Skip Header

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

DNA double-strand break repair Rad50 ATPase

Gene

rad50

Organism
Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Part of the Rad50/Mre11 complex, which is involved in the early steps of DNA double-strand break (DSB) repair (PubMed:11029422, PubMed:18957200). The complex may facilitate opening of the processed DNA ends to aid in the recruitment of HerA and NurA (PubMed:18957200). Rad50 controls the balance between DNA end bridging and DNA resection via ATP-dependent structural rearrangements of the Rad50/Mre11 complex (PubMed:24493214). The ATP-bound conformation promotes DNA end binding and end tethering, and alters Mre11 nuclease activity (PubMed:24493214). ATP hydrolysis promotes both Mre11 activity as well as HerA/NurA activity (PubMed:24493214). Has also reversible adenylate kinase activity (PubMed:17349953).4 Publications

Cofactori

Zn2+UniRule annotation1 PublicationNote: Binds 1 zinc ion per homodimer.UniRule annotation1 Publication

Enzyme regulationi

The adenylate kinase inhibitor P1,P(5)-di(adenosine-5') pentaphosphate (Ap5A) inhibits adenylate kinase activity, but does not affect ATPase activity.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei12 – 121ATPCombined sources3 Publications
Binding sitei140 – 1401ATPCombined sources2 Publications
Metal bindingi444 – 4441ZincUniRule annotation1 Publication
Metal bindingi447 – 4471ZincUniRule annotation1 Publication

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi32 – 387ATPCombined sources3 Publications
Nucleotide bindingi60 – 645ATPCombined sources3 Publications
Nucleotide bindingi763 – 7642ATPCombined sources2 Publications
Nucleotide bindingi791 – 7966ATPCombined sources2 Publications

GO - Molecular functioni

  • ATPase activity Source: UniProtKB-HAMAP
  • ATP binding Source: UniProtKB-HAMAP
  • identical protein binding Source: IntAct
  • zinc ion binding Source: UniProtKB-HAMAP

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

DNA damage, DNA repair

Keywords - Ligandi

ATP-binding, Metal-binding, Nucleotide-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
DNA double-strand break repair Rad50 ATPaseUniRule annotationCurated
Alternative name(s):
pfRad501 Publication
Gene namesi
Name:rad501 PublicationUniRule annotation
Ordered Locus Names:PF1167
OrganismiPyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
Taxonomic identifieri186497 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
Proteomesi
  • UP000001013 Componenti: Chromosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi793 – 7931S → R: Prevents ATP binding and disrupts the communication among the other ATP-binding loops. Prevents also Rad50 dimerization. Decreases both ATPase and adenylate kinase activities. 3 Publications
Mutagenesisi797 – 7971R → G: Decreases ATP-induced dimerization. Increases DNA end tethering. 1 Publication
Mutagenesisi802 – 8021L → W: Destabilizes the ATP-dimerized state. Promotes HerA/NurA activity. 1 Publication
Mutagenesisi805 – 8051R → E: Increases ATP-induced dimerization. Increases DNA end tethering. Fails to promote HerA/NurA activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 882882DNA double-strand break repair Rad50 ATPasePRO_0000138661Add
BLAST

Proteomic databases

PRIDEiP58301.

Interactioni

Subunit structurei

Homodimer (PubMed:10892749, PubMed:14698290). Forms a heterotetramer composed of two Mre11 subunits and two Rad50 subunits (PubMed:11371344, PubMed:21441914, PubMed:22102415). Homodimerization is promoted by ATP binding (PubMed:10892749).5 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
itself3EBI-2505704,EBI-2505704
mre11Q8U1N92EBI-2505704,EBI-2014945

GO - Molecular functioni

  • identical protein binding Source: IntAct

Protein-protein interaction databases

DIPiDIP-54373N.
IntActiP58301. 2 interactions.
STRINGi186497.PF1167.

Structurei

Secondary structure

1
882
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 1110Combined sources
Beta strandi14 – 207Combined sources
Beta strandi23 – 297Combined sources
Helixi36 – 4813Combined sources
Helixi58 – 614Combined sources
Beta strandi63 – 675Combined sources
Beta strandi69 – 779Combined sources
Beta strandi80 – 889Combined sources
Beta strandi93 – 953Combined sources
Beta strandi96 – 1049Combined sources
Beta strandi107 – 1126Combined sources
Helixi116 – 12611Combined sources
Helixi129 – 1357Combined sources
Beta strandi137 – 1393Combined sources
Helixi142 – 1465Combined sources
Helixi152 – 16110Combined sources
Helixi167 – 1737Combined sources
Helixi181 – 1866Combined sources
Helixi397 – 43741Combined sources
Beta strandi441 – 4433Combined sources
Turni445 – 4473Combined sources
Helixi453 – 49745Combined sources
Turni717 – 7226Combined sources
Helixi727 – 7348Combined sources
Helixi741 – 75919Combined sources
Turni760 – 7623Combined sources
Beta strandi766 – 7716Combined sources
Beta strandi774 – 7829Combined sources
Beta strandi785 – 7873Combined sources
Helixi789 – 7913Combined sources
Helixi794 – 81320Combined sources
Beta strandi817 – 8237Combined sources
Beta strandi825 – 8284Combined sources
Helixi830 – 84213Combined sources
Helixi844 – 8463Combined sources
Beta strandi847 – 8559Combined sources
Helixi857 – 8626Combined sources
Beta strandi864 – 8729Combined sources
Beta strandi875 – 8828Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1F2TX-ray1.60A1-149[»]
B735-882[»]
1F2UX-ray1.60A/C1-149[»]
B/D735-882[»]
1II8X-ray3.02A1-195[»]
B709-882[»]
1L8DX-ray2.20A/B396-506[»]
1US8X-ray2.10A1-147[»]
B739-882[»]
3QKRX-ray3.40A1-195[»]
B704-882[»]
3QKSX-ray2.10A1-195[»]
B704-882[»]
3QKTX-ray1.90A/B/C/D1-177[»]
A/B/C/D726-882[»]
3QKUX-ray3.30A/B1-187[»]
A/B716-882[»]
4NCHX-ray2.30A/B1-177[»]
A/B726-882[»]
4NCIX-ray2.30A1-177[»]
A726-882[»]
4NCJX-ray2.00A/B/C/D1-177[»]
A/B/C/D726-882[»]
4NCKX-ray1.99A/B1-177[»]
A/B726-882[»]
ProteinModelPortaliP58301.
SMRiP58301. Positions 1-195, 396-498, 709-882.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP58301.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini399 – 49698Zinc-hookUniRule annotationAdd
BLAST

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili257 – 588332UniRule annotationAdd
BLAST
Coiled coili629 – 735107UniRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi792 – 82938Ala/Asp-rich (DA-box)Add
BLAST

Domaini

Binding of ATP induces a closed, compact conformation of the Rad50/Mre11 complex. ATP hydrolysis opens the complex.1 Publication
The two conserved Cys that bind zinc constitute the zinc-hook, which separates the large intramolecular coiled coil regions. The 2 Cys residues coordinate one molecule of zinc with the help of the 2 Cys residues of the zinc-hook of another Rad50 molecule, thereby forming a V-shaped homodimer.UniRule annotation1 Publication

Sequence similaritiesi

Belongs to the SMC family. RAD50 subfamily.UniRule annotationCurated
Contains 1 zinc-hook domain.UniRule annotation

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiarCOG00368. Archaea.
COG0419. LUCA.
HOGENOMiHOG000073889.
KOiK03546.
OMAiVYGNDAY.

Family and domain databases

Gene3Di3.40.50.300. 3 hits.
HAMAPiMF_00449. RAD50. 1 hit.
InterProiIPR003959. ATPase_AAA_core.
IPR027417. P-loop_NTPase.
IPR022982. Rad50_ATPase_archaeal.
IPR013134. Zn_hook_RAD50.
[Graphical view]
PfamiPF13304. AAA_21. 1 hit.
PF04423. Rad50_zn_hook. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 3 hits.
PROSITEiPS51131. ZN_HOOK. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P58301-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKLERVTVKN FRSHSDTVVE FKEGINLIIG QNGSGKSSLL DAILVGLYWP
60 70 80 90 100
LRIKDIKKDE FTKVGARDTY IDLIFEKDGT KYRITRRFLK GYSSGEIHAM
110 120 130 140 150
KRLVGNEWKH VTEPSSKAIS AFMEKLIPYN IFLNAIYIRQ GQIDAILESD
160 170 180 190 200
EAREKVVREV LNLDKFETAY KKLSELKKTI NNRIKEYRDI LARTENIEEL
210 220 230 240 250
IKENEQELIQ VLQEISKIEE VLPSKRSKVD MLRKEVLRLE ETKVEIENSE
260 270 280 290 300
RLLEKRRGDK RTLEERIKNT EEYLEKLKEK EKELEEQVKE ITSIKKDVDA
310 320 330 340 350
YLALKEFKNE YLDKKYKIEK ELTRVEELIN EIQKRIEELN EKESEKEKLE
360 370 380 390 400
NEKKEILNKL AILEKDHQLY EEIKAKKENL RQLKEKLGDK SPEDIKKLLE
410 420 430 440 450
ELETKKTTIE EERNEITQRI GELKNKIGDL KTAIEELKKA KGKCPVCGRE
460 470 480 490 500
LTDEHREELL SKYHLDLNNS KNTLAKLIDR KSELERELRR IDMEIKRLTP
510 520 530 540 550
LLTVAEQIRS IEEELNVVNL EKIEKNATEY EKLLEELRTL EGRIRGLAED
560 570 580 590 600
LKKLAPLEKK LAALIHKKQE LEKELKELNT KLESFGFKSV EDLDSKLREL
610 620 630 640 650
EEIYKRYLTL LNSKKELEIT QREIAKAKET LEMSFEELAE VEADIERIEK
660 670 680 690 700
KLSQLKQKYN EEEYKKKREE KEELEKELAR LEAQKKELEK RRDTIKSTLE
710 720 730 740 750
KLKAEKENRE RVKKEIKDLE KAKDFTEELI EKVKKYKALA REAALSKIGE
760 770 780 790 800
LASEIFAEFT EGKYSEVVVR AEENKVRLFV VWEGKERPLT FLSGGERIAL
810 820 830 840 850
GLAFRLAMSL YLAGEISLLI LDEPTPYLDE ERRRKLITIM ERYLKKIPQV
860 870 880
ILVSHDEELK DAADHVIRIS LENGSSKVEV VS
Length:882
Mass (Da):103,840
Last modified:September 26, 2001 - v1
Checksum:i3ADCBD250382A99E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE009950 Genomic DNA. Translation: AAL81291.1.
RefSeqiWP_011012307.1. NC_003413.1.

Genome annotation databases

EnsemblBacteriaiAAL81291; AAL81291; PF1167.
GeneIDi1469036.
KEGGipfu:PF1167.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE009950 Genomic DNA. Translation: AAL81291.1.
RefSeqiWP_011012307.1. NC_003413.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1F2TX-ray1.60A1-149[»]
B735-882[»]
1F2UX-ray1.60A/C1-149[»]
B/D735-882[»]
1II8X-ray3.02A1-195[»]
B709-882[»]
1L8DX-ray2.20A/B396-506[»]
1US8X-ray2.10A1-147[»]
B739-882[»]
3QKRX-ray3.40A1-195[»]
B704-882[»]
3QKSX-ray2.10A1-195[»]
B704-882[»]
3QKTX-ray1.90A/B/C/D1-177[»]
A/B/C/D726-882[»]
3QKUX-ray3.30A/B1-187[»]
A/B716-882[»]
4NCHX-ray2.30A/B1-177[»]
A/B726-882[»]
4NCIX-ray2.30A1-177[»]
A726-882[»]
4NCJX-ray2.00A/B/C/D1-177[»]
A/B/C/D726-882[»]
4NCKX-ray1.99A/B1-177[»]
A/B726-882[»]
ProteinModelPortaliP58301.
SMRiP58301. Positions 1-195, 396-498, 709-882.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-54373N.
IntActiP58301. 2 interactions.
STRINGi186497.PF1167.

Proteomic databases

PRIDEiP58301.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAL81291; AAL81291; PF1167.
GeneIDi1469036.
KEGGipfu:PF1167.

Phylogenomic databases

eggNOGiarCOG00368. Archaea.
COG0419. LUCA.
HOGENOMiHOG000073889.
KOiK03546.
OMAiVYGNDAY.

Miscellaneous databases

EvolutionaryTraceiP58301.

Family and domain databases

Gene3Di3.40.50.300. 3 hits.
HAMAPiMF_00449. RAD50. 1 hit.
InterProiIPR003959. ATPase_AAA_core.
IPR027417. P-loop_NTPase.
IPR022982. Rad50_ATPase_archaeal.
IPR013134. Zn_hook_RAD50.
[Graphical view]
PfamiPF13304. AAA_21. 1 hit.
PF04423. Rad50_zn_hook. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 3 hits.
PROSITEiPS51131. ZN_HOOK. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRAD50_PYRFU
AccessioniPrimary (citable) accession number: P58301
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 26, 2001
Last sequence update: September 26, 2001
Last modified: September 7, 2016
This is version 116 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, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. 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.