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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 the ATP-dependent amidation of deamido-NAD to form NAD. Uses ammonia as a nitrogen source.UniRule annotation1 Publication

Catalytic activityi

ATP + deamido-NAD+ + NH3 = AMP + diphosphate + NAD+.UniRule annotation1 Publication

Kineticsi

  1. KM=0.62 mM for NH4+1 Publication
  2. KM=0.28 mM for deamido-NAD1 Publication
  3. KM=0.21 mM for ATP1 Publication

    pH dependencei

    Optimum pH is 8.2-8.7.1 Publication

    Temperature dependencei

    Optimum temperature is 40-45 degrees Celsius.1 Publication

    Pathwayi: NAD(+) biosynthesis

    This protein is involved in step 1 of the subpathway that synthesizes NAD(+) from deamido-NAD(+) (ammonia route).UniRule annotation1 Publication
    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)DescriptionActionsGraphical viewLength
    Binding sitei33Deamido-NAD; shared with neighboring subunitCombined sources1
    Metal bindingi51MagnesiumUniRule annotationCombined sources1
    Binding sitei79ATPCombined sources1
    Binding sitei85ATPCombined sources1
    Binding sitei138Deamido-NADUniRule annotationCombined sources1
    Binding sitei158ATPUniRule annotationCombined sources1
    Metal bindingi163MagnesiumUniRule annotationCombined sources1
    Binding sitei171Deamido-NADUniRule annotationCombined sources1
    Binding sitei178Deamido-NAD; shared with neighboring subunitUniRule annotationCombined sources1
    Binding sitei187ATPUniRule annotationCombined sources1
    Binding sitei209ATP; via amide nitrogen and carbonyl oxygenUniRule annotationCombined sources1
    Binding sitei224Deamido-NADCombined sources1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi45 – 52ATPUniRule annotationCombined sources8
    Nucleotide bindingi258 – 259Deamido-NADUniRule annotationCombined sources2

    GO - Molecular functioni

    GO - Biological processi

    Keywordsi

    Molecular functionLigase
    Biological processSporulation, Stress response
    LigandATP-binding, Magnesium, Metal-binding, NAD, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciBSUB:BSU03130-MONOMER.
    BRENDAi6.3.1.5. 658.
    SABIO-RKiP08164.
    UniPathwayiUPA00253; UER00333.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    NH(3)-dependent NAD(+) synthetase1 PublicationUniRule annotation (EC:6.3.1.5UniRule annotation1 Publication)
    Alternative name(s):
    General stress protein 38
    Short name:
    GSP38
    Spore outgrowth factor B
    Sporulation protein OutB
    Gene namesi
    Name:nadEUniRule annotation
    Synonyms:outB1 Publication
    Ordered Locus Names:BSU03130
    OrganismiBacillus subtilis (strain 168)
    Taxonomic identifieri224308 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
    Proteomesi
    • UP000001570 Componenti: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    Pathology & Biotechi

    Chemistry databases

    ChEMBLiCHEMBL4615.
    DrugBankiDB04099. Deamido-Nad+.
    DB00798. Gentamicin.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Initiator methionineiRemoved2 Publications
    ChainiPRO_00001521592 – 272NH(3)-dependent NAD(+) synthetaseAdd BLAST271

    Post-translational modificationi

    Phosphorylated.1 Publication

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    PaxDbiP08164.
    PRIDEiP08164.

    Expressioni

    Developmental stagei

    Synthesis starts during germination and outgrowth, and is highest at the end of exponential growth. Present in dormant spores.1 Publication

    Inductioni

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

    Interactioni

    Subunit structurei

    Homodimer.UniRule annotation5 Publications

    Protein-protein interaction databases

    STRINGi224308.Bsubs1_010100001753.

    Chemistry databases

    BindingDBiP08164.

    Structurei

    Secondary structure

    1272
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi3 – 11Combined sources9
    Helixi19 – 37Combined sources19
    Beta strandi41 – 45Combined sources5
    Helixi50 – 68Combined sources19
    Beta strandi74 – 79Combined sources6
    Beta strandi82 – 84Combined sources3
    Helixi88 – 98Combined sources11
    Beta strandi101 – 105Combined sources5
    Helixi109 – 123Combined sources15
    Helixi129 – 151Combined sources23
    Beta strandi154 – 156Combined sources3
    Helixi161 – 164Combined sources4
    Turni165 – 167Combined sources3
    Turni171 – 175Combined sources5
    Turni181 – 184Combined sources4
    Helixi187 – 196Combined sources10
    Helixi202 – 205Combined sources4
    Beta strandi214 – 216Combined sources3
    Helixi221 – 225Combined sources5
    Helixi229 – 236Combined sources8
    Helixi243 – 255Combined sources13
    Helixi257 – 260Combined sources4
    Beta strandi261 – 264Combined sources4

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB 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.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP08164.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the NAD synthetase family.UniRule annotationCurated

    Phylogenomic databases

    eggNOGiENOG4107RA1. Bacteria.
    COG0171. LUCA.
    HOGENOMiHOG000238070.
    InParanoidiP08164.
    KOiK01916.
    OMAiCAINPIG.
    PhylomeDBiP08164.

    Family and domain databases

    CDDicd00553. NAD_synthase. 1 hit.
    Gene3Di3.40.50.620. 1 hit.
    HAMAPiMF_00193. NadE_ammonia_dep. 1 hit.
    InterProiView protein in InterPro
    IPR022310. NAD/GMP_synthase.
    IPR003694. NAD_synthase.
    IPR022926. NH(3)-dep_NAD(+)_synth.
    IPR014729. Rossmann-like_a/b/a_fold.
    PANTHERiPTHR23090. PTHR23090. 1 hit.
    PfamiView protein in Pfam
    PF02540. NAD_synthase. 1 hit.
    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.
    PATRICifig|224308.179.peg.327.

    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
    PDB 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.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi224308.Bsubs1_010100001753.

    Chemistry databases

    BindingDBiP08164.
    ChEMBLiCHEMBL4615.
    DrugBankiDB04099. Deamido-Nad+.
    DB00798. Gentamicin.

    Proteomic databases

    PaxDbiP08164.
    PRIDEiP08164.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiCAB12107; CAB12107; BSU03130.
    GeneIDi938339.
    KEGGibsu:BSU03130.
    PATRICifig|224308.179.peg.327.

    Phylogenomic databases

    eggNOGiENOG4107RA1. Bacteria.
    COG0171. LUCA.
    HOGENOMiHOG000238070.
    InParanoidiP08164.
    KOiK01916.
    OMAiCAINPIG.
    PhylomeDBiP08164.

    Enzyme and pathway databases

    UniPathwayiUPA00253; UER00333.
    BioCyciBSUB:BSU03130-MONOMER.
    BRENDAi6.3.1.5. 658.
    SABIO-RKiP08164.

    Miscellaneous databases

    EvolutionaryTraceiP08164.

    Family and domain databases

    CDDicd00553. NAD_synthase. 1 hit.
    Gene3Di3.40.50.620. 1 hit.
    HAMAPiMF_00193. NadE_ammonia_dep. 1 hit.
    InterProiView protein in InterPro
    IPR022310. NAD/GMP_synthase.
    IPR003694. NAD_synthase.
    IPR022926. NH(3)-dep_NAD(+)_synth.
    IPR014729. Rossmann-like_a/b/a_fold.
    PANTHERiPTHR23090. PTHR23090. 1 hit.
    PfamiView protein in Pfam
    PF02540. NAD_synthase. 1 hit.
    TIGRFAMsiTIGR00552. nadE. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiNADE_BACSU
    AccessioniPrimary (citable) accession number: P08164
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 1, 1988
    Last sequence update: January 23, 2007
    Last modified: June 7, 2017
    This is version 145 of the entry and version 5 of the sequence. See 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.