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Protein

2,3-dihydroxybenzoate-AMP ligase

Gene

dhbE

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Activation of the carboxylate group of 2,3-dihydroxy-benzoate (DHB), via ATP-dependent PPi exchange reactions, to the acyladenylate.

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei240 – 2401Substrate
Binding sitei329 – 3291ATP; via carbonyl oxygen
Binding sitei413 – 4131ATP
Binding sitei428 – 4281ATP
Binding sitei519 – 5191ATP
Binding sitei519 – 5191Substrate

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi191 – 1922ATP
Nucleotide bindingi307 – 3093ATP

GO - Molecular functioni

  1. (2,3-dihydroxybenzoyl)adenylate synthase activity Source: InterPro
  2. ATP binding Source: UniProtKB-KW
  3. ligase activity Source: UniProtKB-KW

GO - Biological processi

  1. siderophore biosynthetic process Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciBSUB:BSU31980-MONOMER.
MetaCyc:MONOMER-13920.
SABIO-RKP40871.
UniPathwayiUPA00013.

Names & Taxonomyi

Protein namesi
Recommended name:
2,3-dihydroxybenzoate-AMP ligase (EC:6.3.2.-)
Alternative name(s):
Dihydroxybenzoic acid-activating enzyme
Gene namesi
Name:dhbE
Synonyms:entE
Ordered Locus Names:BSU31980
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
ProteomesiUP000001570 Componenti: Chromosome

Organism-specific databases

GenoListiBSU31980. [Micado]

Subcellular locationi

Cytoplasm Curated

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 5395392,3-dihydroxybenzoate-AMP ligasePRO_0000193074Add
BLAST

Proteomic databases

PaxDbiP40871.

Interactioni

Protein-protein interaction databases

IntActiP40871. 1 interaction.
MINTiMINT-8366125.
STRINGi224308.BSU31980.

Structurei

Secondary structure

1
539
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi10 – 189Combined sources
Helixi27 – 3812Combined sources
Beta strandi41 – 466Combined sources
Beta strandi49 – 524Combined sources
Helixi53 – 7018Combined sources
Beta strandi77 – 804Combined sources
Beta strandi84 – 863Combined sources
Helixi87 – 9812Combined sources
Beta strandi101 – 1044Combined sources
Helixi111 – 12010Combined sources
Beta strandi124 – 1329Combined sources
Helixi137 – 14711Combined sources
Beta strandi154 – 1585Combined sources
Beta strandi163 – 1653Combined sources
Helixi166 – 1683Combined sources
Beta strandi183 – 1897Combined sources
Beta strandi193 – 1964Combined sources
Beta strandi199 – 2035Combined sources
Helixi204 – 21815Combined sources
Beta strandi225 – 2284Combined sources
Helixi235 – 2395Combined sources
Helixi242 – 2487Combined sources
Beta strandi252 – 2554Combined sources
Beta strandi257 – 2604Combined sources
Helixi261 – 27111Combined sources
Beta strandi274 – 2785Combined sources
Helixi280 – 29213Combined sources
Beta strandi302 – 3087Combined sources
Helixi312 – 3154Combined sources
Helixi318 – 3214Combined sources
Beta strandi324 – 3318Combined sources
Beta strandi337 – 3393Combined sources
Beta strandi342 – 3443Combined sources
Helixi346 – 3516Combined sources
Beta strandi355 – 3584Combined sources
Beta strandi362 – 3665Combined sources
Beta strandi379 – 3846Combined sources
Helixi396 – 4027Combined sources
Beta strandi409 – 4179Combined sources
Beta strandi419 – 4213Combined sources
Beta strandi423 – 4286Combined sources
Helixi429 – 4313Combined sources
Beta strandi433 – 4353Combined sources
Beta strandi438 – 4403Combined sources
Helixi442 – 4498Combined sources
Beta strandi455 – 46511Combined sources
Turni466 – 4683Combined sources
Beta strandi469 – 48113Combined sources
Helixi485 – 49410Combined sources
Helixi499 – 5013Combined sources
Beta strandi504 – 5085Combined sources
Helixi522 – 53413Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1MD9X-ray2.80A1-539[»]
1MDBX-ray2.15A1-539[»]
1MDFX-ray2.50A1-539[»]
ProteinModelPortaliP40871.
SMRiP40871. Positions 1-536.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP40871.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni234 – 2352Substrate binding

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG1021.
HOGENOMiHOG000230011.
InParanoidiP40871.
KOiK02363.
OMAiPWPDELA.
OrthoDBiEOG600DJW.
PhylomeDBiP40871.

Family and domain databases

InterProiIPR025110. AMP-bd_C.
IPR020845. AMP-binding_CS.
IPR000873. AMP-dep_Synth/Lig.
IPR011963. DHB_AMP_lig.
[Graphical view]
PfamiPF00501. AMP-binding. 1 hit.
PF13193. AMP-binding_C. 1 hit.
[Graphical view]
TIGRFAMsiTIGR02275. DHB_AMP_lig. 1 hit.
PROSITEiPS00455. AMP_BINDING. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P40871-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLKGFTPWPD ELAETYRKNG CWAGETFGDL LRDRAAKYGD RIAITCGNTH
60 70 80 90 100
WSYRELDTRA DRLAAGFQKL GIQQMDRVVV QLPNIKEFFE VIFALFRLGA
110 120 130 140 150
LPVFALPSHR SSEITYFCEF AEAAAYIIPD AYSGFDYRSL ARQVQSKLPT
160 170 180 190 200
LKNIIVAGEA EEFLPLEDLH AEPVKLPEVK SSDVAFLQLS GGSTGLSKLI
210 220 230 240 250
PRTHDDYIYS LKRSVEVCWL DHSTVYLAAL PMAHNYPLSS PGVLGVLYAG
260 270 280 290 300
GRVVLSPSPS PDDAFPLIER EKVTITALVP PLAMVWMDAA SSRRDDLSSL
310 320 330 340 350
QVLQVGGAKF SAEAARRVKA VFGCTLQQVF GMAEGLVNYT RLDDPEEIIV
360 370 380 390 400
NTQGKPMSPY DEMRVWDDHD RDVKPGETGH LLTRGPYTIR GYYKAEEHNA
410 420 430 440 450
ASFTEDGFYR TGDIVRLTRD GYIVVEGRAK DQINRGGEKV AAEEVENHLL
460 470 480 490 500
AHPAVHDAAM VSMPDQFLGE RSCVFIIPRD EAPKAAELKA FLRERGLAAY
510 520 530
KIPDRVEFVE SFPQTGVGKV SKKALREAIS EKLLAGFKK
Length:539
Mass (Da):59,928
Last modified:October 31, 1995 - v2
Checksum:i027D286940B192F8
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti360 – 3601Y → I in AAA79759 (PubMed:8224884).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U26444 Genomic DNA. Translation: AAC44632.1.
AL009126 Genomic DNA. Translation: CAB15188.1.
L08645 Genomic DNA. Translation: AAA79759.1.
PIRiD69615.
RefSeqiNP_391078.1. NC_000964.3.
WP_003243083.1. NZ_JNCM01000033.1.

Genome annotation databases

EnsemblBacteriaiCAB15188; CAB15188; BSU31980.
GeneIDi936509.
KEGGibsu:BSU31980.
PATRICi18978368. VBIBacSub10457_3347.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U26444 Genomic DNA. Translation: AAC44632.1.
AL009126 Genomic DNA. Translation: CAB15188.1.
L08645 Genomic DNA. Translation: AAA79759.1.
PIRiD69615.
RefSeqiNP_391078.1. NC_000964.3.
WP_003243083.1. NZ_JNCM01000033.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1MD9X-ray2.80A1-539[»]
1MDBX-ray2.15A1-539[»]
1MDFX-ray2.50A1-539[»]
ProteinModelPortaliP40871.
SMRiP40871. Positions 1-536.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP40871. 1 interaction.
MINTiMINT-8366125.
STRINGi224308.BSU31980.

Proteomic databases

PaxDbiP40871.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB15188; CAB15188; BSU31980.
GeneIDi936509.
KEGGibsu:BSU31980.
PATRICi18978368. VBIBacSub10457_3347.

Organism-specific databases

GenoListiBSU31980. [Micado]

Phylogenomic databases

eggNOGiCOG1021.
HOGENOMiHOG000230011.
InParanoidiP40871.
KOiK02363.
OMAiPWPDELA.
OrthoDBiEOG600DJW.
PhylomeDBiP40871.

Enzyme and pathway databases

UniPathwayiUPA00013.
BioCyciBSUB:BSU31980-MONOMER.
MetaCyc:MONOMER-13920.
SABIO-RKP40871.

Miscellaneous databases

EvolutionaryTraceiP40871.

Family and domain databases

InterProiIPR025110. AMP-bd_C.
IPR020845. AMP-binding_CS.
IPR000873. AMP-dep_Synth/Lig.
IPR011963. DHB_AMP_lig.
[Graphical view]
PfamiPF00501. AMP-binding. 1 hit.
PF13193. AMP-binding_C. 1 hit.
[Graphical view]
TIGRFAMsiTIGR02275. DHB_AMP_lig. 1 hit.
PROSITEiPS00455. AMP_BINDING. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Sequence and genetic organization of a Bacillus subtilis operon encoding 2,3-dihydroxybenzoate biosynthetic enzymes."
    Rowland B.M., Grossman T.H., Osburne M.S., Taber H.W.
    Gene 178:119-123(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 168 / Marburg / ATCC 6051 / DSM 10 / JCM 1465 / NBRC 13719 / NCIMB 3610 / VKM B-501.
  2. "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(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 168.
  3. "Cloning and mapping of the Bacillus subtilis locus homologous to Escherichia coli ent genes."
    Adams R., Schumann W.
    Gene 133:119-121(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 341-533.
    Strain: 168.
  4. "Crystal structure of DhbE, an archetype for aryl acid activating domains of modular nonribosomal peptide synthetases."
    May J.J., Kessler N., Marahiel M.A., Stubbs M.T.
    Proc. Natl. Acad. Sci. U.S.A. 99:12120-12125(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS) IN COMPLEXES WITH AMP AND 2,3-DIHYDROXYBENZOATE.

Entry informationi

Entry nameiDHBE_BACSU
AccessioniPrimary (citable) accession number: P40871
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 31, 1995
Last sequence update: October 31, 1995
Last modified: January 6, 2015
This is version 111 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.