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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)DescriptionActionsGraphical viewLength
Binding sitei12ATPCombined sources3 Publications1
Binding sitei140ATPCombined sources2 Publications1
Metal bindingi444ZincUniRule annotation1 Publication1
Metal bindingi447ZincUniRule annotation1 Publication1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi32 – 38ATPCombined sources3 Publications7
Nucleotide bindingi60 – 64ATPCombined sources3 Publications5
Nucleotide bindingi763 – 764ATPCombined sources2 Publications2
Nucleotide bindingi791 – 796ATPCombined sources2 Publications6

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)DescriptionActionsGraphical viewLength
Mutagenesisi793S → 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 Publications1
Mutagenesisi797R → G: Decreases ATP-induced dimerization. Increases DNA end tethering. 1 Publication1
Mutagenesisi802L → W: Destabilizes the ATP-dimerized state. Promotes HerA/NurA activity. 1 Publication1
Mutagenesisi805R → E: Increases ATP-induced dimerization. Increases DNA end tethering. Fails to promote HerA/NurA activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001386611 – 882DNA double-strand break repair Rad50 ATPaseAdd BLAST882

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 interactors.
STRINGi186497.PF1167.

Structurei

Secondary structure

1882
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 11Combined sources10
Beta strandi14 – 20Combined sources7
Beta strandi23 – 29Combined sources7
Helixi36 – 48Combined sources13
Helixi58 – 61Combined sources4
Beta strandi63 – 67Combined sources5
Beta strandi69 – 77Combined sources9
Beta strandi80 – 88Combined sources9
Beta strandi93 – 95Combined sources3
Beta strandi96 – 104Combined sources9
Beta strandi107 – 112Combined sources6
Helixi116 – 126Combined sources11
Helixi129 – 135Combined sources7
Beta strandi137 – 139Combined sources3
Helixi142 – 146Combined sources5
Helixi152 – 161Combined sources10
Helixi167 – 173Combined sources7
Helixi181 – 186Combined sources6
Helixi397 – 437Combined sources41
Beta strandi441 – 443Combined sources3
Turni445 – 447Combined sources3
Helixi453 – 497Combined sources45
Turni717 – 722Combined sources6
Helixi727 – 734Combined sources8
Helixi741 – 759Combined sources19
Turni760 – 762Combined sources3
Beta strandi766 – 771Combined sources6
Beta strandi774 – 782Combined sources9
Beta strandi785 – 787Combined sources3
Helixi789 – 791Combined sources3
Helixi794 – 813Combined sources20
Beta strandi817 – 823Combined sources7
Beta strandi825 – 828Combined sources4
Helixi830 – 842Combined sources13
Helixi844 – 846Combined sources3
Beta strandi847 – 855Combined sources9
Helixi857 – 862Combined sources6
Beta strandi864 – 872Combined sources9
Beta strandi875 – 882Combined sources8

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP58301.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini399 – 496Zinc-hookUniRule annotationAdd BLAST98

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili257 – 588UniRule annotationAdd BLAST332
Coiled coili629 – 735UniRule annotationAdd BLAST107

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi792 – 829Ala/Asp-rich (DA-box)Add BLAST38

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
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-54373N.
IntActiP58301. 2 interactors.
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: November 2, 2016
This is version 118 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.