P08164 (NADE_BACSU) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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 names

Name:	nadE
Synonyms:	outB
Ordered Locus Names:	BSU03130

Organism

Bacillus subtilis (strain 168) [Reference proteome] [HAMAP]

Taxonomic identifier

224308 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Firmicutes › Bacilli › Bacillales › Bacillaceae › Bacillus › Bacillus subtilis group › Bacillus subtilis › Bacillus subtilis subsp. subtilis

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-Rule MF_00193
Catalytic activity	ATP + deamido-NAD+ + NH3 = AMP + diphosphate + NAD+. HAMAP-Rule MF_00193
Pathway	Cofactor biosynthesis; NAD(+) biosynthesis; NAD(+) from deamido-NAD(+) (ammonia route): step 1/1. HAMAP-Rule MF_00193
Subunit structure	Homodimer.
Induction	By heat shock, salt stress, oxidative stress, glucose limitation and oxygen limitation. HAMAP-Rule 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-Rule 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 Reference proteome
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: HAMAP
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.4 Ref.5

Chain

2 – 272

271

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

PRO_0000152159

Regions

Nucleotide binding

45 – 52

8

ATP HAMAP-Rule MF_00193

Nucleotide binding

168 – 178

11

NAD HAMAP-Rule MF_00193

Sites

Binding site

33

1

NAD

Binding site

79

1

ATP

Binding site

85

1

ATP

Binding site

138

1

NAD

Binding site

158

1

ATP

Binding site

209

1

ATP

Binding site

224

1

NAD

Binding site

259

1

NAD

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

Beta strand

261 – 264

4

Sequences

	Sequence		Length	Mass (Da)
	P08164 [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] [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.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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

PIR

A26936.

RefSeq

NP_388195.1. NC_000964.3.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

P08164.

SMR

P08164. Positions 2-272.

ModBase

Search...

Protein-protein interaction databases

STRING

224308.BSU03130.

Proteomic databases

PaxDb

P08164.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

CAB12107; CAB12107; BSU03130.

GeneID

938339.

KEGG

bsu:BSU03130.

PATRIC

18972185. VBIBacSub10457_0321.

Organism-specific databases

GenoList

BSU03130. [Micado]

Phylogenomic databases

eggNOG

COG0171.

HOGENOM

HOG000238070.

KO

K01916.

OMA

DFVRGNI.

ProtClustDB

PRK00768.

Enzyme and pathway databases

BioCyc

BSUB:BSU03130-MONOMER.

UniPathway

UPA00253; UER00333.

Family and domain databases

Gene3D

3.40.50.620. 1 hit.

HAMAP

MF_00193. NadE.

InterPro

IPR022310. NAD/GMP_synthase.
IPR003694. NAD_synthase.
IPR022926. NH(3)-dep_NAD(+)_synth.
IPR014729. Rossmann-like_a/b/a_fold.
[Graphical view]

Pfam

PF02540. NAD_synthase. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00552. nadE. 1 hit.

ProtoNet

Search...

Other

BindingDB

P08164.

ChEMBL

CHEMBL4615.

DrugBank

DB00131. Adenosine monophosphate.

EvolutionaryTrace

P08164.

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:	May 1, 2013
This is version 119 of the entry and version 5 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program