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P23478 (ADDA_BACSU) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 113. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
ATP-dependent helicase/nuclease subunit A

EC=3.1.-.-
EC=3.6.4.12
Alternative name(s):
ATP-dependent helicase/nuclease AddA
Gene names
Name:addA
Ordered Locus Names:BSU10630
OrganismBacillus subtilis (strain 168) [Reference proteome] [HAMAP]
Taxonomic identifier224308 [NCBI]
Taxonomic lineageBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus

Protein attributes

Sequence length1232 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

An essential component of the DNA double-stranded break repair machinery, the heterodimer acts as both an ATP-dependent DNA helicase and an ATP-dependent, dual-direction single-stranded exonuclease. Recognizes the B.subtilis chi site (5'-AGCGG-3') which transforms the enzyme from a helicase which degrades both DNA strands to one with only 5' -> 3' exonuclease activity. This generates a double-stranded DNA with a protruding 3'-terminated single-stranded tail suitable for the initiation of homologous recombination (chi fragment). The AddA nuclease domain in particular is required for chi fragment generation; this subunit has 3' -> 5' nuclease and helicase activity. RecA thread formation during DNA double-strand break repair requires RecJ or AddAB. Ref.6 Ref.7 Ref.10

Catalytic activity

ATP + H2O = ADP + phosphate. HAMAP-Rule MF_01451

Cofactor

Magnesium. At low magnesium concentrations there is no nuclease activity, but helicase activity is unaffected. Ref.7

Subunit structure

Heterodimer of AddA and AddB. Ref.6 Ref.11

Miscellaneous

This enzyme is a functional homolog of the E.coli RecBCD enzyme; unlike the RecBCD enzyme it degrades both duplex strands symmetrically.

Sequence similarities

Belongs to the helicase family. AddA subfamily.

Contains 1 uvrD-like helicase ATP-binding domain.

Contains 1 uvrD-like helicase C-terminal domain.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 12321232ATP-dependent helicase/nuclease subunit A HAMAP-Rule MF_01451
PRO_0000064449

Regions

Domain9 – 481473UvrD-like helicase ATP-binding
Domain508 – 798291UvrD-like helicase C-terminal
Nucleotide binding30 – 378ATP Potential

Experimental info

Mutagenesis361K → A: Loss of helicase and nuclease activity. DNA-binding is unaltered. Ref.10
Mutagenesis11721D → A: Some loss of nuclease activity, helicase and DNA-binding are unaltered. No production of chi fragments; when associated with A-961 in AddB nearly complete loss of nuclease activity. Ref.10
Sequence conflict7801A → G in AAA22201. Ref.1
Sequence conflict7801A → G in CAA74482. Ref.2

Secondary structure

................................................................................................................................................................................................................. 1232
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P23478 [UniParc].

Last modified June 16, 2009. Version 2.
Checksum: 2A1B70FA4E645FE4

FASTA1,232141,087
        10         20         30         40         50         60 
MNIPKPADST WTDDQWNAIV STGQDILVAA AAGSGKTAVL VERMIRKITA EENPIDVDRL 

        70         80         90        100        110        120 
LVVTFTNASA AEMKHRIAEA LEKELVQRPG SLHIRRQLSL LNRASISTLH SFCLQVLKKY 

       130        140        150        160        170        180 
YYLIDLDPGF RIADQTEGEL IGDEVLDELF EDEYAKGEKA FFELVDRYTT DRHDLDLQFL 

       190        200        210        220        230        240 
VKQVYEYSRS HPNPEAWLES FVHLYDVSEK SAIEELPFYQ YVKEDIAMVL NGAKEKLLRA 

       250        260        270        280        290        300 
LELTKAPGGP APRADNFLDD LAQIDELIQH QDDFSELYKR VPAVSFKRAK AVKGDEFDPA 

       310        320        330        340        350        360 
LLDEATDLRN GAKKLLEKLK TDYFTRSPEQ HLKSLAEMKP VIETLVQLVI SYGKRFEAAK 

       370        380        390        400        410        420 
QEKSIIDFSD LEHYCLAILT AENDKGEREP SEAARFYQEQ FHEVLVDEYQ DTNLVQESIL 

       430        440        450        460        470        480 
QLVTSGPEET GNLFMVGDVK QSIYRFRLAE PLLFLSKYKR FTESGEGTGR KIDLNKNFRS 

       490        500        510        520        530        540 
RADILDSTNF LFKQLMGGKI GEVDYDEQAE LKLGAAYPDN DETETELLLI DNAEDTDASE 

       550        560        570        580        590        600 
EAEELETVQF EAKAIAKEIR KLISSPFKVY DGKKKTHRNI QYRDIVILLR SMPWAPQIME 

       610        620        630        640        650        660 
ELRAQGIPVY ANLTSGYFEA VEVAVALSVL KVIDNPYQDI PLASVLRSPI VGADENELSL 

       670        680        690        700        710        720 
IRLENKKAPY YEAMKDYLAA GDRSDELYQK LNTFYGHLQK WRAFSKNHSV SELIWEVYRD 

       730        740        750        760        770        780 
TKYMDYVGGM PGGKQRQANL RVLYDRARQY ESTAFRGLFR FLRFIERMQE RGDDLGTARA 

       790        800        810        820        830        840 
LSEQEDVVRL MTIHSSKGLE FPVVFVAGLG RNFNMMDLNK SYLLDKELGF GTKYIHPQLR 

       850        860        870        880        890        900 
ISYPTLPLIA MKKKMRRELL SEELRVLYVA LTRAKEKLFL IGSCKDHQKQ LAKWQASASQ 

       910        920        930        940        950        960 
TDWLLPEFDR YQARTYLDFI GPALARHRDL GDLAGVPAHA DISGHPARFA VQMIHSYDLL 

       970        980        990       1000       1010       1020 
DDDLEERMEE KSERLEAIRR GEPVPGSFAF DEKAREQLSW TYPHQEVTQI RTKQSVSEIK 

      1030       1040       1050       1060       1070       1080 
RKREYEDEYS GRAPVKPADG SILYRRPAFM MKKGLTAAEK GTAMHTVMQH IPLSHVPSIE 

      1090       1100       1110       1120       1130       1140 
EAEQTVHRLY EKELLTEEQK DAIDIEEIVQ FFHTEIGGQL IGAKWKDREI PFSLALPAKE 

      1150       1160       1170       1180       1190       1200 
IYPDAHEADE PLLVQGIIDC LYETEDGLYL LDYKSDRIEG KFQHGFEGAA PILKKRYETQ 

      1210       1220       1230 
IQLYTKAVEQ IAKTKVKGCA LYFFDGGHIL TL 

« Hide

References

« Hide 'large scale' references
[1]"Cloning, sequencing, and expression of Bacillus subtilis genes involved in ATP-dependent nuclease synthesis."
Kooistra J., Venema G.
J. Bacteriol. 173:3644-3655(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: OG1.
[2]"The 172 kb prkA-addAB region from 83 degrees to 97 degrees of the Bacillus subtilis chromosome contains several dysfunctional genes, the glyB marker, many genes encoding transporter proteins, and the ubiquitous hit gene."
Noback M.A., Holsappel S., Kiewiet R., Terpstra P., Wambutt R., Wedler H., Venema G., Bron S.
Microbiology 144:859-875(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: 168.
[3]"The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V. expand/collapse author list , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: 168.
[4]"From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later."
Barbe V., Cruveiller S., Kunst F., Lenoble P., Meurice G., Sekowska A., Vallenet D., Wang T., Moszer I., Medigue C., Danchin A.
Microbiology 155:1758-1775(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: SEQUENCE REVISION TO 780.
[5]"Sequencing of regions downstream of addA (98 degrees) and citG (289 degrees) in Bacillus subtilis."
Medina N., Vannier F., Roche B., Autret S., Levine A., Seror S.J.
Microbiology 143:3305-3308(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1000-1232.
Strain: 168.
[6]"The Bacillus subtilis addAB genes are fully functional in Escherichia coli."
Kooistra J., Haijema B.J., Venema G.
Mol. Microbiol. 7:915-923(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBUNIT, FUNCTION IN E.COLI.
[7]"The Bacillus subtilis AddAB helicase/nuclease is regulated by its cognate Chi sequence in vitro."
Chedin F., Ehrlich S.D., Kowalczykowski S.C.
J. Mol. Biol. 298:7-20(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION AS AN EXONUCLEASE AND HELICASE, COFACTOR, ATP-DEPENDENCE.
[8]"Dynamic formation of RecA filaments at DNA double strand break repair centers in live cells."
Kidane D., Graumann P.L.
J. Cell Biol. 170:357-366(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: RECRUITS RECA TO DNA DOUBLE-STRAND BREAKS.
Strain: 168 / YB886 / BG214.
[9]"Recruitment of Bacillus subtilis RecN to DNA double-strand breaks in the absence of DNA end processing."
Sanchez H., Kidane D., Castillo Cozar M., Graumann P.L., Alonso J.C.
J. Bacteriol. 188:353-360(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: CHARACTERIZATION.
Strain: 168 / YB886 / BG214.
[10]"A dual-nuclease mechanism for DNA break processing by AddAB-type helicase-nucleases."
Yeeles J.T.P., Dillingham M.S.
J. Mol. Biol. 371:66-78(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, MUTAGENESIS OF LYS-36 AND ASP-1172.
[11]"An iron-sulfur cluster is essential for the binding of broken DNA by AddAB-type helicase-nucleases."
Yeeles J.T.P., Cammack R., Dillingham M.S.
J. Biol. Chem. 284:7746-7755(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBUNIT, DNA-BINDING.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
M63489 Genomic DNA. Translation: AAA22201.1.
Y14081 Genomic DNA. Translation: CAA74482.1.
AL009126 Genomic DNA. Translation: CAB12903.2.
Y09476 Genomic DNA. Translation: CAA70668.1.
PIRB39432.
RefSeqNP_388944.2. NC_000964.3.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3U44X-ray3.20A1-1232[»]
3U4QX-ray2.80A1-1232[»]
4CEHX-ray3.24A1-1232[»]
4CEIX-ray2.80A1-1232[»]
4CEJX-ray3.00A1-1232[»]
ProteinModelPortalP23478.
SMRP23478. Positions 11-79.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING224308.BSU10630.

Proteomic databases

PaxDbP23478.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaCAB12903; CAB12903; BSU10630.
GeneID939793.
KEGGbsu:BSU10630.
PATRIC18973828. VBIBacSub10457_1108.

Organism-specific databases

GenoListBSU10630. [Micado]

Phylogenomic databases

eggNOGCOG1074.
HOGENOMHOG000015621.
KOK16898.
OrthoDBEOG6HJ22G.
PhylomeDBP23478.

Enzyme and pathway databases

BioCycBSUB:BSU10630-MONOMER.

Family and domain databases

Gene3D3.40.50.300. 4 hits.
3.90.320.10. 1 hit.
HAMAPMF_01451. AddA.
InterProIPR014152. DNA_helicase_suAddA.
IPR014017. DNA_helicase_UvrD-like_C.
IPR000212. DNA_helicase_UvrD/REP.
IPR011604. Exonuc_phg/RecB_C.
IPR027417. P-loop_NTPase.
IPR011335. Restrct_endonuc-II-like.
IPR014016. UvrD-like_ATP-bd.
[Graphical view]
PANTHERPTHR11070. PTHR11070. 1 hit.
PfamPF00580. UvrD-helicase. 1 hit.
PF13361. UvrD_C. 1 hit.
[Graphical view]
SUPFAMSSF52540. SSF52540. 3 hits.
SSF52980. SSF52980. 1 hit.
TIGRFAMsTIGR02785. addA_Gpos. 1 hit.
PROSITEPS51198. UVRD_HELICASE_ATP_BIND. 1 hit.
PS51217. UVRD_HELICASE_CTER. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameADDA_BACSU
AccessionPrimary (citable) accession number: P23478
Entry history
Integrated into UniProtKB/Swiss-Prot: November 1, 1991
Last sequence update: June 16, 2009
Last modified: July 9, 2014
This is version 113 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Bacillus subtilis

Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList