NDK_MYXXA
ID NDK_MYXXA Reviewed; 145 AA.
AC P15266;
DT 01-APR-1990, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 03-AUG-2022, entry version 120.
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};
OS Myxococcus xanthus.
OC Bacteria; Proteobacteria; Deltaproteobacteria; Myxococcales;
OC Cystobacterineae; Myxococcaceae; Myxococcus.
OX NCBI_TaxID=34;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 2-21.
RC STRAIN=FB / DZF1;
RX PubMed=2154455; DOI=10.1016/s0021-9258(19)39858-8;
RA Munoz-Dorado J., Inouye M., Inouye S.;
RT "Nucleoside diphosphate kinase from Myxococcus xanthus. I. Cloning and
RT sequencing of the gene.";
RL J. Biol. Chem. 265:2702-2706(1990).
RN [2]
RP CHARACTERIZATION.
RX PubMed=2154456; DOI=10.1016/s0021-9258(19)39859-x;
RA Munoz-Dorado J., Inouye M., Inouye S.;
RT "Nucleoside diphosphate kinase from Myxococcus xanthus. II. Biochemical
RT characterization.";
RL J. Biol. Chem. 265:2707-2712(1990).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH SUBSTRATE.
RX PubMed=8263923; DOI=10.1006/jmbi.1993.1673;
RA Williams R.L., Oren D.A., Munoz-Dorado J., Inouye S., Inouye M., Arnold E.;
RT "Crystal structure of Myxococcus xanthus nucleoside diphosphate kinase and
RT its interaction with a nucleotide substrate at 2.0-A resolution.";
RL J. Mol. Biol. 234:1230-1247(1993).
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 -!- SUBUNIT: Homotetramer. {ECO:0000255|HAMAP-Rule:MF_00451,
CC ECO:0000269|PubMed:8263923}.
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 ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; J05207; AAA25400.1; -; Genomic_DNA.
DR PIR; A35539; A35539.
DR RefSeq; WP_011553572.1; NZ_JABFNT010000005.1.
DR PDB; 1NHK; X-ray; 1.90 A; L/R=2-145.
DR PDB; 1NLK; X-ray; 2.00 A; L/R=2-145.
DR PDB; 2NCK; X-ray; 2.00 A; L/R=2-145.
DR PDBsum; 1NHK; -.
DR PDBsum; 1NLK; -.
DR PDBsum; 2NCK; -.
DR AlphaFoldDB; P15266; -.
DR SMR; P15266; -.
DR GeneID; 41360888; -.
DR OMA; KIVAMKM; -.
DR EvolutionaryTrace; P15266; -.
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; Direct protein sequencing; Kinase;
KW Magnesium; Metal-binding; Nucleotide metabolism; Nucleotide-binding;
KW Phosphoprotein; Transferase.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:2154455"
FT CHAIN 2..145
FT /note="Nucleoside diphosphate kinase"
FT /id="PRO_0000137011"
FT ACT_SITE 117
FT /note="Pros-phosphohistidine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
FT BINDING 11
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
FT BINDING 59
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
FT BINDING 87
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
FT BINDING 93
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
FT BINDING 104
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
FT BINDING 114
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
FT STRAND 3..10
FT /evidence="ECO:0007829|PDB:1NHK"
FT HELIX 12..16
FT /evidence="ECO:0007829|PDB:1NHK"
FT HELIX 20..29
FT /evidence="ECO:0007829|PDB:1NHK"
FT STRAND 33..40
FT /evidence="ECO:0007829|PDB:1NHK"
FT HELIX 44..50
FT /evidence="ECO:0007829|PDB:1NHK"
FT HELIX 52..54
FT /evidence="ECO:0007829|PDB:1NHK"
FT HELIX 60..67
FT /evidence="ECO:0007829|PDB:1NHK"
FT STRAND 72..80
FT /evidence="ECO:0007829|PDB:1NHK"
FT HELIX 82..90
FT /evidence="ECO:0007829|PDB:1NHK"
FT HELIX 95..97
FT /evidence="ECO:0007829|PDB:1NHK"
FT HELIX 103..107
FT /evidence="ECO:0007829|PDB:1NHK"
FT STRAND 110..113
FT /evidence="ECO:0007829|PDB:1NHK"
FT STRAND 115..118
FT /evidence="ECO:0007829|PDB:1NHK"
FT HELIX 122..132
FT /evidence="ECO:0007829|PDB:1NHK"
FT HELIX 135..137
FT /evidence="ECO:0007829|PDB:1NHK"
SQ SEQUENCE 145 AA; 16135 MW; 29EA957F3E473FBA CRC64;
MAIERTLSII KPDGLEKGVI GKIISRFEEK GLKPVAIRLQ HLSQAQAEGF YAVHKARPFF
KDLVQFMISG PVVLMVLEGE NAVLANRDIM GATNPAQAAE GTIRKDFATS IDKNTVHGSD
SLENAKIEIA YFFRETEIHS YPYQK
