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Protein

Nucleoside diphosphate kinase III, chloroplastic/mitochondrial

Gene

NDPK3

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate. Shows the highest specificity towards GDP (By similarity).By similarity

Catalytic activityi

ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.

Cofactori

Mg2+By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei96 – 961ATPBy similarity
Binding sitei144 – 1441ATPBy similarity
Binding sitei172 – 1721ATPBy similarity
Binding sitei178 – 1781ATPBy similarity
Binding sitei189 – 1891ATPBy similarity
Binding sitei199 – 1991ATPBy similarity
Active sitei202 – 2021Pros-phosphohistidine intermediateBy similarity

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • cobalt ion binding Source: TAIR
  • nucleoside diphosphate kinase activity Source: GO_Central
  • zinc ion binding Source: TAIR

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Kinase, Transferase

Keywords - Biological processi

Nucleotide metabolism

Keywords - Ligandi

ATP-binding, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciARA:AT4G11010-MONOMER.
ReactomeiR-ATH-499943. Synthesis and interconversion of nucleotide di- and triphosphates.

Names & Taxonomyi

Protein namesi
Recommended name:
Nucleoside diphosphate kinase III, chloroplastic/mitochondrial (EC:2.7.4.6)
Short name:
NDK III
Short name:
NDP kinase III
Short name:
NDPK III
Gene namesi
Name:NDPK3
Ordered Locus Names:At4g11010
ORF Names:F25I24.220, F8M12.12
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 4

Organism-specific databases

TAIRiAT4G11010.

Subcellular locationi

GO - Cellular componenti

  • chloroplast thylakoid lumen Source: UniProtKB-SubCell
  • mitochondrial inner membrane Source: TAIR
  • mitochondrial intermembrane space Source: UniProtKB-SubCell
  • mitochondrion Source: TAIR
  • plastid Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Chloroplast, Mitochondrion, Plastid, Thylakoid

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 8585Chloroplast and mitochondrion1 PublicationAdd
BLAST
Chaini86 – 238153Nucleoside diphosphate kinase III, chloroplastic/mitochondrialPRO_0000019435Add
BLAST

Proteomic databases

PaxDbiO49203.
PRIDEiO49203.

Expressioni

Gene expression databases

GenevisibleiO49203. AT.

Interactioni

Subunit structurei

Homohexamer.Curated

Protein-protein interaction databases

BioGridi12001. 1 interaction.
STRINGi3702.AT4G11010.1.

Structurei

3D structure databases

ProteinModelPortaliO49203.
SMRiO49203. Positions 86-236.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the NDK family.Curated

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiKOG0888. Eukaryota.
COG0105. LUCA.
HOGENOMiHOG000224564.
InParanoidiO49203.
KOiK00940.
OMAiWFKPQEL.
PhylomeDBiO49203.

Family and domain databases

HAMAPiMF_00451. NDP_kinase.
InterProiIPR001564. Nucleoside_diP_kinase.
IPR023005. Nucleoside_diP_kinase_AS.
[Graphical view]
PfamiPF00334. NDK. 1 hit.
[Graphical view]
PRINTSiPR01243. NUCDPKINASE.
SMARTiSM00562. NDK. 1 hit.
[Graphical view]
PROSITEiPS00469. NDP_KINASES. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

O49203-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSSQICRSAS KAAKSLLSSA KNARFFSEGR AIGAAAAVSA SGKIPLYASN
60 70 80 90 100
FARSSGSGVA SKSWITGLLA LPAAAYMIQD QEVLAAEMER TFIAIKPDGV
110 120 130 140 150
QRGLISEIIS RFERKGFKLV GIKVIVPSKD FAQKHYHDLK ERPFFNGLCD
160 170 180 190 200
FLSSGPVIAM VWEGDGVIRY GRKLIGATDP QKSEPGTIRG DLAVTVGRNI
210 220 230
IHGSDGPETA KDEISLWFKP QELVSYTSNS EKWLYGDN
Length:238
Mass (Da):25,734
Last modified:June 1, 1998 - v1
Checksum:i6F05190005F7A1D9
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF044265 mRNA. Translation: AAC00512.1.
AF080118 Genomic DNA. Translation: AAC33956.1.
AL049525 Genomic DNA. Translation: CAB40069.1.
AL161518 Genomic DNA. Translation: CAB81202.1.
CP002687 Genomic DNA. Translation: AEE82961.1.
AY062964 mRNA. Translation: AAL33810.1.
AY035184 mRNA. Translation: AAK59688.1.
PIRiT01877.
RefSeqiNP_192839.1. NM_117171.3.
UniGeneiAt.47514.

Genome annotation databases

EnsemblPlantsiAT4G11010.1; AT4G11010.1; AT4G11010.
GeneIDi826702.
GrameneiAT4G11010.1; AT4G11010.1; AT4G11010.
KEGGiath:AT4G11010.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF044265 mRNA. Translation: AAC00512.1.
AF080118 Genomic DNA. Translation: AAC33956.1.
AL049525 Genomic DNA. Translation: CAB40069.1.
AL161518 Genomic DNA. Translation: CAB81202.1.
CP002687 Genomic DNA. Translation: AEE82961.1.
AY062964 mRNA. Translation: AAL33810.1.
AY035184 mRNA. Translation: AAK59688.1.
PIRiT01877.
RefSeqiNP_192839.1. NM_117171.3.
UniGeneiAt.47514.

3D structure databases

ProteinModelPortaliO49203.
SMRiO49203. Positions 86-236.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi12001. 1 interaction.
STRINGi3702.AT4G11010.1.

Proteomic databases

PaxDbiO49203.
PRIDEiO49203.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT4G11010.1; AT4G11010.1; AT4G11010.
GeneIDi826702.
GrameneiAT4G11010.1; AT4G11010.1; AT4G11010.
KEGGiath:AT4G11010.

Organism-specific databases

TAIRiAT4G11010.

Phylogenomic databases

eggNOGiKOG0888. Eukaryota.
COG0105. LUCA.
HOGENOMiHOG000224564.
InParanoidiO49203.
KOiK00940.
OMAiWFKPQEL.
PhylomeDBiO49203.

Enzyme and pathway databases

BioCyciARA:AT4G11010-MONOMER.
ReactomeiR-ATH-499943. Synthesis and interconversion of nucleotide di- and triphosphates.

Miscellaneous databases

PROiO49203.

Gene expression databases

GenevisibleiO49203. AT.

Family and domain databases

HAMAPiMF_00451. NDP_kinase.
InterProiIPR001564. Nucleoside_diP_kinase.
IPR023005. Nucleoside_diP_kinase_AS.
[Graphical view]
PfamiPF00334. NDK. 1 hit.
[Graphical view]
PRINTSiPR01243. NUCDPKINASE.
SMARTiSM00562. NDK. 1 hit.
[Graphical view]
PROSITEiPS00469. NDP_KINASES. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Multiple evidence for nucleotide metabolism in the chloroplast thylakoid lumen."
    Spetea C., Hundal T., Lundin B., Heddad M., Adamska I., Andersson B.
    Proc. Natl. Acad. Sci. U.S.A. 101:1409-1414(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], SUBCELLULAR LOCATION, CHARACTERIZATION.
    Strain: cv. Columbia.
  2. Lee J., Song P.-S., Hahn T.R., Choi G.
    Submitted (JAN-1998) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: cv. Columbia.
  3. "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana."
    Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T., Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B., Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M., de Simone V., Obermaier B.
    , Mache R., Mueller M., Kreis M., Delseny M., Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D., Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J., Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B., Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J., Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R., Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M., Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C., Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J., Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S., Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A., Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M., Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D., Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E., Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S., Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R., Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M., Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E., Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P., Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K., Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K., de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K., Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M., Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G., Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K., Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K., Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W., Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H., Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B., Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J., Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K., O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N., Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A., Martienssen R., McCombie W.R.
    Nature 402:769-777(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  4. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  5. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
    Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
    , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
    Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  6. "Proteomic approach to identify novel mitochondrial proteins in Arabidopsis."
    Kruft V., Eubel H., Jaensch L., Werhahn W., Braun H.-P.
    Plant Physiol. 127:1694-1710(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 86-103 AND 122-135, SUBCELLULAR LOCATION.
    Tissue: Leaf and Stem.
  7. "Experimental analysis of the Arabidopsis mitochondrial proteome highlights signaling and regulatory components, provides assessment of targeting prediction programs, and indicates plant-specific mitochondrial proteins."
    Heazlewood J.L., Tonti-Filippini J.S., Gout A.M., Day D.A., Whelan J., Millar A.H.
    Plant Cell 16:241-256(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
    Strain: cv. Landsberg erecta.

Entry informationi

Entry nameiNDK3_ARATH
AccessioniPrimary (citable) accession number: O49203
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: June 1, 1998
Last modified: February 17, 2016
This is version 138 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Caution

PubMed:14736920 demonstrates a thylakoid lumen location, while PubMed:14671022 shows a mitochondrial location.Curated

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. 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.