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P23477 (ADDB_BACSU) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 111. 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/deoxyribonuclease subunit B

EC=3.1.-.-
EC=3.6.4.12
Alternative name(s):
ATP-dependent helicase/nuclease AddB
Gene names
Name:addB
Ordered Locus Names:BSU10620
OrganismBacillus subtilis (strain 168) [Reference proteome] [HAMAP]
Taxonomic identifier224308 [NCBI]
Taxonomic lineageBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus

Protein attributes

Sequence length1166 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

The heterodimer acts as both an ATP-dependent DNA helicase and an ATP-dependent single-stranded exonuclease, acting in both directions. 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' to 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 AddB nuclease domain is not required for chi fragment generation; this subunit has 5' -> 3' nuclease activity. RecA thread formation during DNA double-strand break repair requires RecJ or AddAB. Ref.5 Ref.6 Ref.9

Catalytic activity

ATP + H2O = ADP + phosphate. HAMAP-Rule MF_01452

Cofactor

Binds 1 4Fe-4S cluster. Ref.6 Ref.10

Magnesium. At low magnesium concentrations there is no nuclease activity, but helicase activity is unaffected. Ref.6 Ref.10

Subunit structure

Heterodimer of AddA and AddB. Ref.5 Ref.10

Miscellaneous

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

Sequence similarities

Belongs to the helicase family. AddB/RexB type 1 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 – 11661166ATP-dependent helicase/deoxyribonuclease subunit B HAMAP-Rule MF_01452
PRO_0000064450

Regions

Domain1 – 278278UvrD-like helicase ATP-binding
Domain281 – 586306UvrD-like helicase C-terminal
Nucleotide binding8 – 158ATP Potential

Sites

Metal binding8011Iron-sulfur (4Fe-4S)
Metal binding11211Iron-sulfur (4Fe-4S)
Metal binding11241Iron-sulfur (4Fe-4S)
Metal binding11301Iron-sulfur (4Fe-4S)

Experimental info

Mutagenesis8011C → A: Loss of iron-sulfur group binding, loss of DNA-binding. Ref.10
Mutagenesis9611D → A: Some loss of nuclease activity, helicase and DNA-binding are unaltered; when associated with A-1172 in AddA nearly complete loss of nuclease activity. Ref.9
Mutagenesis11211C → A: Loss of iron-sulfur group binding, loss of DNA-binding. Ref.10
Mutagenesis11241C → A: Loss of iron-sulfur group binding, loss of DNA-binding. Ref.10
Mutagenesis11301C → A: Loss of iron-sulfur group binding, loss of DNA-binding. Ref.10
Sequence conflict843 – 8442EQ → DE in AAA22200. Ref.1
Sequence conflict843 – 8442EQ → DE in CAA74481. Ref.2

Secondary structure

....................................................................................................................................................................................... 1166
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P23477 [UniParc].

Last modified June 16, 2009. Version 2.
Checksum: FA63593585A4CA73

FASTA1,166134,645
        10         20         30         40         50         60 
MGAEFLVGRS GSGKTKLIIN SIQDELRRAP FGKPIIFLVP DQMTFLMEYE LAKTPDMGGM 

        70         80         90        100        110        120 
IRAQVFSFSR LAWRVLQHTG GMSRPFLTST GVQMLLRKLI EEHKQEFKVY QKASDKSGFT 

       130        140        150        160        170        180 
AQVERMLTEF KRYCLEPEDI RRMAESGTAS EYRGERVLSE KLHDLSILYQ QMEKSLADQY 

       190        200        210        220        230        240 
LHSEDYLTLL AEHIPLAEDI KGAHIYVDGF YQFTPQEFRV LEQLMVHAEH ITFSLTADKP 

       250        260        270        280        290        300 
SYEREPHELE LFRMTGKTYY RLHQKAKELN LDITYKELSG TERHTKTPEL AHLEAQYEAR 

       310        320        330        340        350        360 
PAIPYAEKQE ALTVMQAANR RAELEGIARE IHALVREKGY RYKDVAILAR QPEDYKDMVK 

       370        380        390        400        410        420 
EVFADYEIPY FIDGKASMLN HPLIEFIRSS LDVLKGNWRY EAVFRCVKTE LLFPLNEPKA 

       430        440        450        460        470        480 
KVREQVDQLE NYCIAYGIKG DRWTKGDRFQ YRRFVSLDDD FAQTDQEIEM ENMLNDTRDW 

       490        500        510        520        530        540 
IVPPLFQLQK RMKKAKTVQE KAEALYRYLE ETDVPLKLDQ ERQRAEDDGR IIEAQQHQQA 

       550        560        570        580        590        600 
WDAVIQLLEE FVEMMGDDEI SLDLFQQMIE AGAESLTFSL IPPALDQVFV GNMDLSRMYG 

       610        620        630        640        650        660 
TSCTFVLGAN DGVLPARPDE NGVLSDDDRE WLKTIGVELS SGGRERLLDE HFLIYMAFSS 

       670        680        690        700        710        720 
PSDRLYVSYP IADAEGKTLL PSMIVKRLEE LFPHHKERLL TNEPEQVSDE EQLMYVVNKS 

       730        740        750        760        770        780 
VAQSFTASQL RLWTREYDIS DVWWSTYNVL MSEQDRLQSK KLFSSLFFRN EVKQLERSVS 

       790        800        810        820        830        840 
RQLYGERIQG SVSRMETFNA CPFSHFASHG LHLKERQFFK LEAPDIGQLF HSSLKLISDR 

       850        860        870        880        890        900 
LREQKLDWRD LTKEQCELFS YDAVERLAPK LQKEILLSSN RHYYVKEKLQ KIVTRVSGIL 

       910        920        930        940        950        960 
SEHAKASGFV PIGLELGFGG KGPLPPLTFQ LKNGCTMELV GRIDRVDKAE SSKGLLLRIV 

       970        980        990       1000       1010       1020 
DYKSSDKGLD LAEVYYGLAL QMLTYLDLSI THSADWLGMR ATPAGVLYFH IHDPMIQSNL 

      1030       1040       1050       1060       1070       1080 
PLGLDEIEQE IFKKFKMKGL LLGDQEVVRL MDTTLQEGRS NIINAGLKKD GSLRSDSAAV 

      1090       1100       1110       1120       1130       1140 
GEKEFDLLTK HVRRTFQEAG EQITDGRVSI EPYKMKNKTP CTYCAFKSVC QFDESLEENE 

      1150       1160 
YRPLKAEKDK TILEWIKKEA DGNEHS 

« 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 844.
[5]"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.
[6]"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, MAGNESIUM COFACTOR, ATP-DEPENDENCE.
[7]"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.
[8]"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.
[9]"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 ASP-961.
[10]"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: COFACTOR, SUBUNIT, DNA-BINDING, MUTAGENESIS OF CYS-801; CYS-1121; CYS-1124 AND CYS-1130.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
M63489 Genomic DNA. Translation: AAA22200.1.
Y14081 Genomic DNA. Translation: CAA74481.1.
AL009126 Genomic DNA. Translation: CAB12902.2.
PIRA39432.
RefSeqNP_388943.2. NC_000964.3.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3U44X-ray3.20B1-1166[»]
3U4QX-ray2.80B1-1166[»]
4CEHX-ray3.24B1-1166[»]
4CEIX-ray2.80B1-1166[»]
4CEJX-ray3.00B1-1166[»]
ProteinModelPortalP23477.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

IntActP23477. 1 interaction.
STRING224308.BSU10620.

Proteomic databases

PaxDbP23477.
PRIDEP23477.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaCAB12902; CAB12902; BSU10620.
GeneID936341.
KEGGbsu:BSU10620.
PATRIC18973826. VBIBacSub10457_1107.

Organism-specific databases

GenoListBSU10620. [Micado]

Phylogenomic databases

eggNOGCOG3857.
HOGENOMHOG000285805.
KOK16899.
OrthoDBEOG6DC6FN.
PhylomeDBP23477.

Enzyme and pathway databases

BioCycBSUB:BSU10620-MONOMER.

Family and domain databases

Gene3D3.40.50.300. 2 hits.
HAMAPMF_01452. AddB_type1.
InterProIPR014140. DNA_helicase_suAddB.
IPR014017. DNA_helicase_UvrD-like_C.
IPR027417. P-loop_NTPase.
[Graphical view]
PfamPF13361. UvrD_C. 1 hit.
[Graphical view]
SUPFAMSSF52540. SSF52540. 1 hit.
TIGRFAMsTIGR02773. addB_Gpos. 1 hit.
PROSITEPS51198. UVRD_HELICASE_ATP_BIND. 1 hit.
PS51217. UVRD_HELICASE_CTER. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameADDB_BACSU
AccessionPrimary (citable) accession number: P23477
Entry history
Integrated into UniProtKB/Swiss-Prot: November 1, 1991
Last sequence update: June 16, 2009
Last modified: July 9, 2014
This is version 111 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