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Protein

NAD kinase 1

Gene

nadK1

Organism
Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in the regulation of the intracellular balance of NAD and NADP, and is a key enzyme in the biosynthesis of NADP. Catalyzes specifically the phosphorylation on 2'-hydroxyl of the adenosine moiety of NAD to yield NADP.UniRule annotation2 Publications

Catalytic activityi

ATP + NAD+ = ADP + NADP+.UniRule annotation1 Publication

Cofactori

a divalent metal cationUniRule annotation

Enzyme regulationi

Competitively inhibited by 5'-thioacetyladenosine (TAA) and di-(5'-thioadenosine) (DTA).2 Publications

Kineticsi

Kcat is 13.78 sec(-1) for kinase activity with ATP (at pH 7.5 and 30 degrees Celsius). Kcat is 13.12 sec(-1) for kinase activity with NAD (at pH 7.5 and 30 degrees Celsius).

  1. KM=2.8 mM for ATP (at pH 7.5 and 30 degrees Celsius)1 Publication

Vmax=6.67 µmol/min/mg enzyme (at pH 7.5 and 30 degrees Celsius)1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei45 – 451Proton acceptorUniRule annotation1 Publication
Binding sitei46 – 461NAD; via amide nitrogenUniRule annotation1 Publication
Binding sitei148 – 1481NADUniRule annotation
Binding sitei150 – 1501NAD1 Publication
Binding sitei158 – 1581NAD; via carbonyl oxygenUniRule annotation1 Publication
Binding sitei223 – 2231NADUniRule annotation1 Publication

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi45 – 462NADUniRule annotation1 Publication
Nucleotide bindingi122 – 1232NADUniRule annotation1 Publication
Nucleotide bindingi161 – 1666NADUniRule annotation1 Publication

GO - Molecular functioni

  1. ATP binding Source: UniProtKB
  2. metal ion binding Source: UniProtKB-HAMAP
  3. NAD+ kinase activity Source: UniProtKB
  4. NAD binding Source: UniProtKB

GO - Biological processi

  1. NAD metabolic process Source: InterPro
  2. NADP biosynthetic process Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Kinase, Transferase

Keywords - Ligandi

ATP-binding, NAD, NADP, Nucleotide-binding

Enzyme and pathway databases

BioCyciLMON169963:LMO0968-MONOMER.
BRENDAi2.7.1.23. 3045.

Names & Taxonomyi

Protein namesi
Recommended name:
NAD kinase 1UniRule annotation (EC:2.7.1.23UniRule annotation)
Alternative name(s):
ATP-dependent NAD kinaseUniRule annotation
Gene namesi
Name:nadK1UniRule annotation
Ordered Locus Names:lmo0968
OrganismiListeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)
Taxonomic identifieri169963 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesListeriaceaeListeria
ProteomesiUP000000817 Componenti: Chromosome

Organism-specific databases

GenoListiLMO0968.

Subcellular locationi

  1. Cytoplasm UniRule annotation

GO - Cellular componenti

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

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi45 – 451D → N: Only minor changes in the structure and a 10-fold decrease in the kinase activity. 1 Publication
Mutagenesisi223 – 2231H → E: Twice less active than the wild-type. Its activity toward DTA is increased 2-fold. 2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 264264NAD kinase 1PRO_0000120632Add
BLAST

Interactioni

Subunit structurei

Homotetramer.2 Publications

Protein-protein interaction databases

STRINGi169963.lmo0968.

Structurei

Secondary structure

1
264
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 76Combined sources
Helixi11 – 2414Combined sources
Turni26 – 283Combined sources
Beta strandi33 – 353Combined sources
Beta strandi37 – 448Combined sources
Helixi45 – 5410Combined sources
Helixi56 – 583Combined sources
Turni59 – 613Combined sources
Beta strandi63 – 719Combined sources
Beta strandi74 – 763Combined sources
Helixi80 – 823Combined sources
Helixi83 – 919Combined sources
Beta strandi96 – 11217Combined sources
Beta strandi115 – 13117Combined sources
Beta strandi133 – 1397Combined sources
Beta strandi142 – 15514Combined sources
Helixi158 – 1614Combined sources
Helixi163 – 1664Combined sources
Beta strandi178 – 1858Combined sources
Beta strandi189 – 1913Combined sources
Beta strandi199 – 2024Combined sources
Beta strandi207 – 2137Combined sources
Beta strandi217 – 2215Combined sources
Beta strandi224 – 2285Combined sources
Beta strandi230 – 24718Combined sources
Helixi253 – 2619Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2I1WX-ray2.34A/B/C/D1-264[»]
2I29X-ray2.10A1-264[»]
2I2AX-ray2.10A1-264[»]
2I2BX-ray2.10A1-264[»]
2I2CX-ray1.85A1-264[»]
2I2DX-ray2.22A1-264[»]
2I2FX-ray1.90A1-264[»]
2Q5FX-ray1.90A1-264[»]
3V7UX-ray1.97A1-264[»]
3V7WX-ray2.01A1-264[»]
3V7YX-ray1.97A1-264[»]
3V80X-ray2.03A1-264[»]
3V8MX-ray2.48A1-264[»]
3V8NX-ray2.38A1-264[»]
3V8PX-ray2.29A1-264[»]
3V8QX-ray2.37A1-264[»]
3V8RX-ray2.39A1-264[»]
4DY6X-ray2.20A1-264[»]
SMRiQ8Y8D7. Positions 1-264.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ8Y8D7.

Family & Domainsi

Sequence similaritiesi

Belongs to the NAD kinase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0061.
HOGENOMiHOG000275803.
KOiK00858.
OMAiHRYENQV.
OrthoDBiEOG6PZXDR.
PhylomeDBiQ8Y8D7.

Family and domain databases

Gene3Di2.60.200.30. 1 hit.
3.40.50.10330. 1 hit.
HAMAPiMF_00361. NAD_kinase.
InterProiIPR017438. ATP-NAD_kinase_dom_1.
IPR017437. ATP-NAD_kinase_PpnK-typ_all-b.
IPR016064. NAD/diacylglycerol_kinase.
IPR002504. NADK.
[Graphical view]
PANTHERiPTHR20275. PTHR20275. 1 hit.
PfamiPF01513. NAD_kinase. 1 hit.
[Graphical view]
SUPFAMiSSF111331. SSF111331. 1 hit.

Sequencei

Sequence statusi: Complete.

Q8Y8D7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKYMITSKGD EKSDLLRLNM IAGFGEYDME YDDVEPEIVI SIGGDGTFLS
60 70 80 90 100
AFHQYEERLD EIAFIGIHTG HLGFYADWRP AEADKLVKLL AKGEYQKVSY
110 120 130 140 150
PLLKTTVKYG IGKKEATYLA LNESTVKSSG GPFVVDVVIN DIHFERFRGD
160 170 180 190 200
GLCMSTPSGT TAYNKSLGGA LMHPSIEAMQ LTEMASINNR VYRTIGSPLV
210 220 230 240 250
FPKHHVVSLQ PVNDKDFQIS VDHLSILHRD VQEIRYEVSA KKIHFARFRS
260
FPFWRRVHDS FIED
Length:264
Mass (Da):29,933
Last modified:March 1, 2002 - v1
Checksum:i00E0BCC4CAD30653
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL591977 Genomic DNA. Translation: CAC99046.1.
PIRiAH1195.
RefSeqiNP_464493.1. NC_003210.1.

Genome annotation databases

GeneIDi986453.
KEGGilmo:lmo0968.
PATRICi20311034. VBILisMon69206_0995.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL591977 Genomic DNA. Translation: CAC99046.1.
PIRiAH1195.
RefSeqiNP_464493.1. NC_003210.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2I1WX-ray2.34A/B/C/D1-264[»]
2I29X-ray2.10A1-264[»]
2I2AX-ray2.10A1-264[»]
2I2BX-ray2.10A1-264[»]
2I2CX-ray1.85A1-264[»]
2I2DX-ray2.22A1-264[»]
2I2FX-ray1.90A1-264[»]
2Q5FX-ray1.90A1-264[»]
3V7UX-ray1.97A1-264[»]
3V7WX-ray2.01A1-264[»]
3V7YX-ray1.97A1-264[»]
3V80X-ray2.03A1-264[»]
3V8MX-ray2.48A1-264[»]
3V8NX-ray2.38A1-264[»]
3V8PX-ray2.29A1-264[»]
3V8QX-ray2.37A1-264[»]
3V8RX-ray2.39A1-264[»]
4DY6X-ray2.20A1-264[»]
SMRiQ8Y8D7. Positions 1-264.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi169963.lmo0968.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi986453.
KEGGilmo:lmo0968.
PATRICi20311034. VBILisMon69206_0995.

Organism-specific databases

GenoListiLMO0968.

Phylogenomic databases

eggNOGiCOG0061.
HOGENOMiHOG000275803.
KOiK00858.
OMAiHRYENQV.
OrthoDBiEOG6PZXDR.
PhylomeDBiQ8Y8D7.

Enzyme and pathway databases

BioCyciLMON169963:LMO0968-MONOMER.
BRENDAi2.7.1.23. 3045.

Miscellaneous databases

EvolutionaryTraceiQ8Y8D7.

Family and domain databases

Gene3Di2.60.200.30. 1 hit.
3.40.50.10330. 1 hit.
HAMAPiMF_00361. NAD_kinase.
InterProiIPR017438. ATP-NAD_kinase_dom_1.
IPR017437. ATP-NAD_kinase_PpnK-typ_all-b.
IPR016064. NAD/diacylglycerol_kinase.
IPR002504. NADK.
[Graphical view]
PANTHERiPTHR20275. PTHR20275. 1 hit.
PfamiPF01513. NAD_kinase. 1 hit.
[Graphical view]
SUPFAMiSSF111331. SSF111331. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC BAA-679 / EGD-e.
  2. "NAD kinases use substrate-assisted catalysis for specific recognition of NAD."
    Poncet-Montange G., Assairi L., Arold S., Pochet S., Labesse G.
    J. Biol. Chem. 282:33925-33934(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) OF WILD-TYPE AND MUTANT ASN-45 IN COMPLEX WITH NAD AND NAD ANALOGS, FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF ASP-45 AND HIS-223, ACTIVE SITE, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT.
  3. "Screening and in situ synthesis using crystals of a NAD kinase lead to a potent antistaphylococcal compound."
    Gelin M., Poncet-Montange G., Assairi L., Morellato L., Huteau V., Dugue L., Dussurget O., Pochet S., Labesse G.
    Structure 20:1107-1117(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.97 ANGSTROMS) OF WILD-TYPE AND MUTANT GLU-223 IN COMPLEX WITH NAD ANALOGS, FUNCTION, MUTAGENESIS OF HIS-223, ENZYME REGULATION.

Entry informationi

Entry nameiNADK1_LISMO
AccessioniPrimary (citable) accession number: Q8Y8D7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 25, 2002
Last sequence update: March 1, 2002
Last modified: April 29, 2015
This is version 82 of the entry and version 1 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. 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.