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Q8Y8D7

- NADK1_LISMO

UniProt

Q8Y8D7 - NADK1_LISMO

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Protein
NAD kinase 1
Gene
nadK1, lmo0968
Organism
Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)
Status
Reviewed - 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.2 Publications

Catalytic activityi

ATP + NAD+ = ADP + NADP+.1 Publication

Cofactori

Divalent metal ions By similarity.UniRule 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)

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei45 – 451Proton acceptor1 Publication
Binding sitei46 – 461NAD; via amide nitrogen
Binding sitei148 – 1481NAD By similarity
Binding sitei150 – 1501NAD Inferred
Binding sitei158 – 1581NAD; via carbonyl oxygen
Binding sitei223 – 2231NAD

Regions

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

GO - Molecular functioni

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

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.

Names & Taxonomyi

Protein namesi
Recommended name:
NAD kinase 1 (EC:2.7.1.23)
Alternative name(s):
ATP-dependent NAD kinase
Gene namesi
Name:nadK1
Ordered Locus Names:lmo0968
OrganismiListeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)
Taxonomic identifieri169963 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesListeriaceaeListeria
ProteomesiUP000000817: Chromosome

Organism-specific databases

GenoListiLMO0968.

Subcellular locationi

Cytoplasm By similarity 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 1UniRule annotation
PRO_0000120632Add
BLAST

Interactioni

Subunit structurei

Homotetramer.1 Publication

Protein-protein interaction databases

STRINGi169963.lmo0968.

Structurei

Secondary structure

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

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
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[»]
ProteinModelPortaliQ8Y8D7.
SMRiQ8Y8D7. Positions 1-264.

Miscellaneous databases

EvolutionaryTraceiQ8Y8D7.

Family & Domainsi

Sequence similaritiesi

Belongs to the NAD kinase family.

Phylogenomic databases

eggNOGiCOG0061.
HOGENOMiHOG000275803.
KOiK00858.
OMAiQWITIVP.
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.
IPR016064. ATP-NAD_kinase_PpnK-typ.
IPR017437. ATP-NAD_kinase_PpnK-typ_all-b.
IPR002504. PolyP/ATP_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

MKYMITSKGD EKSDLLRLNM IAGFGEYDME YDDVEPEIVI SIGGDGTFLS    50
AFHQYEERLD EIAFIGIHTG HLGFYADWRP AEADKLVKLL AKGEYQKVSY 100
PLLKTTVKYG IGKKEATYLA LNESTVKSSG GPFVVDVVIN DIHFERFRGD 150
GLCMSTPSGT TAYNKSLGGA LMHPSIEAMQ LTEMASINNR VYRTIGSPLV 200
FPKHHVVSLQ PVNDKDFQIS VDHLSILHRD VQEIRYEVSA KKIHFARFRS 250
FPFWRRVHDS FIED 264
Length:264
Mass (Da):29,933
Last modified:March 1, 2002 - v1
Checksum:i00E0BCC4CAD30653
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AL591977 Genomic DNA. Translation: CAC99046.1.
PIRiAH1195.
RefSeqiNP_464493.1. NC_003210.1.

Genome annotation databases

EnsemblBacteriaiCAC99046; CAC99046; CAC99046.
GeneIDi986453.
KEGGilmo:lmo0968.
PATRICi20311034. VBILisMon69206_0995.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AL591977 Genomic DNA. Translation: CAC99046.1 .
PIRi AH1195.
RefSeqi NP_464493.1. NC_003210.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2I1W X-ray 2.34 A/B/C/D 1-264 [» ]
2I29 X-ray 2.10 A 1-264 [» ]
2I2A X-ray 2.10 A 1-264 [» ]
2I2B X-ray 2.10 A 1-264 [» ]
2I2C X-ray 1.85 A 1-264 [» ]
2I2D X-ray 2.22 A 1-264 [» ]
2I2F X-ray 1.90 A 1-264 [» ]
2Q5F X-ray 1.90 A 1-264 [» ]
3V7U X-ray 1.97 A 1-264 [» ]
3V7W X-ray 2.01 A 1-264 [» ]
3V7Y X-ray 1.97 A 1-264 [» ]
3V80 X-ray 2.03 A 1-264 [» ]
3V8M X-ray 2.48 A 1-264 [» ]
3V8N X-ray 2.38 A 1-264 [» ]
3V8P X-ray 2.29 A 1-264 [» ]
3V8Q X-ray 2.37 A 1-264 [» ]
3V8R X-ray 2.39 A 1-264 [» ]
4DY6 X-ray 2.20 A 1-264 [» ]
ProteinModelPortali Q8Y8D7.
SMRi Q8Y8D7. Positions 1-264.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 169963.lmo0968.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai CAC99046 ; CAC99046 ; CAC99046 .
GeneIDi 986453.
KEGGi lmo:lmo0968.
PATRICi 20311034. VBILisMon69206_0995.

Organism-specific databases

GenoListi LMO0968.

Phylogenomic databases

eggNOGi COG0061.
HOGENOMi HOG000275803.
KOi K00858.
OMAi QWITIVP.
OrthoDBi EOG6PZXDR.
PhylomeDBi Q8Y8D7.

Enzyme and pathway databases

BioCyci LMON169963:LMO0968-MONOMER.

Miscellaneous databases

EvolutionaryTracei Q8Y8D7.

Family and domain databases

Gene3Di 2.60.200.30. 1 hit.
3.40.50.10330. 1 hit.
HAMAPi MF_00361. NAD_kinase.
InterProi IPR017438. ATP-NAD_kinase_dom_1.
IPR016064. ATP-NAD_kinase_PpnK-typ.
IPR017437. ATP-NAD_kinase_PpnK-typ_all-b.
IPR002504. PolyP/ATP_NADK.
[Graphical view ]
PANTHERi PTHR20275. PTHR20275. 1 hit.
Pfami PF01513. NAD_kinase. 1 hit.
[Graphical view ]
SUPFAMi SSF111331. SSF111331. 1 hit.
ProtoNeti Search...

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: July 9, 2014
This is version 76 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

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