 582140DOD-type homing endonuclease 1PROSITE-ProRule annotationAdd
BLAST
Domaini1063 – 1194132DOD-type homing endonuclease 2PROSITE-ProRule annotationAdd
BLAST

Region

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

Sequence similaritiesi

Contains 1 ATP-cone domain.PROSITE-ProRule annotation
Contains 2 DOD-type homing endonuclease domains.PROSITE-ProRule annotation

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

        10         20         30         40         50
MAVEKVMKRD GRIVPFDESR IRWAVQRAMW EVGIRDEKKL DEVVKSIVQR
60 70 80 90 100
INELYDGKIP HIENIQDIVE LELMRAGLFE VAKAYILYRK KKAEIREEKK
110 120 130 140 150
RILNKKELDE IDKRFSINAL RVLASRYLKK DENGNIVESP RELFERVAIL
160 170 180 190 200
AVIPDLLYDE RVFDKNGNYS QDLKRVEYYL EHFEEFDRKY SIGKYKLNKY
210 220 230 240 250
HFERMVNLYK ELAEQGKMKV SIDEFLAMLE KGEFNEYEKE INEYFRLMTN
260 270 280 290 300
QIFMPNTPAL INSGRPLGML SACFVVPIED DMESIMKAAH DVAMIQKMGG
310 320 330 340 350
GCIDGKAKII FENEGEEHLT TMEEMYERYK HLGEFYDEEY NRWGIDVSNV
360 370 380 390 400
PIYVKSFDPE SKRVVKGKVN VIWKYELGKD VTKYEIITNK GTKILTSPWH
410 420 430 440 450
PFFVLTPDFK IVEKRADELK EGDILIGGMP DGEDYKFIFD YWLAGFIAGD
460 470 480 490 500
GCFDKYHSHV KGHEYIYDRL RIYDYRIETF EIINDYLEKT FGRKYSIQKD
510 520 530 540 550
RNIYYIDIKA RNITSHYLKL LEGIDNGIPP QILKEGKNAV LSFIAGLFDA
560 570 580 590 600
EGHVSNKPGI ELGMVNKRLI EDVTHYLNAL GIKARIREKL RKDGIDYVLH
610 620 630 640 650
VEEYSSLLRF YELIGKNLQN EEKREKLEKV LSNHKGGNFG LPLNFNAFKE
660 670 680 690 700
WASEYGVEFK TNGSQTIAII NDERISLGQW HTRNRVSKAV LVKMLRKLYE
710 720 730 740 750
ATKDEEVKRM LHLIEGLEVV RHITTTNEPR TFYDLTVENY QNYLAGENGM
760 770 780 790 800
IFVHNTGLNF SKLRPEGDIV GTTTGAASGP VSFMHLIDAV SDVIKQGGVR
810 820 830 840 850
RGANMGILEI WHPDIEKFIH AKEKNIGTNV LSNFNISVGI WEDFWEALKE
860 870 880 890 900
GKKYPLINPR TGEVVKEVDP KTLFEELAYM AWAKADPGVI FFDVINRRNV
910 920 930 940 950
LKKAKGGPIR ATNPCVVGDT RILTPEGYLK AEEIFSLAKE RGKKEAVAVE
960 970 980 990 1000
GIAEEGEPYA YSVEILLPGE EKVEYETVHG KVLAVADPVA VPAYVWKVGR
1010 1020 1030 1040 1050
KKVARVKTKE GYEITATLDH KLMTPEGWKE VGKLKEGDKI LLPRFEVEEE
1060 1070 1080 1090 1100
FGSESIGEDL AFVLGWFIGD GYLNVNDKRA WFYFNAEKEE EIAVRIRDIL
1110 1120 1130 1140 1150
VKHFGIKAEL HRYGNQIKLG VRGEAYRWLE NIVKNNEKRI PEIVYRLKPR
1160 1170 1180 1190 1200
EIAAFLRGLF SADGYVDKDM AIRLTSKSRE LLREVQDLLL LFGILSKIYE
1210 1220 1230 1240 1250
KPYESEFHYT TKNGEERIYR SKGYYELVIT NYSRKLFAEK IGLEGYKMEK
1260 1270 1280 1290 1300
LSLKKTKVDQ PIVTVESVEV LGEEIVYDFT VPNYHMYISN GFMSHNCGEE
1310 1320 1330 1340 1350
PLYEYESCNL ASINLAKFVK YDENGKPYFD WDEYAYVIQK VAKYLDNSID
1360 1370 1380 1390 1400
VNKFPLPEID YNTKLTRRIG VGMMGLADAL FKLGIPYNSE EGFKFMRKVT
1410 1420 1430 1440 1450
EYLTFYAYKY SVEAAKKRGT FPLYDKTEYP EGKLPVEGFY HPEIWNLPWD
1460 1470 1480 1490 1500
KLVEEIKKYG LRNAMVTTCP PTGSVSMIAD TSSGIEPVYA LVYKKSVTVG
1510 1520 1530 1540 1550
EFYYVDPVFE EELKKRGLYS EELLKKISDN YGSVQGLEEI PEDMQRVFVT
1560 1570 1580 1590 1600
ALDIHWLDHI IAQASIQMWL TDSASKTINM INEATVEDVK AAYLIARFLG
1610 1620 1630 1640 1650
CKGVTVYRDG SLSVQVYSVE GEKKKRRFKP KPSEYAKKIL LEIVEKEPWI
1660 1670 1680 1690 1700
KNFINVDEIL NGKKEQLLFS LRPANESKLK VPGREEEVRP GNIPEEKIRE
1710 1720 1730 1740
LLGVVYCPVC YEKEGKLVEL KMESGCATCP VCGWSKCVIS
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: October 29, 2014
This is version 33 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