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Protein

NH(3)-dependent NAD(+) synthetase

Gene

nadE

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

Functioni

Catalyzes a key step in NAD biosynthesis, transforming deamido-NAD into NAD by a two-step reaction.

Catalytic activityi

ATP + deamido-NAD+ + NH3 = AMP + diphosphate + NAD+.

pH dependencei

Optimum pH is 8.5.

Pathwayi: NAD(+) biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes NAD(+) from deamido-NAD(+) (ammonia route).
Proteins known to be involved in this subpathway in this organism are:
  1. NH(3)-dependent NAD(+) synthetase (nadE)
This subpathway is part of the pathway NAD(+) biosynthesis, which is itself part of Cofactor biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes NAD(+) from deamido-NAD(+) (ammonia route), the pathway NAD(+) biosynthesis and in Cofactor biosynthesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei33 – 331NAD
Binding sitei79 – 791ATP
Binding sitei85 – 851ATP
Binding sitei138 – 1381NAD
Binding sitei158 – 1581ATP
Binding sitei209 – 2091ATP
Binding sitei224 – 2241NAD
Binding sitei259 – 2591NAD

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi45 – 528ATP
Nucleotide bindingi168 – 17811NADAdd
BLAST

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

Sporulation, Stress response

Keywords - Ligandi

ATP-binding, NAD, Nucleotide-binding

Enzyme and pathway databases

BioCyciBSUB:BSU03130-MONOMER.
BRENDAi6.3.1.5. 658.
SABIO-RKP08164.
UniPathwayiUPA00253; UER00333.

Names & Taxonomyi

Protein namesi
Recommended name:
NH(3)-dependent NAD(+) synthetase (EC:6.3.1.5)
Alternative name(s):
General stress protein 38
Short name:
GSP38
Spore outgrowth factor B
Sporulation protein OutB
Gene namesi
Name:nadE
Synonyms:outB
Ordered Locus Names:BSU03130
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
Proteomesi
  • UP000001570 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Pathology & Biotechi

Chemistry

ChEMBLiCHEMBL4615.
DrugBankiDB00798. Gentamicin.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved2 Publications
Chaini2 – 272271NH(3)-dependent NAD(+) synthetasePRO_0000152159Add
BLAST

Post-translational modificationi

Phosphorylated.1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiP08164.

Expressioni

Inductioni

By heat shock, salt stress, oxidative stress, glucose limitation and oxygen limitation.

Interactioni

Subunit structurei

Homodimer.3 Publications

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100001753.

Chemistry

BindingDBiP08164.

Structurei

Secondary structure

1
272
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi3 – 119Combined sources
Helixi19 – 3719Combined sources
Beta strandi41 – 455Combined sources
Helixi50 – 6819Combined sources
Beta strandi74 – 796Combined sources
Beta strandi82 – 843Combined sources
Helixi88 – 9811Combined sources
Beta strandi101 – 1055Combined sources
Helixi109 – 12315Combined sources
Helixi129 – 15123Combined sources
Beta strandi154 – 1563Combined sources
Helixi161 – 1644Combined sources
Turni165 – 1673Combined sources
Turni171 – 1755Combined sources
Turni181 – 1844Combined sources
Helixi187 – 19610Combined sources
Helixi202 – 2054Combined sources
Beta strandi214 – 2163Combined sources
Helixi221 – 2255Combined sources
Helixi229 – 2368Combined sources
Helixi243 – 25513Combined sources
Helixi257 – 2604Combined sources
Beta strandi261 – 2644Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1EE1X-ray2.06A/B2-272[»]
1FYDX-ray2.25A/B2-272[»]
1IFXX-ray2.25A/B2-272[»]
1IH8X-ray1.90A/B2-272[»]
1KQPX-ray1.03A/B2-272[»]
1NSYX-ray2.00A/B2-272[»]
2NSYX-ray2.00A/B2-272[»]
ProteinModelPortaliP08164.
SMRiP08164. Positions 2-272.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP08164.

Family & Domainsi

Sequence similaritiesi

Belongs to the NAD synthetase family.Curated

Phylogenomic databases

eggNOGiENOG4107RA1. Bacteria.
COG0171. LUCA.
HOGENOMiHOG000238070.
InParanoidiP08164.
KOiK01916.
OMAiITEHKRQ.
OrthoDBiEOG64JFM7.
PhylomeDBiP08164.

Family and domain databases

Gene3Di3.40.50.620. 1 hit.
HAMAPiMF_00193. NadE.
InterProiIPR022310. NAD/GMP_synthase.
IPR003694. NAD_synthase.
IPR022926. NH(3)-dep_NAD(+)_synth.
IPR014729. Rossmann-like_a/b/a_fold.
[Graphical view]
PfamiPF02540. NAD_synthase. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00552. nadE. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P08164-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSMQEKIMRE LHVKPSIDPK QEIEDRVNFL KQYVKKTGAK GFVLGISGGQ
60 70 80 90 100
DSTLAGRLAQ LAVESIREEG GDAQFIAVRL PHGTQQDEDD AQLALKFIKP
110 120 130 140 150
DKSWKFDIKS TVSAFSDQYQ QETGDQLTDF NKGNVKARTR MIAQYAIGGQ
160 170 180 190 200
EGLLVLGTDH AAEAVTGFFT KYGDGGADLL PLTGLTKRQG RTLLKELGAP
210 220 230 240 250
ERLYLKEPTA DLLDEKPQQS DETELGISYD EIDDYLEGKE VSAKVSEALE
260 270
KRYSMTEHKR QVPASMFDDW WK
Length:272
Mass (Da):30,395
Last modified:January 23, 2007 - v5
Checksum:i8021E88B5946C2E0
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M15811 Genomic DNA. Translation: AAA22635.1.
D50453 Genomic DNA. Translation: BAA08947.1.
AL009126 Genomic DNA. Translation: CAB12107.1.
PIRiA26936.
RefSeqiNP_388195.1. NC_000964.3.
WP_003246440.1. NZ_JNCM01000030.1.

Genome annotation databases

EnsemblBacteriaiCAB12107; CAB12107; BSU03130.
GeneIDi938339.
KEGGibsu:BSU03130.
PATRICi18972185. VBIBacSub10457_0321.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M15811 Genomic DNA. Translation: AAA22635.1.
D50453 Genomic DNA. Translation: BAA08947.1.
AL009126 Genomic DNA. Translation: CAB12107.1.
PIRiA26936.
RefSeqiNP_388195.1. NC_000964.3.
WP_003246440.1. NZ_JNCM01000030.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1EE1X-ray2.06A/B2-272[»]
1FYDX-ray2.25A/B2-272[»]
1IFXX-ray2.25A/B2-272[»]
1IH8X-ray1.90A/B2-272[»]
1KQPX-ray1.03A/B2-272[»]
1NSYX-ray2.00A/B2-272[»]
2NSYX-ray2.00A/B2-272[»]
ProteinModelPortaliP08164.
SMRiP08164. Positions 2-272.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100001753.

Chemistry

BindingDBiP08164.
ChEMBLiCHEMBL4615.
DrugBankiDB00798. Gentamicin.

Proteomic databases

PaxDbiP08164.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB12107; CAB12107; BSU03130.
GeneIDi938339.
KEGGibsu:BSU03130.
PATRICi18972185. VBIBacSub10457_0321.

Phylogenomic databases

eggNOGiENOG4107RA1. Bacteria.
COG0171. LUCA.
HOGENOMiHOG000238070.
InParanoidiP08164.
KOiK01916.
OMAiITEHKRQ.
OrthoDBiEOG64JFM7.
PhylomeDBiP08164.

Enzyme and pathway databases

UniPathwayiUPA00253; UER00333.
BioCyciBSUB:BSU03130-MONOMER.
BRENDAi6.3.1.5. 658.
SABIO-RKP08164.

Miscellaneous databases

EvolutionaryTraceiP08164.

Family and domain databases

Gene3Di3.40.50.620. 1 hit.
HAMAPiMF_00193. NadE.
InterProiIPR022310. NAD/GMP_synthase.
IPR003694. NAD_synthase.
IPR022926. NH(3)-dep_NAD(+)_synth.
IPR014729. Rossmann-like_a/b/a_fold.
[Graphical view]
PfamiPF02540. NAD_synthase. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00552. nadE. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Nucleotide sequence of the outB locus of Bacillus subtilis and regulation of its expression."
    Albertini A.M., Caramori T., Henner D.J., Ferrari E., Galizzi A.
    J. Bacteriol. 169:1480-1484(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "The 25 degrees-36 degrees region of the Bacillus subtilis chromosome: determination of the sequence of a 146 kb segment and identification of 113 genes."
    Yamane K., Kumano M., Kurita K.
    Microbiology 142:3047-3056(1996) [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. "First steps from a two-dimensional protein index towards a response-regulation map for Bacillus subtilis."
    Antelmann H., Bernhardt J., Schmid R., Mach H., Voelker U., Hecker M.
    Electrophoresis 18:1451-1463(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-19.
    Strain: 168 / IS58.
  5. "Identification of proteins phosphorylated by ATP during sporulation of Bacillus subtilis."
    Mitchell C., Morris P.W., Vary J.C.
    J. Bacteriol. 174:2474-2477(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-11, PHOSPHORYLATION.
  6. "The Bacillus subtilis outB gene is highly homologous to an Escherichia coli ntr-like gene."
    Albertini A.M., Galizzi A.
    J. Bacteriol. 172:5482-5485(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: SIMILARITY TO E.COLI NADE.
  7. "The outB gene of Bacillus subtilis codes for NAD synthetase."
    Nessi C., Albertini A.M., Speranza M.L., Galizzi A.
    J. Biol. Chem. 270:6181-6185(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION.
  8. "Crystal structure of NH3-dependent NAD+ synthetase from Bacillus subtilis."
    Rizzi M., Nessi C., Mattevi A., Coda A., Bolognesi M., Galizzi A.
    EMBO J. 15:5125-5134(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
  9. "A novel deamido-NAD+-binding site revealed by the trapped NAD-adenylate intermediate in the NAD+ synthetase structure."
    Rizzi M., Bolognesi M., Coda A.
    Structure 6:1129-1140(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.3 ANGSTROMS) IN COMPLEX WITH SUBSTRATE.
  10. "Stabilization of active-site loops in NH3-dependent NAD+ synthetase from Bacillus subtilis."
    Devedjiev Y., Symersky J., Singh R., Jedrzejas M., Brouillette C., Brouillette W., Muccio D., Chattopadhyay D., DeLucas L.
    Acta Crystallogr. D 57:806-812(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH SUBSTRATES.
  11. "NH3-dependent NAD+ synthetase from Bacillus subtilis at 1 A resolution."
    Symersky J., Devedjiev Y., Moore K., Brouillette C., DeLucas L.
    Acta Crystallogr. D 58:1138-1146(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.0 ANGSTROMS) IN COMPLEX WITH SUBSTRATES.

Entry informationi

Entry nameiNADE_BACSU
AccessioniPrimary (citable) accession number: P08164
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1988
Last sequence update: January 23, 2007
Last modified: February 17, 2016
This is version 138 of the entry and version 5 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, 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

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.