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Protein

DNA double-strand break repair Rad50 ATPase

Gene

rad50

Organism
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
Status
Reviewed-Annotation score: -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. The complex may facilitate opening of the processed DNA ends to aid in the recruitment of HerA and NurA. Rad50 controls the balance between DNA end bridging and DNA resection via ATP-dependent structural rearrangements of the Rad50/Mre11 complex.UniRule annotation

Cofactori

Zn2+UniRule annotationNote: Binds 1 zinc ion per homodimer.UniRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei14ATPUniRule annotationCombined sources1
Binding sitei134ATPUniRule annotation1
Metal bindingi502ZincUniRule annotation1
Metal bindingi505ZincUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi35 – 40ATPCombined sources6
Nucleotide bindingi62 – 64ATPCombined sources3

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionHydrolase
Biological processDNA damage, DNA repair
LigandATP-binding, Metal-binding, Nucleotide-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
DNA double-strand break repair Rad50 ATPaseUniRule annotation
Gene namesi
Name:rad50UniRule annotation
Ordered Locus Names:MJ1322
OrganismiMethanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
Taxonomic identifieri243232 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaMethanococciMethanococcalesMethanocaldococcaceaeMethanocaldococcus
Proteomesi
  • UP000000805 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001386541 – 1005DNA double-strand break repair Rad50 ATPaseAdd BLAST1005

Proteomic databases

PRIDEiQ58718

Interactioni

Subunit structurei

Homodimer. Forms a heterotetramer composed of two Mre11 subunits and two Rad50 subunits.UniRule annotation

Protein-protein interaction databases

STRINGi243232.MJ_1322

Structurei

Secondary structure

11005
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 13Combined sources11
Beta strandi16 – 22Combined sources7
Beta strandi25 – 32Combined sources8
Helixi38 – 50Combined sources13
Beta strandi54 – 56Combined sources3
Turni58 – 61Combined sources4
Beta strandi67 – 77Combined sources11
Beta strandi80 – 89Combined sources10
Beta strandi92 – 99Combined sources8
Beta strandi102 – 105Combined sources4
Helixi108 – 119Combined sources12
Helixi123 – 130Combined sources8
Helixi136 – 142Combined sources7
Helixi145 – 156Combined sources12
Helixi158 – 185Combined sources28
Turni186 – 188Combined sources3
Helixi193 – 224Combined sources32
Turni228 – 230Combined sources3
Helixi231 – 247Combined sources17
Beta strandi255 – 257Combined sources3
Beta strandi262 – 266Combined sources5
Beta strandi269 – 271Combined sources3
Helixi273 – 275Combined sources3
Helixi278 – 296Combined sources19
Beta strandi300 – 306Combined sources7
Turni307 – 310Combined sources4
Helixi313 – 324Combined sources12
Beta strandi331 – 338Combined sources8
Helixi340 – 345Combined sources6
Beta strandi347 – 355Combined sources9

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3AUXX-ray2.80A1-190[»]
A825-1005[»]
3AUYX-ray2.70A/B11-190[»]
A/B825-1005[»]
3AV0X-ray3.10B1-190[»]
B825-1005[»]
5DNYX-ray3.11B/D1-190[»]
B/D825-1005[»]
5F3WX-ray3.11B/D1-190[»]
B/D825-1005[»]
ProteinModelPortaliQ58718
SMRiQ58718
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ58718

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini457 – 554Zinc-hookUniRule annotationAdd BLAST98

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili189 – 230UniRule annotationAdd BLAST42
Coiled coili292 – 321UniRule annotationAdd BLAST30
Coiled coili346 – 379UniRule annotationAdd BLAST34
Coiled coili404 – 498UniRule annotationAdd BLAST95
Coiled coili523 – 600UniRule annotationAdd BLAST78
Coiled coili656 – 692UniRule annotationAdd BLAST37
Coiled coili800 – 834UniRule annotationAdd BLAST35

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi915 – 953Ala/Asp-rich (DA-box)Add BLAST39

Domaini

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 annotation

Sequence similaritiesi

Belongs to the SMC family. RAD50 subfamily.UniRule annotation

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiarCOG00368 Archaea
COG0419 LUCA
InParanoidiQ58718
KOiK03546
OMAiFELPYSH
OrthoDBiPOG093Z01RC
PhylomeDBiQ58718

Family and domain databases

HAMAPiMF_00449 RAD50, 1 hit
InterProiView protein in InterPro
IPR003593 AAA+_ATPase
IPR027417 P-loop_NTPase
IPR038729 Rad50/SbcC_AAA
IPR022982 Rad50_ATPase_archaeal
IPR027050 SbcC-like
IPR013134 Zn_hook_RAD50
PANTHERiPTHR32114 PTHR32114, 1 hit
PfamiView protein in Pfam
PF13476 AAA_23, 1 hit
PF04423 Rad50_zn_hook, 1 hit
SMARTiView protein in SMART
SM00382 AAA, 1 hit
SUPFAMiSSF52540 SSF52540, 3 hits
PROSITEiView protein in PROSITE
PS51131 ZN_HOOK, 1 hit

Sequencei

Sequence statusi: Complete.

Q58718-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSMILKEIRM NNFKSHVNSR IKFEKGIVAI IGENGSGKSS IFEAVFFALF
60 70 80 90 100
GAGSNFNYDT IITKGKKSVY VELDFEVNGN NYKIIREYDS GRGGAKLYKN
110 120 130 140 150
GKPYATTISA VNKAVNEILG VDRNMFLNSI YIKQGEIAKF LSLKPSEKLE
160 170 180 190 200
TVAKLLGIDE FEKCYQKMGE IVKEYEKRLE RIEGELNYKE NYEKELKNKM
210 220 230 240 250
SQLEEKNKKL MEINDKLNKI KKEFEDIEKL FNEWENKKLL YEKFINKLEE
260 270 280 290 300
RKRALELKNQ ELKILEYDLN TVVEARETLN RHKDEYEKYK SLVDEIRKIE
310 320 330 340 350
SRLRELKSHY EDYLKLTKQL EIIKGDIEKL KEFINKSKYR DDIDNLDTLL
360 370 380 390 400
NKIKDEIERV ETIKDLLEEL KNLNEEIEKI EKYKRICEEC KEYYEKYLEL
410 420 430 440 450
EEKAVEYNKL TLEYITLLQE KKSIEKNIND LETRINKLLE ETKNIDIESI
460 470 480 490 500
ENSLKEIEEK KKVLENLQKE KIELNKKLGE INSEIKRLKK ILDELKEVEG
510 520 530 540 550
KCPLCKTPID ENKKMELINQ HKTQLNNKYT ELEEINKKIR EIEKDIEKLK
560 570 580 590 600
KEIDKEENLK TLKTLYLEKQ SQIEELELKL KNYKEQLDEI NKKISNYVIN
610 620 630 640 650
GKPVDEILED IKSQLNKFKN FYNQYLSAVS YLNSVDEEGI RNRIKEIENI
660 670 680 690 700
VSGWNKEKCR EELNKLREDE REINRLKDKL NELKNKEKEL IEIENRRSLK
710 720 730 740 750
FDKYKEYLGL TEKLEELKNI KDGLEEIYNI CNSKILAIDN IKRKYNKEDI
760 770 780 790 800
EIYLNNKILE VNKEINDIEE RISYINQKLD EINYNEEEHK KIKELYENKR
810 820 830 840 850
QELDNVREQK TEIETGIEYL KKDVESLKAR LKEMSNLEKE KEKLTKFVEY
860 870 880 890 900
LDKVRRIFGR NGFQAYLREK YVPLIQKYLN EAFSEFDLPY SFVELTKDFE
910 920 930 940 950
VRVHAPNGVL TIDNLSGGEQ IAVALSLRLA IANALIGNRV ECIILDEPTV
960 970 980 990 1000
YLDENRRAKL AEIFRKVKSI PQMIIITHHR ELEDVADVII NVKKDGNVSK

VKING
Length:1,005
Mass (Da):119,388
Last modified:November 1, 1996 - v1
Checksum:i9BBBB48173E788F3
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L77117 Genomic DNA Translation: AAB99331.1
PIRiA64465

Genome annotation databases

EnsemblBacteriaiAAB99331; AAB99331; MJ_1322
KEGGimja:MJ_1322

Similar proteinsi

Entry informationi

Entry nameiRAD50_METJA
AccessioniPrimary (citable) accession number: Q58718
Entry historyiIntegrated into UniProtKB/Swiss-Prot: September 26, 2001
Last sequence update: November 1, 1996
Last modified: June 20, 2018
This is version 125 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Methanococcus jannaschii
    Methanococcus jannaschii: entries and gene names
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

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