NDK_PYRHO
ID NDK_PYRHO Reviewed; 157 AA.
AC O58429;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 26-SEP-2001, sequence version 2.
DT 03-AUG-2022, entry version 122.
DE RecName: Full=Nucleoside diphosphate kinase {ECO:0000255|HAMAP-Rule:MF_00451};
DE Short=NDK {ECO:0000255|HAMAP-Rule:MF_00451};
DE Short=NDP kinase {ECO:0000255|HAMAP-Rule:MF_00451};
DE EC=2.7.4.6 {ECO:0000255|HAMAP-Rule:MF_00451};
DE AltName: Full=Nucleoside-2-P kinase {ECO:0000255|HAMAP-Rule:MF_00451};
GN Name=ndk {ECO:0000255|HAMAP-Rule:MF_00451}; OrderedLocusNames=PH0698;
OS Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC
OS 100139 / OT-3).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Pyrococcus.
OX NCBI_TaxID=70601;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3;
RX PubMed=9679194; DOI=10.1093/dnares/5.2.55;
RA Kawarabayasi Y., Sawada M., Horikawa H., Haikawa Y., Hino Y., Yamamoto S.,
RA Sekine M., Baba S., Kosugi H., Hosoyama A., Nagai Y., Sakai M., Ogura K.,
RA Otsuka R., Nakazawa H., Takamiya M., Ohfuku Y., Funahashi T., Tanaka T.,
RA Kudoh Y., Yamazaki J., Kushida N., Oguchi A., Aoki K., Yoshizawa T.,
RA Nakamura Y., Robb F.T., Horikoshi K., Masuchi Y., Shizuya H., Kikuchi H.;
RT "Complete sequence and gene organization of the genome of a hyper-
RT thermophilic archaebacterium, Pyrococcus horikoshii OT3.";
RL DNA Res. 5:55-76(1998).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS).
RG RIKEN structural genomics initiative (RSGI);
RT "Crystal structure of nucleotide diphosphate kinase from Pyrococcus
RT horikoshii.";
RL Submitted (DEC-2005) to the PDB data bank.
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. {ECO:0000255|HAMAP-Rule:MF_00451}.
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|HAMAP-
CC Rule:MF_00451};
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|HAMAP-Rule:MF_00451};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00451};
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00451}.
CC -!- SIMILARITY: Belongs to the NDK family. {ECO:0000255|HAMAP-
CC Rule:MF_00451, ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAA29789.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; BA000001; BAA29789.1; ALT_INIT; Genomic_DNA.
DR PIR; C71116; C71116.
DR RefSeq; WP_048053198.1; NC_000961.1.
DR PDB; 2CWK; X-ray; 1.75 A; A/B=1-157.
DR PDB; 2DXD; X-ray; 1.77 A; A/B=1-157.
DR PDB; 2DXE; X-ray; 1.70 A; A/B=1-157.
DR PDB; 2DXF; X-ray; 1.70 A; A/B=1-157.
DR PDB; 2DY9; X-ray; 2.01 A; A/B=1-157.
DR PDB; 2DYA; X-ray; 1.77 A; A/B=1-157.
DR PDBsum; 2CWK; -.
DR PDBsum; 2DXD; -.
DR PDBsum; 2DXE; -.
DR PDBsum; 2DXF; -.
DR PDBsum; 2DY9; -.
DR PDBsum; 2DYA; -.
DR AlphaFoldDB; O58429; -.
DR SMR; O58429; -.
DR STRING; 70601.3257106; -.
DR EnsemblBacteria; BAA29789; BAA29789; BAA29789.
DR GeneID; 1443028; -.
DR KEGG; pho:PH0698; -.
DR eggNOG; arCOG04313; Archaea.
DR OMA; KIVAMKM; -.
DR OrthoDB; 106462at2157; -.
DR EvolutionaryTrace; O58429; -.
DR Proteomes; UP000000752; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004550; F:nucleoside diphosphate kinase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0006241; P:CTP biosynthetic process; IEA:UniProtKB-UniRule.
DR GO; GO:0006183; P:GTP biosynthetic process; IEA:UniProtKB-UniRule.
DR GO; GO:0006165; P:nucleoside diphosphate phosphorylation; IEA:InterPro.
DR GO; GO:0006228; P:UTP biosynthetic process; IEA:UniProtKB-UniRule.
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; Cytoplasm; Kinase; Magnesium; Metal-binding;
KW Nucleotide metabolism; Nucleotide-binding; Phosphoprotein; Transferase.
FT CHAIN 1..157
FT /note="Nucleoside diphosphate kinase"
FT /id="PRO_0000137099"
FT ACT_SITE 121
FT /note="Pros-phosphohistidine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
FT BINDING 12
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
FT BINDING 60
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
FT BINDING 88
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
FT BINDING 94
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
FT BINDING 105
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
FT STRAND 4..11
FT /evidence="ECO:0007829|PDB:2DXE"
FT HELIX 13..17
FT /evidence="ECO:0007829|PDB:2DXE"
FT HELIX 21..31
FT /evidence="ECO:0007829|PDB:2DXE"
FT STRAND 34..41
FT /evidence="ECO:0007829|PDB:2DXE"
FT HELIX 45..51
FT /evidence="ECO:0007829|PDB:2DXE"
FT HELIX 53..55
FT /evidence="ECO:0007829|PDB:2DXE"
FT HELIX 61..68
FT /evidence="ECO:0007829|PDB:2DXE"
FT STRAND 73..81
FT /evidence="ECO:0007829|PDB:2DXE"
FT HELIX 83..91
FT /evidence="ECO:0007829|PDB:2DXE"
FT HELIX 96..98
FT /evidence="ECO:0007829|PDB:2DXE"
FT HELIX 104..108
FT /evidence="ECO:0007829|PDB:2DXE"
FT STRAND 113..115
FT /evidence="ECO:0007829|PDB:2DXE"
FT STRAND 119..122
FT /evidence="ECO:0007829|PDB:2DXE"
FT HELIX 126..136
FT /evidence="ECO:0007829|PDB:2DXE"
FT HELIX 139..141
FT /evidence="ECO:0007829|PDB:2DXE"
FT HELIX 150..153
FT /evidence="ECO:0007829|PDB:2DXE"
SQ SEQUENCE 157 AA; 17908 MW; 66D242C6BB46AAF5 CRC64;
MSETERTLVI IKPDAVVRGL IGEIISRFEK KGLKIVGMKM IWIDRELAEK HYEEHREKPF
FKALIDYITK TPVVVMVLEG RYAVEVVRKM AGATDPKDAA PGTIRGDFGL EVSDAICNVI
HASDSKESAE REISLFFKPE ELFEYPRAAD WFYKKGI
