NDK1_MAIZE
ID NDK1_MAIZE Reviewed; 149 AA.
AC B4FK49; A0A0A7DIX5;
DT 05-DEC-2018, integrated into UniProtKB/Swiss-Prot.
DT 23-SEP-2008, sequence version 1.
DT 03-AUG-2022, entry version 78.
DE RecName: Full=Nucleoside diphosphate kinase 1 {ECO:0000303|PubMed:25679041};
DE EC=2.7.4.6 {ECO:0000255|RuleBase:RU004013, ECO:0000269|PubMed:25679041};
DE AltName: Full=Nucleoside diphosphate kinase I {ECO:0000305};
DE Short=NDK I {ECO:0000305};
DE Short=NDP kinase I {ECO:0000305};
DE Short=NDPK I {ECO:0000305};
DE AltName: Full=ZmNDPK1 {ECO:0000303|PubMed:25679041};
GN Name=ndpk1 {ECO:0000303|PubMed:25679041};
GN ORFNames=ZEAMMB73_Zm00001d029968 {ECO:0000312|EMBL:ONL99892.1};
OS Zea mays (Maize).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; PACMAD clade;
OC Panicoideae; Andropogonodae; Andropogoneae; Tripsacinae; Zea.
OX NCBI_TaxID=4577;
RN [1] {ECO:0000312|EMBL:AIL33795.1, ECO:0007744|PDB:1VYA}
RP NUCLEOTIDE SEQUENCE [MRNA], X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS),
RP FUNCTION, CATALYTIC ACTIVITY, SUBUNIT, ACTIVE SITE, AND MUTAGENESIS OF
RP HIS-115 AND LYS-149.
RC STRAIN=W23 {ECO:0000303|PubMed:25679041};
RC TISSUE=Tassel {ECO:0000312|EMBL:AIL33795.1};
RX PubMed=25679041; DOI=10.1021/bi501284g;
RA Kopylov M., Bass H.W., Stroupe M.E.;
RT "The maize (Zea mays L.) nucleoside diphosphate kinase1 (ZmNDPK1) gene
RT encodes a human NM23-H2 homologue that binds and stabilizes G-quadruplex
RT DNA.";
RL Biochemistry 54:1743-1757(2015).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. B73; TISSUE=Seedling {ECO:0000312|EMBL:ONL99892.1};
RX PubMed=19965430; DOI=10.1126/science.1178534;
RA Schnable P.S., Ware D., Fulton R.S., Stein J.C., Wei F., Pasternak S.,
RA Liang C., Zhang J., Fulton L., Graves T.A., Minx P., Reily A.D.,
RA Courtney L., Kruchowski S.S., Tomlinson C., Strong C., Delehaunty K.,
RA Fronick C., Courtney B., Rock S.M., Belter E., Du F., Kim K., Abbott R.M.,
RA Cotton M., Levy A., Marchetto P., Ochoa K., Jackson S.M., Gillam B.,
RA Chen W., Yan L., Higginbotham J., Cardenas M., Waligorski J., Applebaum E.,
RA Phelps L., Falcone J., Kanchi K., Thane T., Scimone A., Thane N., Henke J.,
RA Wang T., Ruppert J., Shah N., Rotter K., Hodges J., Ingenthron E.,
RA Cordes M., Kohlberg S., Sgro J., Delgado B., Mead K., Chinwalla A.,
RA Leonard S., Crouse K., Collura K., Kudrna D., Currie J., He R.,
RA Angelova A., Rajasekar S., Mueller T., Lomeli R., Scara G., Ko A.,
RA Delaney K., Wissotski M., Lopez G., Campos D., Braidotti M., Ashley E.,
RA Golser W., Kim H., Lee S., Lin J., Dujmic Z., Kim W., Talag J., Zuccolo A.,
RA Fan C., Sebastian A., Kramer M., Spiegel L., Nascimento L., Zutavern T.,
RA Miller B., Ambroise C., Muller S., Spooner W., Narechania A., Ren L.,
RA Wei S., Kumari S., Faga B., Levy M.J., McMahan L., Van Buren P.,
RA Vaughn M.W., Ying K., Yeh C.-T., Emrich S.J., Jia Y., Kalyanaraman A.,
RA Hsia A.-P., Barbazuk W.B., Baucom R.S., Brutnell T.P., Carpita N.C.,
RA Chaparro C., Chia J.-M., Deragon J.-M., Estill J.C., Fu Y., Jeddeloh J.A.,
RA Han Y., Lee H., Li P., Lisch D.R., Liu S., Liu Z., Nagel D.H., McCann M.C.,
RA SanMiguel P., Myers A.M., Nettleton D., Nguyen J., Penning B.W.,
RA Ponnala L., Schneider K.L., Schwartz D.C., Sharma A., Soderlund C.,
RA Springer N.M., Sun Q., Wang H., Waterman M., Westerman R., Wolfgruber T.K.,
RA Yang L., Yu Y., Zhang L., Zhou S., Zhu Q., Bennetzen J.L., Dawe R.K.,
RA Jiang J., Jiang N., Presting G.G., Wessler S.R., Aluru S.,
RA Martienssen R.A., Clifton S.W., McCombie W.R., Wing R.A., Wilson R.K.;
RT "The B73 maize genome: complexity, diversity, and dynamics.";
RL Science 326:1112-1115(2009).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RX PubMed=18937034; DOI=10.1007/s11103-008-9415-4;
RA Alexandrov N.N., Brover V.V., Freidin S., Troukhan M.E., Tatarinova T.V.,
RA Zhang H., Swaller T.J., Lu Y.-P., Bouck J., Flavell R.B., Feldmann K.A.;
RT "Insights into corn genes derived from large-scale cDNA sequencing.";
RL Plant Mol. Biol. 69:179-194(2009).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. B73 {ECO:0000312|EMBL:ACF82492.1};
RX PubMed=19936069; DOI=10.1371/journal.pgen.1000740;
RA Soderlund C., Descour A., Kudrna D., Bomhoff M., Boyd L., Currie J.,
RA Angelova A., Collura K., Wissotski M., Ashley E., Morrow D., Fernandes J.,
RA Walbot V., Yu Y.;
RT "Sequencing, mapping, and analysis of 27,455 maize full-length cDNAs.";
RL PLoS Genet. 5:E1000740-E1000740(2009).
CC -!- FUNCTION: Major role in the synthesis of nucleoside triphosphates other
CC than ATP. The ATP gamma phosphate is transferred to the NDP beta
CC phosphate via a ping-pong mechanism, using a phosphorylated active-site
CC intermediate (By similarity). Involved in transcription regulation
CC (Probable). Has G-quadruplex (G4) DNA-binding activity, which is
CC independent of its nucleotide-binding and kinase activity. Binds folded
CC G4 with low nanomolar affinity and corresponding unfolded G-rich DNA
CC more weakly. Stabilizes folded G4s regardless of whether they are
CC prefolded or not (PubMed:25679041). {ECO:0000250|UniProtKB:P36010,
CC ECO:0000269|PubMed:25679041, ECO:0000305}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 2'-deoxyribonucleoside 5'-diphosphate + ATP = a 2'-
CC deoxyribonucleoside 5'-triphosphate + ADP; Xref=Rhea:RHEA:44640,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:61560, ChEBI:CHEBI:73316,
CC ChEBI:CHEBI:456216; EC=2.7.4.6;
CC Evidence={ECO:0000255|RuleBase:RU004013,
CC ECO:0000269|PubMed:25679041};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'-
CC triphosphate + ADP; Xref=Rhea:RHEA:18113, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:57930, ChEBI:CHEBI:61557, ChEBI:CHEBI:456216; EC=2.7.4.6;
CC Evidence={ECO:0000255|RuleBase:RU004013,
CC ECO:0000269|PubMed:25679041};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000250|UniProtKB:P22392};
CC -!- SUBUNIT: Homohexamer. Can also form dodecamers.
CC {ECO:0000269|PubMed:25679041}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the NDK family. {ECO:0000255|RuleBase:RU004011,
CC ECO:0000305}.
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DR EMBL; KM347972; AIL33795.1; -; mRNA.
DR EMBL; CM007647; ONL99892.1; -; Genomic_DNA.
DR EMBL; EU954075; ACG26193.1; -; mRNA.
DR EMBL; EU954306; ACG26424.1; -; mRNA.
DR EMBL; EU957798; ACG29916.1; -; mRNA.
DR EMBL; EU961140; ACG33258.1; -; mRNA.
DR EMBL; BT037487; ACF82492.1; -; mRNA.
DR EMBL; BT061314; ACN26011.1; -; mRNA.
DR RefSeq; NP_001296954.1; NM_001310025.1.
DR PDB; 1VYA; X-ray; 2.05 A; A/B/C/D/E/F/G/H/I/J/K/L=1-149.
DR PDBsum; 1VYA; -.
DR AlphaFoldDB; B4FK49; -.
DR SMR; B4FK49; -.
DR PRIDE; B4FK49; -.
DR EnsemblPlants; Zm00001eb023820_T002; Zm00001eb023820_P002; Zm00001eb023820.
DR GeneID; 100217209; -.
DR Gramene; Zm00001eb023820_T002; Zm00001eb023820_P002; Zm00001eb023820.
DR KEGG; zma:100217209; -.
DR HOGENOM; CLU_060216_6_3_1; -.
DR OMA; KIVAMKM; -.
DR OrthoDB; 1334716at2759; -.
DR Proteomes; UP000007305; Chromosome 1.
DR ExpressionAtlas; B4FK49; baseline and differential.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0004550; F:nucleoside diphosphate kinase activity; IDA:UniProtKB.
DR GO; GO:0006241; P:CTP biosynthetic process; IEA:InterPro.
DR GO; GO:0006183; P:GTP biosynthetic process; IEA:InterPro.
DR GO; GO:0006165; P:nucleoside diphosphate phosphorylation; IDA:UniProtKB.
DR GO; GO:0009142; P:nucleoside triphosphate biosynthetic process; IDA:UniProtKB.
DR GO; GO:0034214; P:protein hexamerization; IDA:UniProtKB.
DR GO; GO:0006228; P:UTP biosynthetic process; IEA:InterPro.
DR Gene3D; 3.30.70.141; -; 1.
DR HAMAP; MF_00451; NDP_kinase; 1.
DR InterPro; IPR034907; NDK-like_dom.
DR InterPro; IPR036850; NDK-like_dom_sf.
DR InterPro; IPR001564; Nucleoside_diP_kinase.
DR InterPro; IPR023005; Nucleoside_diP_kinase_AS.
DR Pfam; PF00334; NDK; 1.
DR PRINTS; PR01243; NUCDPKINASE.
DR SMART; SM00562; NDK; 1.
DR SUPFAM; SSF54919; SSF54919; 1.
DR PROSITE; PS00469; NDP_KINASES; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; DNA-binding; Kinase; Nucleotide-binding;
KW Nucleus; Reference proteome; Transcription; Transcription regulation;
KW Transferase.
FT CHAIN 1..149
FT /note="Nucleoside diphosphate kinase 1"
FT /id="PRO_0000445391"
FT ACT_SITE 115
FT /note="Pros-phosphohistidine intermediate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10030,
FT ECO:0000269|PubMed:25679041"
FT BINDING 9
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P22392"
FT BINDING 57
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P22392"
FT BINDING 85
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P22392"
FT BINDING 91
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P22392"
FT BINDING 102
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P22392"
FT BINDING 112
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P22392"
FT MUTAGEN 115
FT /note="H->A: Loss of kinase activity. No effect on binding
FT to prefolded G-quadruplex (G4) DNA or to unfolded G4 DNA."
FT /evidence="ECO:0000269|PubMed:25679041"
FT MUTAGEN 149
FT /note="K->A: No effect on kinase activity. 5-fold reduction
FT in binding to prefolded G-quadruplex (G4) DNA. Loss fo
FT binding to unfolded G4 DNA."
FT /evidence="ECO:0000269|PubMed:25679041"
FT CONFLICT 135
FT /note="P -> L (in Ref. 1; AIL33795)"
FT /evidence="ECO:0000305"
FT STRAND 3..8
FT /evidence="ECO:0007829|PDB:1VYA"
FT HELIX 10..14
FT /evidence="ECO:0007829|PDB:1VYA"
FT HELIX 18..28
FT /evidence="ECO:0007829|PDB:1VYA"
FT STRAND 31..39
FT /evidence="ECO:0007829|PDB:1VYA"
FT HELIX 42..48
FT /evidence="ECO:0007829|PDB:1VYA"
FT HELIX 50..52
FT /evidence="ECO:0007829|PDB:1VYA"
FT HELIX 58..65
FT /evidence="ECO:0007829|PDB:1VYA"
FT STRAND 67..77
FT /evidence="ECO:0007829|PDB:1VYA"
FT HELIX 80..88
FT /evidence="ECO:0007829|PDB:1VYA"
FT TURN 93..95
FT /evidence="ECO:0007829|PDB:1VYA"
FT HELIX 101..105
FT /evidence="ECO:0007829|PDB:1VYA"
FT STRAND 114..116
FT /evidence="ECO:0007829|PDB:1VYA"
FT HELIX 120..130
FT /evidence="ECO:0007829|PDB:1VYA"
FT HELIX 143..146
FT /evidence="ECO:0007829|PDB:1VYA"
SQ SEQUENCE 149 AA; 16541 MW; 18980971F0474014 CRC64;
MESTFIMIKP DGVQRGLIGE IISRFEKKGF YLKALKLVNV ERSFAEKHYA DLASKPFFQG
LVDYIISGPV VAMVWEGKSV VTTGRKIIGA TNPLASEPGT IRGDFAVDIG RNVIHGSDSI
ESANKEIALW FPEGPADWQS SQHPWIYEK
