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P23477

- ADDB_BACSU

UniProt

P23477 - ADDB_BACSU

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Protein

ATP-dependent helicase/deoxyribonuclease subunit B

Gene

addB

Organism
Bacillus subtilis (strain 168)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

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.3 Publications

Catalytic activityi

ATP + H2O = ADP + phosphate.

Cofactori

Binds 1 4Fe-4S cluster.1 Publication
Magnesium. At low magnesium concentrations there is no nuclease activity, but helicase activity is unaffected.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi801 – 8011Iron-sulfur (4Fe-4S)
Metal bindingi1121 – 11211Iron-sulfur (4Fe-4S)
Metal bindingi1124 – 11241Iron-sulfur (4Fe-4S)
Metal bindingi1130 – 11301Iron-sulfur (4Fe-4S)

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi8 – 158ATPSequence Analysis

GO - Molecular functioni

  1. 4 iron, 4 sulfur cluster binding Source: UniProtKB-KW
  2. 5'-3' exonuclease activity Source: UniProtKB-HAMAP
  3. ATP binding Source: UniProtKB-HAMAP
  4. double-stranded DNA binding Source: UniProtKB-HAMAP
  5. helicase activity Source: UniProtKB-HAMAP
  6. metal ion binding Source: UniProtKB-KW

GO - Biological processi

  1. double-strand break repair via homologous recombination Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Exonuclease, Hydrolase, Nuclease

Keywords - Biological processi

DNA damage, DNA repair

Keywords - Ligandi

4Fe-4S, ATP-binding, DNA-binding, Iron, Iron-sulfur, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciBSUB:BSU10620-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
ATP-dependent helicase/deoxyribonuclease subunit B (EC:3.1.-.-, EC:3.6.4.12)
Alternative name(s):
ATP-dependent helicase/nuclease AddB
Gene namesi
Name:addB
Ordered Locus Names:BSU10620
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
ProteomesiUP000001570: Chromosome

Organism-specific databases

GenoListiBSU10620. [Micado]

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi801 – 8011C → A: Loss of iron-sulfur group binding, loss of DNA-binding. 1 Publication
Mutagenesisi961 – 9611D → 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. 1 Publication
Mutagenesisi1121 – 11211C → A: Loss of iron-sulfur group binding, loss of DNA-binding. 1 Publication
Mutagenesisi1124 – 11241C → A: Loss of iron-sulfur group binding, loss of DNA-binding. 1 Publication
Mutagenesisi1130 – 11301C → A: Loss of iron-sulfur group binding, loss of DNA-binding. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 11661166ATP-dependent helicase/deoxyribonuclease subunit BPRO_0000064450Add
BLAST

Proteomic databases

PaxDbiP23477.
PRIDEiP23477.

Interactioni

Subunit structurei

Heterodimer of AddA and AddB.2 Publications

Protein-protein interaction databases

DIPiDIP-60826N.
IntActiP23477. 1 interaction.
STRINGi224308.BSU10620.

Structurei

Secondary structure

1
1166
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 86
Helixi14 – 2815
Beta strandi35 – 384
Helixi41 – 433
Helixi44 – 518
Turni55 – 573
Beta strandi58 – 669
Helixi68 – 7912
Helixi89 – 10214
Helixi103 – 1064
Turni110 – 1134
Beta strandi114 – 1163
Helixi118 – 13215
Helixi137 – 1448
Helixi155 – 17521
Turni177 – 1793
Helixi183 – 1853
Helixi186 – 1938
Turni194 – 1963
Helixi198 – 2003
Beta strandi204 – 2074
Helixi215 – 22713
Beta strandi229 – 2368
Beta strandi242 – 2443
Beta strandi248 – 2514
Helixi253 – 26816
Beta strandi273 – 2786
Turni283 – 2864
Helixi288 – 2958
Beta strandi296 – 2983
Beta strandi310 – 31910
Helixi320 – 33617
Helixi342 – 3443
Beta strandi345 – 3506
Helixi352 – 3543
Helixi356 – 36510
Beta strandi370 – 3745
Helixi382 – 39514
Helixi400 – 4078
Turni408 – 4103
Beta strandi411 – 4133
Beta strandi415 – 4173
Helixi419 – 43618
Helixi441 – 4444
Beta strandi445 – 4473
Beta strandi457 – 4593
Helixi465 – 49430
Helixi498 – 51114
Helixi514 – 52714
Helixi531 – 55424
Helixi562 – 57514
Beta strandi584 – 5863
Beta strandi588 – 5958
Beta strandi602 – 6076
Turni611 – 6166
Beta strandi622 – 6243
Helixi626 – 6349
Helixi645 – 65814
Beta strandi662 – 67211
Beta strandi674 – 6763
Helixi683 – 6919
Beta strandi698 – 7003
Helixi704 – 7063
Helixi709 – 7124
Helixi713 – 7153
Helixi719 – 73416
Helixi742 – 7509
Helixi756 – 7638
Turni764 – 7674
Helixi777 – 7837
Beta strandi786 – 7883
Helixi792 – 8009
Helixi802 – 8087
Helixi824 – 84320
Helixi848 – 8503
Helixi853 – 86715
Helixi868 – 8703
Turni872 – 8743
Helixi875 – 8784
Helixi880 – 90425
Beta strandi910 – 92415
Beta strandi927 – 9315
Turni932 – 9343
Beta strandi935 – 95117
Beta strandi954 – 96613
Helixi971 – 9755
Helixi981 – 99717
Beta strandi1001 – 101010
Helixi1024 – 103310
Beta strandi1037 – 10426
Helixi1045 – 10517
Beta strandi1056 – 10594
Beta strandi1061 – 10644
Beta strandi1071 – 10733
Helixi1082 – 110423
Beta strandi1113 – 11153
Helixi1121 – 11233
Helixi1127 – 11304
Beta strandi1134 – 11363
Helixi1149 – 115911

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3U44X-ray3.20B1-1166[»]
3U4QX-ray2.80B1-1166[»]
4CEHX-ray3.24B1-1166[»]
4CEIX-ray2.80B1-1166[»]
4CEJX-ray3.00B1-1166[»]
ProteinModelPortaliP23477.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 278278UvrD-like helicase ATP-bindingAdd
BLAST
Domaini281 – 586306UvrD-like helicase C-terminalAdd
BLAST

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG3857.
HOGENOMiHOG000285805.
KOiK16899.
OrthoDBiEOG6DC6FN.
PhylomeDBiP23477.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
HAMAPiMF_01452. AddB_type1.
InterProiIPR014140. DNA_helicase_suAddB.
IPR014017. DNA_helicase_UvrD-like_C.
IPR027417. P-loop_NTPase.
[Graphical view]
PfamiPF13361. UvrD_C. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
TIGRFAMsiTIGR02773. addB_Gpos. 1 hit.
PROSITEiPS51198. UVRD_HELICASE_ATP_BIND. 1 hit.
PS51217. UVRD_HELICASE_CTER. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P23477-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MGAEFLVGRS GSGKTKLIIN SIQDELRRAP FGKPIIFLVP DQMTFLMEYE
60 70 80 90 100
LAKTPDMGGM IRAQVFSFSR LAWRVLQHTG GMSRPFLTST GVQMLLRKLI
110 120 130 140 150
EEHKQEFKVY QKASDKSGFT AQVERMLTEF KRYCLEPEDI RRMAESGTAS
160 170 180 190 200
EYRGERVLSE KLHDLSILYQ QMEKSLADQY LHSEDYLTLL AEHIPLAEDI
210 220 230 240 250
KGAHIYVDGF YQFTPQEFRV LEQLMVHAEH ITFSLTADKP SYEREPHELE
260 270 280 290 300
LFRMTGKTYY RLHQKAKELN LDITYKELSG TERHTKTPEL AHLEAQYEAR
310 320 330 340 350
PAIPYAEKQE ALTVMQAANR RAELEGIARE IHALVREKGY RYKDVAILAR
360 370 380 390 400
QPEDYKDMVK EVFADYEIPY FIDGKASMLN HPLIEFIRSS LDVLKGNWRY
410 420 430 440 450
EAVFRCVKTE LLFPLNEPKA KVREQVDQLE NYCIAYGIKG DRWTKGDRFQ
460 470 480 490 500
YRRFVSLDDD FAQTDQEIEM ENMLNDTRDW IVPPLFQLQK RMKKAKTVQE
510 520 530 540 550
KAEALYRYLE ETDVPLKLDQ ERQRAEDDGR IIEAQQHQQA WDAVIQLLEE
560 570 580 590 600
FVEMMGDDEI SLDLFQQMIE AGAESLTFSL IPPALDQVFV GNMDLSRMYG
610 620 630 640 650
TSCTFVLGAN DGVLPARPDE NGVLSDDDRE WLKTIGVELS SGGRERLLDE
660 670 680 690 700
HFLIYMAFSS PSDRLYVSYP IADAEGKTLL PSMIVKRLEE LFPHHKERLL
710 720 730 740 750
TNEPEQVSDE EQLMYVVNKS VAQSFTASQL RLWTREYDIS DVWWSTYNVL
760 770 780 790 800
MSEQDRLQSK KLFSSLFFRN EVKQLERSVS RQLYGERIQG SVSRMETFNA
810 820 830 840 850
CPFSHFASHG LHLKERQFFK LEAPDIGQLF HSSLKLISDR LREQKLDWRD
860 870 880 890 900
LTKEQCELFS YDAVERLAPK LQKEILLSSN RHYYVKEKLQ KIVTRVSGIL
910 920 930 940 950
SEHAKASGFV PIGLELGFGG KGPLPPLTFQ LKNGCTMELV GRIDRVDKAE
960 970 980 990 1000
SSKGLLLRIV DYKSSDKGLD LAEVYYGLAL QMLTYLDLSI THSADWLGMR
1010 1020 1030 1040 1050
ATPAGVLYFH IHDPMIQSNL PLGLDEIEQE IFKKFKMKGL LLGDQEVVRL
1060 1070 1080 1090 1100
MDTTLQEGRS NIINAGLKKD GSLRSDSAAV GEKEFDLLTK HVRRTFQEAG
1110 1120 1130 1140 1150
EQITDGRVSI EPYKMKNKTP CTYCAFKSVC QFDESLEENE YRPLKAEKDK
1160
TILEWIKKEA DGNEHS
Length:1,166
Mass (Da):134,645
Last modified:June 16, 2009 - v2
Checksum:iFA63593585A4CA73
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti843 – 8442EQ → DE in AAA22200. (PubMed:1646786)Curated
Sequence conflicti843 – 8442EQ → DE in CAA74481. (PubMed:9579061)Curated

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M63489 Genomic DNA. Translation: AAA22200.1.
Y14081 Genomic DNA. Translation: CAA74481.1.
AL009126 Genomic DNA. Translation: CAB12902.2.
PIRiA39432.
RefSeqiNP_388943.2. NC_000964.3.

Genome annotation databases

EnsemblBacteriaiCAB12902; CAB12902; BSU10620.
GeneIDi936341.
KEGGibsu:BSU10620.
PATRICi18973826. VBIBacSub10457_1107.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M63489 Genomic DNA. Translation: AAA22200.1 .
Y14081 Genomic DNA. Translation: CAA74481.1 .
AL009126 Genomic DNA. Translation: CAB12902.2 .
PIRi A39432.
RefSeqi NP_388943.2. NC_000964.3.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
3U44 X-ray 3.20 B 1-1166 [» ]
3U4Q X-ray 2.80 B 1-1166 [» ]
4CEH X-ray 3.24 B 1-1166 [» ]
4CEI X-ray 2.80 B 1-1166 [» ]
4CEJ X-ray 3.00 B 1-1166 [» ]
ProteinModelPortali P23477.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-60826N.
IntActi P23477. 1 interaction.
STRINGi 224308.BSU10620.

Proteomic databases

PaxDbi P23477.
PRIDEi P23477.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai CAB12902 ; CAB12902 ; BSU10620 .
GeneIDi 936341.
KEGGi bsu:BSU10620.
PATRICi 18973826. VBIBacSub10457_1107.

Organism-specific databases

GenoListi BSU10620. [Micado ]

Phylogenomic databases

eggNOGi COG3857.
HOGENOMi HOG000285805.
KOi K16899.
OrthoDBi EOG6DC6FN.
PhylomeDBi P23477.

Enzyme and pathway databases

BioCyci BSUB:BSU10620-MONOMER.

Family and domain databases

Gene3Di 3.40.50.300. 2 hits.
HAMAPi MF_01452. AddB_type1.
InterProi IPR014140. DNA_helicase_suAddB.
IPR014017. DNA_helicase_UvrD-like_C.
IPR027417. P-loop_NTPase.
[Graphical view ]
Pfami PF13361. UvrD_C. 1 hit.
[Graphical view ]
SUPFAMi SSF52540. SSF52540. 1 hit.
TIGRFAMsi TIGR02773. addB_Gpos. 1 hit.
PROSITEi PS51198. UVRD_HELICASE_ATP_BIND. 1 hit.
PS51217. UVRD_HELICASE_CTER. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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.
    , 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.

Entry informationi

Entry nameiADDB_BACSU
AccessioniPrimary (citable) accession number: P23477
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1991
Last sequence update: June 16, 2009
Last modified: October 1, 2014
This is version 112 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

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

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3