NDK_MIMIV
ID NDK_MIMIV Reviewed; 137 AA.
AC Q5UQL3;
DT 13-SEP-2005, integrated into UniProtKB/Swiss-Prot.
DT 07-DEC-2004, sequence version 1.
DT 03-AUG-2022, entry version 88.
DE RecName: Full=Nucleoside diphosphate kinase;
DE Short=NDK;
DE Short=NDP kinase;
DE EC=2.7.4.6;
GN Name=NDK; OrderedLocusNames=MIMI_R418;
OS Acanthamoeba polyphaga mimivirus (APMV).
OC Viruses; Varidnaviria; Bamfordvirae; Nucleocytoviricota; Megaviricetes;
OC Imitervirales; Mimiviridae; Mimivirus.
OX NCBI_TaxID=212035;
OH NCBI_TaxID=5757; Acanthamoeba polyphaga (Amoeba).
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Rowbotham-Bradford;
RX PubMed=15486256; DOI=10.1126/science.1101485;
RA Raoult D., Audic S., Robert C., Abergel C., Renesto P., Ogata H.,
RA La Scola B., Susan M., Claverie J.-M.;
RT "The 1.2-megabase genome sequence of Mimivirus.";
RL Science 306:1344-1350(2004).
RN [2]
RP CHARACTERIZATION, AND BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=Rowbotham-Bradford;
RX PubMed=16957983; DOI=10.1007/s10863-006-9045-y;
RA Jeudy S., Claverie J.-M., Abergel C.;
RT "The nucleoside diphosphate kinase from mimivirus: a peculiar affinity for
RT deoxypyrimidine nucleotides.";
RL J. Bioenerg. Biomembr. 38:247-254(2006).
RN [3]
RP MUTAGENESIS OF ASN-62 AND ARG-107.
RC STRAIN=Rowbotham-Bradford;
RX PubMed=19457438; DOI=10.1016/j.jip.2009.03.011;
RA Claverie J.M., Grzela R., Lartigue A., Bernadac A., Nitsche S., Vacelet J.,
RA Ogata H., Abergel C.;
RT "Mimivirus and Mimiviridae: giant viruses with an increasing number of
RT potential hosts, including corals and sponges.";
RL J. Invertebr. Pathol. 101:172-180(2009).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH ATP ANALOG.
RC STRAIN=Rowbotham-Bradford;
RX PubMed=16511098; DOI=10.1107/s1744309105013904;
RA Jeudy S., Coutard B., Lebrun R., Abergel C.;
RT "Acanthamoeba polyphaga mimivirus NDK: preliminary crystallographic
RT analysis of the first viral nucleoside diphosphate kinase.";
RL Acta Crystallogr. F 61:569-572(2005).
CC -!- FUNCTION: Plays a role in the synthesis of nucleoside triphosphates.
CC This activity may optimize the replication of the AT-rich (73%) viral
CC genome in a thymidine-limited host environment.
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; Evidence={ECO:0000255|PROSITE-
CC ProRule:PRU10030};
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|PROSITE-ProRule:PRU10030};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=140 uM for dGDP {ECO:0000269|PubMed:16957983};
CC KM=41 uM for dGTP {ECO:0000269|PubMed:16957983};
CC KM=5 uM for ADP {ECO:0000269|PubMed:16957983};
CC KM=770 uM for ATP {ECO:0000269|PubMed:16957983};
CC KM=830 uM for GTP {ECO:0000269|PubMed:16957983};
CC KM=100 uM for UDP {ECO:0000269|PubMed:16957983};
CC KM=110 uM for UTP {ECO:0000269|PubMed:16957983};
CC KM=40 uM for CTP {ECO:0000269|PubMed:16957983};
CC KM=50 uM for CDP {ECO:0000269|PubMed:16957983};
CC KM=30 uM for dTTP {ECO:0000269|PubMed:16957983};
CC KM=25 uM for dUTP {ECO:0000269|PubMed:16957983};
CC Vmax=99 umol/min/mg enzyme toward dGDP {ECO:0000269|PubMed:16957983};
CC Vmax=27 umol/min/mg enzyme toward dGTP {ECO:0000269|PubMed:16957983};
CC Vmax=50 umol/min/mg enzyme toward ADP {ECO:0000269|PubMed:16957983};
CC Vmax=140 umol/min/mg enzyme toward ATP {ECO:0000269|PubMed:16957983};
CC Vmax=450 umol/min/mg enzyme toward GTP {ECO:0000269|PubMed:16957983};
CC Vmax=110 umol/min/mg enzyme toward UDP {ECO:0000269|PubMed:16957983};
CC Vmax=41 umol/min/mg enzyme toward UTP {ECO:0000269|PubMed:16957983};
CC Vmax=25 umol/min/mg enzyme toward CTP {ECO:0000269|PubMed:16957983};
CC Vmax=70 umol/min/mg enzyme toward CDP {ECO:0000269|PubMed:16957983};
CC Note=KM values are below 10 uM for dCDP, dCTP and dUTP.;
CC -!- SIMILARITY: Belongs to the NDK family. {ECO:0000305}.
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DR EMBL; AY653733; AAV50687.1; -; Genomic_DNA.
DR RefSeq; YP_003986922.1; NC_014649.1.
DR PDB; 2B8P; X-ray; 2.55 A; A/B=2-137.
DR PDB; 2B8Q; X-ray; 2.50 A; A/B/C/D/E/F=2-137.
DR PDB; 3B6B; X-ray; 2.00 A; A/B/C/D/E/F=2-137.
DR PDB; 3DDI; X-ray; 1.90 A; A/B=2-137.
DR PDB; 3DKD; X-ray; 1.90 A; A/B=2-137.
DR PDB; 3EE3; X-ray; 2.40 A; A/B/C/D/E/F=2-137.
DR PDB; 3EIC; X-ray; 2.30 A; A/B/C/D/E/F=2-137.
DR PDB; 3EJM; X-ray; 1.95 A; A/B=2-137.
DR PDB; 3ELH; X-ray; 2.40 A; A/B/C/D/E/F=2-137.
DR PDB; 3EM1; X-ray; 1.50 A; A/B=2-137.
DR PDB; 3EMT; X-ray; 1.60 A; A/B=2-137.
DR PDB; 3ENA; X-ray; 1.60 A; A/B=2-137.
DR PDB; 3ETM; X-ray; 1.90 A; A/B=2-137.
DR PDB; 3EVM; X-ray; 1.80 A; A/B=2-137.
DR PDB; 3EVO; X-ray; 1.50 A; A/B=2-137.
DR PDB; 3EVW; X-ray; 2.60 A; A/B/C/D/E/F=2-137.
DR PDB; 3FBB; X-ray; 2.40 A; A/B/C/D/E/F=2-137.
DR PDB; 3FBC; X-ray; 2.60 A; A/B/C/D/E/F=2-137.
DR PDB; 3FBE; X-ray; 2.40 A; A/B/C/D/E/F=2-137.
DR PDB; 3FBF; X-ray; 2.60 A; A/B/C/D/E/F=2-137.
DR PDB; 3FC9; X-ray; 2.80 A; A/B/C/D/E/F=2-137.
DR PDB; 3FCV; X-ray; 2.40 A; A/B=2-137.
DR PDB; 3FCW; X-ray; 2.40 A; A/B/C/D/E/F=2-137.
DR PDB; 3G2X; X-ray; 2.70 A; A/B/C/D/E/F=2-137.
DR PDB; 3GP9; X-ray; 1.80 A; A/B/C/D/E/F=2-137.
DR PDB; 3GPA; X-ray; 2.00 A; A/B/C/D/E/F=2-137.
DR PDBsum; 2B8P; -.
DR PDBsum; 2B8Q; -.
DR PDBsum; 3B6B; -.
DR PDBsum; 3DDI; -.
DR PDBsum; 3DKD; -.
DR PDBsum; 3EE3; -.
DR PDBsum; 3EIC; -.
DR PDBsum; 3EJM; -.
DR PDBsum; 3ELH; -.
DR PDBsum; 3EM1; -.
DR PDBsum; 3EMT; -.
DR PDBsum; 3ENA; -.
DR PDBsum; 3ETM; -.
DR PDBsum; 3EVM; -.
DR PDBsum; 3EVO; -.
DR PDBsum; 3EVW; -.
DR PDBsum; 3FBB; -.
DR PDBsum; 3FBC; -.
DR PDBsum; 3FBE; -.
DR PDBsum; 3FBF; -.
DR PDBsum; 3FC9; -.
DR PDBsum; 3FCV; -.
DR PDBsum; 3FCW; -.
DR PDBsum; 3G2X; -.
DR PDBsum; 3GP9; -.
DR PDBsum; 3GPA; -.
DR SMR; Q5UQL3; -.
DR PRIDE; Q5UQL3; -.
DR GeneID; 9925039; -.
DR KEGG; vg:9925039; -.
DR BRENDA; 2.7.4.6; 9231.
DR SABIO-RK; Q5UQL3; -.
DR EvolutionaryTrace; Q5UQL3; -.
DR Proteomes; UP000001134; Genome.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004550; F:nucleoside diphosphate kinase activity; IEA:UniProtKB-EC.
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; IEA:InterPro.
DR GO; GO:0006228; P:UTP biosynthetic process; IEA:InterPro.
DR Gene3D; 3.30.70.141; -; 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; Kinase; Magnesium; Metal-binding;
KW Nucleotide metabolism; Nucleotide-binding; Phosphoprotein;
KW Reference proteome; Transferase.
FT CHAIN 1..137
FT /note="Nucleoside diphosphate kinase"
FT /id="PRO_0000137154"
FT ACT_SITE 112
FT /note="Pros-phosphohistidine intermediate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10030"
FT BINDING 9
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 58
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 86
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 99
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 109
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT MUTAGEN 62
FT /note="N->L: Increased affinity for NTP and decreased
FT affinity for dNTP."
FT /evidence="ECO:0000269|PubMed:19457438"
FT MUTAGEN 107
FT /note="R->G: Complete loss of affinity for pyrimidine
FT bases."
FT /evidence="ECO:0000269|PubMed:19457438"
FT STRAND 2..8
FT /evidence="ECO:0007829|PDB:3EM1"
FT HELIX 10..14
FT /evidence="ECO:0007829|PDB:3EM1"
FT HELIX 18..27
FT /evidence="ECO:0007829|PDB:3EM1"
FT STRAND 31..40
FT /evidence="ECO:0007829|PDB:3EM1"
FT HELIX 43..49
FT /evidence="ECO:0007829|PDB:3EM1"
FT HELIX 51..53
FT /evidence="ECO:0007829|PDB:3EM1"
FT HELIX 59..66
FT /evidence="ECO:0007829|PDB:3EM1"
FT STRAND 71..78
FT /evidence="ECO:0007829|PDB:3EM1"
FT HELIX 81..89
FT /evidence="ECO:0007829|PDB:3EM1"
FT HELIX 98..102
FT /evidence="ECO:0007829|PDB:3EM1"
FT STRAND 105..107
FT /evidence="ECO:0007829|PDB:3EM1"
FT STRAND 110..113
FT /evidence="ECO:0007829|PDB:3EM1"
FT HELIX 117..127
FT /evidence="ECO:0007829|PDB:3EM1"
SQ SEQUENCE 137 AA; 15750 MW; 8C1C6C88964D6BBC CRC64;
MQRTLVLIKP DAFERSLVAE IMGRIEKKNF KIVSMKFWSK APRNLIEQHY KEHSEQSYFN
DNCDFMVSGP IISIVYEGTD AISKIRRLQG NILTPGTIRG DLANDIRENL IHASDSEDSA
VDEISIWFPE TKMETDN
