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Protein

Probable DNA double-strand break repair Rad50 ATPase

Gene

rad50

Organism
Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

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 (By similarity).By similarity

Cofactori

Zn2+By similarityNote: Binds 1 zinc ion per homodimer.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi435ZincPROSITE-ProRule annotation1
Metal bindingi438ZincPROSITE-ProRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi30 – 37ATPBy similarity8

GO - Molecular functioni

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:
Probable DNA double-strand break repair Rad50 ATPase
Gene namesi
Name:rad50
Ordered Locus Names:TM_1636
OrganismiThermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Taxonomic identifieri243274 [NCBI]
Taxonomic lineageiBacteriaThermotogaeThermotogalesThermotogaceaeThermotoga
Proteomesi
  • UP000008183 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001386701 – 852Probable DNA double-strand break repair Rad50 ATPaseAdd BLAST852

Interactioni

Subunit structurei

Homodimer. Forms a complex with Mre11 (By similarity).By similarity

Binary interactionsi

WithEntry#Exp.IntActNotes
sbcDQ9X1X03EBI-3954207,EBI-3954204

Protein-protein interaction databases

IntActiQ9X1X1. 1 interactor.
STRINGi243274.TM1636.

Structurei

Secondary structure

1852
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
Helixi57 – 60Combined sources4
Beta strandi65 – 67Combined sources3
Beta strandi69 – 78Combined sources10
Beta strandi81 – 90Combined sources10
Turni91 – 94Combined sources4
Beta strandi95 – 103Combined sources9
Beta strandi105 – 107Combined sources3
Beta strandi109 – 115Combined sources7
Helixi116 – 127Combined sources12
Helixi131 – 137Combined sources7
Beta strandi138 – 141Combined sources4
Turni145 – 150Combined sources6
Helixi153 – 163Combined sources11
Helixi167 – 189Combined sources23
Helixi686 – 709Combined sources24
Turni711 – 713Combined sources3
Helixi714 – 738Combined sources25
Beta strandi742 – 747Combined sources6
Turni748 – 751Combined sources4
Beta strandi752 – 757Combined sources6
Beta strandi760 – 763Combined sources4
Helixi764 – 766Combined sources3
Helixi769 – 786Combined sources18
Turni787 – 790Combined sources4
Beta strandi793 – 798Combined sources6
Turni799 – 802Combined sources4
Helixi805 – 816Combined sources12
Helixi817 – 820Combined sources4
Beta strandi821 – 830Combined sources10
Helixi832 – 835Combined sources4
Beta strandi841 – 845Combined sources5
Beta strandi848 – 850Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3QF7X-ray1.90A/B1-190[»]
A/B686-852[»]
3QG5X-ray3.40A/B1-190[»]
A/B686-852[»]
3THOX-ray2.61A1-190[»]
A686-852[»]
4W9MX-ray2.70C/E/I/K1-188[»]
C/E/I/K687-852[»]
ProteinModelPortaliQ9X1X1.
SMRiQ9X1X1.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini389 – 488Zinc-hookPROSITE-ProRule annotationAdd BLAST100

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili155 – 345Sequence analysisAdd BLAST191
Coiled coili389 – 427Sequence analysisAdd BLAST39
Coiled coili460 – 488Sequence analysisAdd BLAST29
Coiled coili534 – 711Sequence analysisAdd BLAST178

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi768 – 804Ala/Asp-rich (DA-box)Add BLAST37

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 (By similarity).By similarity

Sequence similaritiesi

Belongs to the SMC family. RAD50 subfamily.Curated
Contains 1 zinc-hook domain.PROSITE-ProRule annotation

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiENOG4107WZZ. Bacteria.
COG0419. LUCA.
InParanoidiQ9X1X1.
KOiK03546.
OMAiTHIEDLM.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR027417. P-loop_NTPase.
IPR013134. Zn_hook_RAD50.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 5 hits.
PROSITEiPS51131. ZN_HOOK. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9X1X1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRPERLTVRN FLGLKNVDIE FQSGITVVEG PNGAGKSSLF EAISFALFGN
60 70 80 90 100
GIRYPNSYDY VNRNAVDGTA RLVFQFERGG KRYEIIREIN ALQRKHNAKL
110 120 130 140 150
SEILENGKKA AIAAKPTSVK QEVEKILGIE HRTFIRTVFL PQGEIDKLLI
160 170 180 190 200
SPPSEITEII SDVFQSKETL EKLEKLLKEK MKKLENEISS LQALYTAIWK
210 220 230 240 250
YLEENDLEVL KSELKTVSEK KKELLKKREE LQKEEEQLKR LLEKYRELVK
260 270 280 290 300
KKERLRVLSL RRNELQKEVI YEQKVKKAKE LEPLFREIYL RQREFERFSQ
310 320 330 340 350
ELNSREKRYK ELESEKEAIS KEIPVHRERL SKLEEIGEKI KEELDLLEKV
360 370 380 390 400
LKASRPLLEQ RIRLKENLTR LEEEFRRLVG EKEKREKELL SIEKTENETK
410 420 430 440 450
NELEKLLDEL SILKKDHMKW LAYQIASSLN EGDTCPVCGG VFHGKVEAVE
460 470 480 490 500
FNIDEFEKLD QKRSELENTL NVLKERKKSL SSLIEDLLMK IEEGKKNLKS
510 520 530 540 550
IRNQIEKIEE ELHRLGYSED LEEKLDEKRK KLRKIEEERH SISQKITAAD
560 570 580 590 600
VQISQIENQL KEIKGEIEAK RETLKEQREE MDQLKSDFFD RLRKIGIGFE
610 620 630 640 650
EFRILVKEEV KDAEKELGVV ETEIRLLEES LKELESENVR DVSEDYEKVR
660 670 680 690 700
NQLEALSQEI SDLERKEGRL NHLIEETLRR ERELKSLEKK LKEMSDEYNN
710 720 730 740 750
LDLLRKYLFD KSNFSRYFTG RVLEAVLKRT KAYLDILTNG RFDIDFDDEK
760 770 780 790 800
GGFIIKDWGI ERPARGLSGG ERALISISLA MSLAEVASGR LDAFFIDEGF
810 820 830 840 850
SSLDTENKEK IASVLKELER LNKVIVFITH DREFSEAFDR KLRITGGVVV

NE
Length:852
Mass (Da):100,002
Last modified:November 1, 1999 - v1
Checksum:i31BA9F72A4EC5CD2
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000512 Genomic DNA. Translation: AAD36703.1.
PIRiD72230.
RefSeqiNP_229436.1. NC_000853.1.
WP_004082116.1. NZ_CP011107.1.

Genome annotation databases

EnsemblBacteriaiAAD36703; AAD36703; TM_1636.
GeneIDi897923.
KEGGitma:TM1636.
PATRICi23938246. VBITheMar51294_1655.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000512 Genomic DNA. Translation: AAD36703.1.
PIRiD72230.
RefSeqiNP_229436.1. NC_000853.1.
WP_004082116.1. NZ_CP011107.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3QF7X-ray1.90A/B1-190[»]
A/B686-852[»]
3QG5X-ray3.40A/B1-190[»]
A/B686-852[»]
3THOX-ray2.61A1-190[»]
A686-852[»]
4W9MX-ray2.70C/E/I/K1-188[»]
C/E/I/K687-852[»]
ProteinModelPortaliQ9X1X1.
SMRiQ9X1X1.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiQ9X1X1. 1 interactor.
STRINGi243274.TM1636.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAD36703; AAD36703; TM_1636.
GeneIDi897923.
KEGGitma:TM1636.
PATRICi23938246. VBITheMar51294_1655.

Phylogenomic databases

eggNOGiENOG4107WZZ. Bacteria.
COG0419. LUCA.
InParanoidiQ9X1X1.
KOiK03546.
OMAiTHIEDLM.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
InterProiIPR027417. P-loop_NTPase.
IPR013134. Zn_hook_RAD50.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 5 hits.
PROSITEiPS51131. ZN_HOOK. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRAD50_THEMA
AccessioniPrimary (citable) accession number: Q9X1X1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 26, 2001
Last sequence update: November 1, 1999
Last modified: November 30, 2016
This is version 110 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.