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Entry version 135 (07 Apr 2021)
Sequence version 1 (01 Nov 1996)
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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:

Annotation score:3 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>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

<p>This subsection of the 'Function' section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei14ATPUniRule annotationCombined sources1
Binding sitei134ATPUniRule annotation1
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the 'Description' field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi502ZincUniRule annotation1
Metal bindingi505ZincUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes a region in the protein which binds nucleotide phosphates. It always involves more than one amino acid and includes all residues involved in nucleotide-binding.<p><a href='/help/np_bind' target='_top'>More...</a></p>Nucleotide bindingi35 – 40ATPCombined sources6
Nucleotide bindingi62 – 64ATPCombined sources3

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

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

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
DNA double-strand break repair Rad50 ATPaseUniRule annotation
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:rad50UniRule annotation
Ordered Locus Names:MJ1322
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiMethanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri243232 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiArchaeaEuryarchaeotaMethanomada groupMethanococciMethanococcalesMethanocaldococcaceaeMethanocaldococcus
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000000805 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001386541 – 1005DNA double-strand break repair Rad50 ATPaseAdd BLAST1005

Proteomic databases

PRoteomics IDEntifications database

More...
PRIDEi
Q58718

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction%5Fsection">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Homodimer.

Forms a heterotetramer composed of two Mre11 subunits and two Rad50 subunits.

UniRule annotation

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
243232.MJ_1322

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

11005
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...
SMRi
Q58718

Database of comparative protein structure models

More...
ModBasei
Search...

Protein Data Bank in Europe - Knowledge Base

More...
PDBe-KBi
Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...
EvolutionaryTracei
Q58718

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family%5Fand%5Fdomains%5Fsection">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini457 – 554Zinc-hookUniRule annotationAdd BLAST98

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and domains' section denotes the positions of regions of coiled coil within the protein.<p><a href='/help/coiled' target='_top'>More...</a></p>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
<p>This subsection of the 'Family and Domains' section describes the position of regions of compositional bias within the protein and the particular amino acids that are over-represented within those regions.<p><a href='/help/compbias' target='_top'>More...</a></p>Compositional biasi915 – 953Ala/Asp-rich (DA-box)Add BLAST39

<p>This subsection of the 'Family and domains' section provides general information on the biological role of a domain. The term 'domain' is intended here in its wide acceptation, it may be a structural domain, a transmembrane region or a functional domain. Several domains are described in this subsection.<p><a href='/help/domain_cc' target='_top'>More...</a></p>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

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the SMC family. RAD50 subfamily.UniRule annotation

Keywords - Domaini

Coiled coil

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
arCOG00368, Archaea

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_004785_0_2_2

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
Q58718

Identification of Orthologs from Complete Genome Data

More...
OMAi
FELPYSH

Database for complete collections of gene phylogenies

More...
PhylomeDBi
Q58718

Family and domain databases

HAMAP database of protein families

More...
HAMAPi
MF_00449, RAD50, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR003593, AAA+_ATPase
IPR027417, P-loop_NTPase
IPR038729, Rad50/SbcC_AAA
IPR022982, Rad50_ATPase_archaeal
IPR013134, Zn_hook_RAD50

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF13476, AAA_23, 1 hit
PF04423, Rad50_zn_hook, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00382, AAA, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF52540, SSF52540, 2 hits

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS51131, ZN_HOOK, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>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
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i9BBBB48173E788F3
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

More...
GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
L77117 Genomic DNA Translation: AAB99331.1

Protein sequence database of the Protein Information Resource

More...
PIRi
A64465

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAB99331; AAB99331; MJ_1322

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
mja:MJ_1322

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

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

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...
PDBei

Protein Data Bank RCSB

More...
RCSB PDBi

Protein Data Bank Japan

More...
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[»]
SMRiQ58718
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

STRINGi243232.MJ_1322

Proteomic databases

PRIDEiQ58718

Genome annotation databases

EnsemblBacteriaiAAB99331; AAB99331; MJ_1322
KEGGimja:MJ_1322

Phylogenomic databases

eggNOGiarCOG00368, Archaea
HOGENOMiCLU_004785_0_2_2
InParanoidiQ58718
OMAiFELPYSH
PhylomeDBiQ58718

Miscellaneous databases

EvolutionaryTraceiQ58718

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
IPR013134, Zn_hook_RAD50
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, 2 hits
PROSITEiView protein in PROSITE
PS51131, ZN_HOOK, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiRAD50_METJA
<p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: Q58718
<p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: September 26, 2001
Last sequence update: November 1, 1996
Last modified: April 7, 2021
This is version 135 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
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