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Protein

ATP-dependent helicase/deoxyribonuclease subunit B

Gene

addB

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: 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

Protein has several cofactor binding sites:
  • [4Fe-4S] cluster1 PublicationNote: Binds 1 [4Fe-4S] cluster.1 Publication
  • Mg2+1 PublicationNote: At low magnesium concentrations there is no nuclease activity, but helicase activity is unaffected.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi801Iron-sulfur (4Fe-4S)1
Metal bindingi1121Iron-sulfur (4Fe-4S)1
Metal bindingi1124Iron-sulfur (4Fe-4S)1
Metal bindingi1130Iron-sulfur (4Fe-4S)1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi8 – 15ATPSequence analysis8

GO - Molecular functioni

GO - Biological processi

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
Proteomesi
  • UP000001570 Componenti: Chromosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi801C → A: Loss of iron-sulfur group binding, loss of DNA-binding. 1 Publication1
Mutagenesisi961D → 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 Publication1
Mutagenesisi1121C → A: Loss of iron-sulfur group binding, loss of DNA-binding. 1 Publication1
Mutagenesisi1124C → A: Loss of iron-sulfur group binding, loss of DNA-binding. 1 Publication1
Mutagenesisi1130C → A: Loss of iron-sulfur group binding, loss of DNA-binding. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000644501 – 1166ATP-dependent helicase/deoxyribonuclease subunit BAdd BLAST1166

Proteomic databases

PaxDbiP23477.
PRIDEiP23477.

Interactioni

Subunit structurei

Heterodimer of AddA and AddB.2 Publications

Protein-protein interaction databases

DIPiDIP-60826N.
IntActiP23477. 2 interactors.
STRINGi224308.Bsubs1_010100005876.

Structurei

Secondary structure

11166
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 8Combined sources6
Helixi14 – 28Combined sources15
Beta strandi35 – 38Combined sources4
Helixi41 – 43Combined sources3
Helixi44 – 51Combined sources8
Turni55 – 57Combined sources3
Beta strandi58 – 66Combined sources9
Helixi68 – 79Combined sources12
Helixi89 – 102Combined sources14
Helixi103 – 106Combined sources4
Turni110 – 113Combined sources4
Beta strandi114 – 116Combined sources3
Helixi118 – 132Combined sources15
Helixi137 – 144Combined sources8
Helixi155 – 175Combined sources21
Turni177 – 179Combined sources3
Helixi183 – 185Combined sources3
Helixi186 – 193Combined sources8
Turni194 – 196Combined sources3
Helixi198 – 200Combined sources3
Beta strandi204 – 207Combined sources4
Helixi215 – 227Combined sources13
Beta strandi229 – 236Combined sources8
Beta strandi242 – 244Combined sources3
Beta strandi248 – 251Combined sources4
Helixi253 – 268Combined sources16
Beta strandi273 – 278Combined sources6
Turni283 – 286Combined sources4
Helixi288 – 295Combined sources8
Beta strandi296 – 298Combined sources3
Beta strandi310 – 319Combined sources10
Helixi320 – 336Combined sources17
Helixi342 – 344Combined sources3
Beta strandi345 – 350Combined sources6
Helixi352 – 354Combined sources3
Helixi356 – 365Combined sources10
Beta strandi370 – 374Combined sources5
Helixi382 – 395Combined sources14
Helixi400 – 407Combined sources8
Turni408 – 410Combined sources3
Beta strandi411 – 413Combined sources3
Beta strandi415 – 417Combined sources3
Helixi419 – 436Combined sources18
Helixi441 – 444Combined sources4
Beta strandi445 – 447Combined sources3
Beta strandi457 – 459Combined sources3
Helixi465 – 494Combined sources30
Helixi498 – 511Combined sources14
Helixi514 – 527Combined sources14
Helixi531 – 554Combined sources24
Helixi562 – 575Combined sources14
Beta strandi584 – 586Combined sources3
Beta strandi588 – 595Combined sources8
Beta strandi602 – 607Combined sources6
Turni611 – 616Combined sources6
Beta strandi622 – 624Combined sources3
Helixi626 – 634Combined sources9
Helixi645 – 658Combined sources14
Beta strandi662 – 672Combined sources11
Beta strandi674 – 676Combined sources3
Helixi683 – 691Combined sources9
Beta strandi698 – 700Combined sources3
Helixi704 – 706Combined sources3
Helixi709 – 712Combined sources4
Helixi713 – 715Combined sources3
Helixi719 – 734Combined sources16
Helixi742 – 750Combined sources9
Helixi756 – 763Combined sources8
Turni764 – 767Combined sources4
Helixi777 – 783Combined sources7
Beta strandi786 – 788Combined sources3
Helixi792 – 800Combined sources9
Helixi802 – 808Combined sources7
Helixi824 – 843Combined sources20
Helixi848 – 850Combined sources3
Helixi853 – 867Combined sources15
Helixi868 – 870Combined sources3
Turni872 – 874Combined sources3
Helixi875 – 878Combined sources4
Helixi880 – 904Combined sources25
Beta strandi910 – 924Combined sources15
Beta strandi927 – 931Combined sources5
Turni932 – 934Combined sources3
Beta strandi935 – 951Combined sources17
Beta strandi954 – 966Combined sources13
Helixi971 – 975Combined sources5
Helixi981 – 997Combined sources17
Beta strandi1001 – 1010Combined sources10
Helixi1024 – 1033Combined sources10
Beta strandi1037 – 1042Combined sources6
Helixi1045 – 1051Combined sources7
Beta strandi1056 – 1059Combined sources4
Beta strandi1061 – 1064Combined sources4
Beta strandi1071 – 1073Combined sources3
Helixi1082 – 1104Combined sources23
Beta strandi1113 – 1115Combined sources3
Helixi1121 – 1123Combined sources3
Helixi1127 – 1130Combined sources4
Beta strandi1134 – 1136Combined sources3
Helixi1149 – 1159Combined sources11

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3U44X-ray3.20B1-1166[»]
3U4QX-ray2.80B1-1166[»]
4CEHX-ray3.24B1-1166[»]
4CEIX-ray2.80B1-1166[»]
4CEJX-ray3.00B1-1166[»]
ProteinModelPortaliP23477.
SMRiP23477.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini1 – 278UvrD-like helicase ATP-bindingAdd BLAST278
Domaini281 – 586UvrD-like helicase C-terminalAdd BLAST306

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG3857. LUCA.
HOGENOMiHOG000285805.
KOiK16899.
OMAiDYKSSAK.
PhylomeDBiP23477.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
HAMAPiMF_01452. AddB_type1. 1 hit.
InterProiIPR014140. DNA_helicase_suAddB.
IPR014017. DNA_helicase_UvrD-like_C.
IPR027417. P-loop_NTPase.
[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)DescriptionActionsGraphical viewLength
Sequence conflicti843 – 844EQ → DE in AAA22200 (PubMed:1646786).Curated2
Sequence conflicti843 – 844EQ → DE in CAA74481 (PubMed:9579061).Curated2

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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.
WP_003244988.1. NZ_JNCM01000035.1.

Genome annotation databases

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

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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.
WP_003244988.1. NZ_JNCM01000035.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3U44X-ray3.20B1-1166[»]
3U4QX-ray2.80B1-1166[»]
4CEHX-ray3.24B1-1166[»]
4CEIX-ray2.80B1-1166[»]
4CEJX-ray3.00B1-1166[»]
ProteinModelPortaliP23477.
SMRiP23477.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-60826N.
IntActiP23477. 2 interactors.
STRINGi224308.Bsubs1_010100005876.

Proteomic databases

PaxDbiP23477.
PRIDEiP23477.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Phylogenomic databases

eggNOGiCOG3857. LUCA.
HOGENOMiHOG000285805.
KOiK16899.
OMAiDYKSSAK.
PhylomeDBiP23477.

Enzyme and pathway databases

BioCyciBSUB:BSU10620-MONOMER.

Family and domain databases

Gene3Di3.40.50.300. 2 hits.
HAMAPiMF_01452. AddB_type1. 1 hit.
InterProiIPR014140. DNA_helicase_suAddB.
IPR014017. DNA_helicase_UvrD-like_C.
IPR027417. P-loop_NTPase.
[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]
ProtoNetiSearch...

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: November 2, 2016
This is version 124 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

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.