P58301 (RAD50_PYRFU) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
DNA double-strand break repair Rad50 ATPase

Gene names

Name:	rad50
Ordered Locus Names:	PF1167

Organism

Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

Taxonomic identifier

186497 [NCBI]

Taxonomic lineage

Archaea › Euryarchaeota › Thermococci › Thermococcales › Thermococcaceae › Pyrococcus

Protein attributes

Sequence length	882 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Involved in DNA double-strand break repair (DSBR). The Rad50/Mre11 complex possesses single-strand endonuclease activity and ATP-dependent double-strand-specific 3'-5' exonuclease activity. Rad50 provides an ATP-dependent control of Mre11 by unwinding and/or repositioning DNA ends into the Mre11 active site. HAMAP MF_00449
Cofactor	Binds 1 zinc ion per heterotetramer Probable. Ref.5
Subunit structure	Heterotetramer composed of two Mre11 subunits and two Rad50 subunits. Ref.4
Domain	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. HAMAP MF_00449
Sequence similarities	Belongs to the SMC family. RAD50 subfamily. Contains 1 zinc-hook domain.

Ontologies

Keywords
Biological process	DNA damage DNA repair
Domain	Coiled coil
Ligand	ATP-binding Metal-binding Nucleotide-binding Zinc
Molecular function	Hydrolase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	DNA repair Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW nuclease activity Inferred from electronic annotation. Source: InterPro zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 882

882

DNA double-strand break repair Rad50 ATPase HAMAP MF_00449

PRO_0000138661

Regions

Domain

399 – 496

98

Zinc-hook

Nucleotide binding

30 – 37

8

ATP HAMAP MF_00449

Coiled coil

148 – 345

198

Potential

Coiled coil

399 – 437

39

Potential

Coiled coil

468 – 496

29

Potential

Coiled coil

534 – 744

211

Potential

Compositional bias

792 – 829

38

Ala/Asp-rich (DA-box) HAMAP MF_00449

Sites

Metal binding

444

1

Zinc

Metal binding

447

1

Zinc

Experimental info

Mutagenesis

793

1

S → R: Prevents ATP binding and disrupts the communication among the other ATP-binding loops. Prevents also Rad50 dimerization.

Secondary structure

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882

Helix Strand Turn

Details...

Beta strand

2 – 11

10

Beta strand

14 – 20

7

Beta strand

23 – 29

7

Helix

36 – 48

13

Beta strand

69 – 77

9

Beta strand

80 – 88

9

Beta strand

96 – 104

9

Beta strand

107 – 112

6

Helix

116 – 126

11

Helix

129 – 135

7

Helix

142 – 146

5

Helix

151 – 160

10

Helix

164 – 194

31

Helix

397 – 437

41

Beta strand

441 – 443

3

Turn

445 – 447

3

Helix

453 – 497

45

Helix

741 – 759

19

Turn

760 – 762

3

Beta strand

766 – 771

6

Beta strand

774 – 782

9

Beta strand

785 – 787

3

Helix

789 – 791

3

Helix

794 – 813

20

Beta strand

817 – 823

7

Helix

830 – 842

13

Helix

844 – 846

3

Beta strand

847 – 855

9

Helix

857 – 862

6

Beta strand

864 – 872

9

Beta strand

875 – 882

8

Sequences

	Sequence		Length	Mass (Da)
	P58301 [UniParc]. Last modified September 26, 2001. Version 1. Checksum: 3ADCBD250382A99E	FASTA	882	103,840
	10 20 30 40 50 60 MKLERVTVKN FRSHSDTVVE FKEGINLIIG QNGSGKSSLL DAILVGLYWP LRIKDIKKDE 70 80 90 100 110 120 FTKVGARDTY IDLIFEKDGT KYRITRRFLK GYSSGEIHAM KRLVGNEWKH VTEPSSKAIS 130 140 150 160 170 180 AFMEKLIPYN IFLNAIYIRQ GQIDAILESD EAREKVVREV LNLDKFETAY KKLSELKKTI 190 200 210 220 230 240 NNRIKEYRDI LARTENIEEL IKENEQELIQ VLQEISKIEE VLPSKRSKVD MLRKEVLRLE 250 260 270 280 290 300 ETKVEIENSE RLLEKRRGDK RTLEERIKNT EEYLEKLKEK EKELEEQVKE ITSIKKDVDA 310 320 330 340 350 360 YLALKEFKNE YLDKKYKIEK ELTRVEELIN EIQKRIEELN EKESEKEKLE NEKKEILNKL 370 380 390 400 410 420 AILEKDHQLY EEIKAKKENL RQLKEKLGDK SPEDIKKLLE ELETKKTTIE EERNEITQRI 430 440 450 460 470 480 GELKNKIGDL KTAIEELKKA KGKCPVCGRE LTDEHREELL SKYHLDLNNS KNTLAKLIDR 490 500 510 520 530 540 KSELERELRR IDMEIKRLTP LLTVAEQIRS IEEELNVVNL EKIEKNATEY EKLLEELRTL 550 560 570 580 590 600 EGRIRGLAED LKKLAPLEKK LAALIHKKQE LEKELKELNT KLESFGFKSV EDLDSKLREL 610 620 630 640 650 660 EEIYKRYLTL LNSKKELEIT QREIAKAKET LEMSFEELAE VEADIERIEK KLSQLKQKYN 670 680 690 700 710 720 EEEYKKKREE KEELEKELAR LEAQKKELEK RRDTIKSTLE KLKAEKENRE RVKKEIKDLE 730 740 750 760 770 780 KAKDFTEELI EKVKKYKALA REAALSKIGE LASEIFAEFT EGKYSEVVVR AEENKVRLFV 790 800 810 820 830 840 VWEGKERPLT FLSGGERIAL GLAFRLAMSL YLAGEISLLI LDEPTPYLDE ERRRKLITIM 850 860 870 880 ERYLKKIPQV ILVSHDEELK DAADHVIRIS LENGSSKVEV VS

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Mre11 and Rad50 from Pyrococcus furiosus: cloning and biochemical characterization reveal an evolutionarily conserved multiprotein machine." Hopfner K.-P., Karcher A., Shin D., Fairley C., Tainer J.A., Carney J.P. J. Bacteriol. 182:6036-6041(2000) [PubMed: 11029422] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], CHARACTERIZATION. 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: 10430560] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1.
[3]	"Structural biology of Rad50 ATPase: ATP-driven conformational control in DNA double-strand break repair and the ABC-ATPase superfamily." Hopfner K.-P., Karcher A., Shin D.S., Craig L., Arthur L.M., Carney J.P., Tainer J.A. Cell 101:789-800(2000) [PubMed: 10892749] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF 1-149. Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1.
[4]	"Structural biochemistry and interaction architecture of the DNA double-strand break repair Mre11 nuclease and Rad50-ATPase." Hopfner K.-P., Karcher A., Craig L., Woo T.T., Carney J.P., Tainer J.A. Cell 105:473-485(2001) [PubMed: 11371344] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.02 ANGSTROMS) OF 1-195 AND 709-882, SUBUNIT.
[5]	"The Rad50 zinc-hook is a structure joining Mre11 complexes in DNA recombination and repair." Hopfner K.-P., Craig L., Moncalian G., Zinkel R.A., Usui T., Owen B.A.L., Karcher A., Henderson B., Bodmer J.-L., McMurray C.T., Carney J.P., Petrini J.H.J., Tainer J.A. Nature 418:562-566(2002) [PubMed: 12152085] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF 396-498, COFACTOR.
[6]	"The rad50 signature motif: essential to ATP binding and biological function." Moncalian G., Lengsfeld B., Bhaskara V., Hopfner K.-P., Karcher A., Alden E., Tainer J.A., Paull T.T. J. Mol. Biol. 335:937-951(2004) [PubMed: 14698290] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 8-147 OF MUTANT ARG-793.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AE009950 Genomic DNA. Translation: AAL81291.1.

RefSeq

NP_578896.1. NC_003413.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1F2T	X-ray	1.60	A	1-149	[»]
			B	735-882	[»]
1F2U	X-ray	1.60	A/C	1-149	[»]
			B/D	735-882	[»]
1II8	X-ray	3.02	A	1-195	[»]
			B	709-882	[»]
1L8D	X-ray	2.20	A/B	396-506	[»]
1US8	X-ray	2.10	A	1-147	[»]
			B	739-882	[»]
3QKR	X-ray	3.40	A	1-195	[»]
			B	704-882	[»]
3QKS	X-ray	2.10	A	1-195	[»]
			B	704-882	[»]
3QKT	X-ray	1.90	A/B/C/D	1-882	[»]
3QKU	X-ray	3.30	A/B	1-882	[»]

ProteinModelPortal

P58301.

SMR

P58301. Positions 1-195, 396-498, 709-882.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-54373N.

IntAct

P58301. 1 interaction.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBPYRT00000005235; EBPYRP00000005096; EBPYRG00000005234.

GeneID

1469036.

GenomeReviews

Gene locus PF1167 in contig AE009950_GR.

KEGG

pfu:PF1167.

NMPDR

fig|186497.1.peg.1207.

Phylogenomic databases

GeneTree

EBGT00050000022195.

HOGENOM

HBG726702.

OMA

RTENIEE.

ProtClustDB

PRK03918.

Family and domain databases

HAMAP

MF_00449. RAD50.
[Tree]

InterPro

IPR022982. Rad50_ATPase.
IPR007517. Rad50_Zn_hook.
IPR003395. RecF/RecN/SMC.
IPR013134. Zn_hook_Rad50.
[Graphical view]

KO

K03546.

Pfam

PF04423. Rad50_zn_hook. 1 hit.
PF02463. SMC_N. 1 hit.
[Graphical view]

PROSITE

PS51131. ZN_HOOK. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

RAD50_PYRFU

Accession

Primary (citable) accession number: P58301

Entry history

Integrated into UniProtKB/Swiss-Prot:	September 26, 2001
Last sequence update:	September 26, 2001
Last modified:	January 25, 2012
This is version 83 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program