Reviewed, UniProtKB/Swiss-Prot P08164 (NADE_BACSU)

Names and origin

Protein names

Recommended name:
    NH(3)-dependent NAD(+) synthetase
    EC=6.3.1.5
Alternative name(s):
    Spore outgrowth factor B
    Sporulation protein outB
    General stress protein 38
      Short name=GSP38

Gene names

Name:	nadE
Synonyms:	outB
Ordered Locus Names:	BSU03130

Organism

Bacillus subtilis [Complete proteome] [HAMAP]

Taxonomic identifier

1423 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Bacillales › Bacillaceae › Bacillus

Protein attributes

Sequence length	272 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Catalyzes a key step in NAD biosynthesis, transforming deamido-NAD into NAD by a two-step reaction. HAMAP MF_00193
Catalytic activity	ATP + deamido-NAD+ + NH3 = AMP + diphosphate + NAD+. HAMAP MF_00193
Pathway	Cofactor biosynthesis; NAD(+) biosynthesis; NAD(+) from deamido-NAD(+) (ammonia route): step 1/1. HAMAP MF_00193
Subunit structure	Homodimer. HAMAP MF_00193
Induction	By heat shock, salt stress, oxidative stress, glucose limitation and oxygen limitation. HAMAP MF_00193
Post-translational modification	Phosphorylated. Ref.5
Sequence similarities	Belongs to the NAD synthetase family.
biophysicochemical properties	pH dependence: Optimum pH is 8.5. HAMAP MF_00193

Ontologies

Keywords
Biological process	Sporulation Stress response
Ligand	ATP-binding NAD Nucleotide-binding
Molecular function	Ligase
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	NAD biosynthetic process Inferred from electronic annotation. Source: HAMAP response to stress Inferred from electronic annotation. Source: UniProtKB-KW sporulation resulting in formation of a cellular spore Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	ATP binding Inferred from electronic annotation. Source: HAMAP NAD+ synthase (glutamine-hydrolyzing) activity Inferred from electronic annotation. Source: InterPro NAD+ synthase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.5 Ref.4

Chain

2 – 272

271

NH(3)-dependent NAD(+) synthetase HAMAP MF_00193

PRO_0000152159

Regions

Nucleotide binding

45 – 52

8

ATP HAMAP MF_00193

Nucleotide binding

168 – 178

11

NAD HAMAP MF_00193

Sites

Binding site

33

1

NAD HAMAP MF_00193

Binding site

79

1

ATP HAMAP MF_00193

Binding site

85

1

ATP HAMAP MF_00193

Binding site

138

1

NAD HAMAP MF_00193

Binding site

158

1

ATP HAMAP MF_00193

Binding site

209

1

ATP HAMAP MF_00193

Binding site

224

1

NAD HAMAP MF_00193

Binding site

259

1

NAD HAMAP MF_00193

Secondary structure

1

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272

Helix Strand Turn

Details...

Helix

3 – 11

9

Helix

19 – 37

19

Beta strand

41 – 45

5

Helix

50 – 68

19

Beta strand

74 – 79

6

Beta strand

82 – 84

3

Helix

88 – 98

11

Beta strand

101 – 105

5

Helix

109 – 123

15

Helix

129 – 151

23

Beta strand

154 – 156

3

Helix

161 – 164

4

Turn

165 – 167

3

Turn

171 – 175

5

Turn

181 – 184

4

Helix

187 – 196

10

Helix

202 – 205

4

Beta strand

214 – 216

3

Helix

221 – 225

5

Helix

229 – 236

8

Helix

243 – 255

13

Helix

257 – 260

4

Sequences

	Sequence		Length	Mass (Da)
	P08164-1 [UniParc]. Last modified January 23, 2007. Version 5. Checksum: 8021E88B5946C2E0	FASTA	272	30,395
	10 20 30 40 50 60 MSMQEKIMRE LHVKPSIDPK QEIEDRVNFL KQYVKKTGAK GFVLGISGGQ DSTLAGRLAQ 70 80 90 100 110 120 LAVESIREEG GDAQFIAVRL PHGTQQDEDD AQLALKFIKP DKSWKFDIKS TVSAFSDQYQ 130 140 150 160 170 180 QETGDQLTDF NKGNVKARTR MIAQYAIGGQ EGLLVLGTDH AAEAVTGFFT KYGDGGADLL 190 200 210 220 230 240 PLTGLTKRQG RTLLKELGAP ERLYLKEPTA DLLDEKPQQS DETELGISYD EIDDYLEGKE 250 260 270 VSAKVSEALE KRYSMTEHKR QVPASMFDDW WK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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: 2435704] [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: 8969502] [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: 9384377] [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: 9298659] [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: 1556067] [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: 2118513] [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: 7890752] [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: 8895556] [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: 9753692] [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: 11375500] [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: 12077433] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.0 ANGSTROMS) IN COMPLEX WITH SUBSTRATES.

Cross-references

Sequence databases

EMBLGenBankDDBJ

M15811 Genomic DNA. Translation: AAA22635.1.
D50453 Genomic DNA. Translation: BAA08947.1.
AL009126 Genomic DNA. Translation: CAB12107.1.

PIR

A26936.

RefSeq

NP_388195.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1EE1	X-ray	2.06	A/B	2-272	[»]
1FYD	X-ray	2.25	A/B	2-272	[»]
1IFX	X-ray	2.25	A/B	2-272	[»]
1IH8	X-ray	1.90	A/B	2-272	[»]
1KQP	X-ray	1.03	A/B	2-272	[»]
1NSY	X-ray	2.00	A/B	2-272	[»]
2NSY	X-ray	2.00	A/B	2-272	[»]

ModBase

Search...

Genome annotation databases

GeneID

938339.

GenomeReviews

Gene locus BSU03130 in contig AL009126_GR.

KEGG

bsu:BSU03130.

NMPDR

fig|224308.1.peg.314.

Organism-specific databases

SubtiList

BG10694. nadE. [Micado]

CMR

Search...

Phylogenomic databases

HOGENOM

P08164.

OMA

P08164. ADLEEDR.

Enzyme and pathway databases

BioCyc

BSUB224308:BSU0314-MON.

BRENDA

6.3.1.5. 150.

Family and domain databases

HAMAP

MF_00193.
[Tree]

InterPro

IPR003694. NAD_synthase.
IPR014729. Rossmann-like_a/b/a_fold.
[Graphical view]

Gene3D

G3DSA:3.40.50.620. Rossmann-like_a/b/a_fold. 1 hit.

Pfam

PF02540. NAD_synthase. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00552. nadE. 1 hit.

ProtoNet

Search...

Other Resources

DrugBank

DB00131. Adenosine monophosphate.

Entry information

Entry name

NADE_BACSU

Accession

Primary (citable) accession number: P08164

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 1, 1988
Last sequence update:	January 23, 2007
Last modified:	June 16, 2009
This is version 87 of the entry and version 5 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)