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Nucleoside diphosphate kinase, NDK superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Ferredoxin-like [ 54861] (59)
Superfamily:   Nucleoside diphosphate kinase, NDK [ 54919]
Families:   Nucleoside diphosphate kinase, NDK [ 54920]


Superfamily statistics
Genomes (2,887) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 5,387 20,862 34
Proteins 4,769 19,666 34


Functional annotation
General category Metabolism
Detailed category Nucleotide metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)cellular aromatic compound metabolic process00Least InformativeDirect
Biological Process (BP)cellular nitrogen compound metabolic process00Least InformativeDirect
Biological Process (BP)primary metabolic process0.0000000000000031440.00000000004962Least InformativeDirect
Biological Process (BP)single-organism metabolic process0.000000000024390Least InformativeDirect
Biological Process (BP)single-organism cellular process0.0000046520.00001406Least InformativeDirect
Biological Process (BP)heterocycle metabolic process00Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process00Least InformativeDirect
Biological Process (BP)biological regulation0.00021350.7547Least InformativeInherited
Biological Process (BP)biosynthetic process0.022580.0008286Least InformativeInherited
Biological Process (BP)response to stimulus0.56030.9778Least InformativeInherited
Biological Process (BP)organonitrogen compound metabolic process0.93361Least InformativeInherited
Biological Process (BP)nucleoside phosphate metabolic process0.00051430.0000002546Moderately InformativeDirect
Biological Process (BP)heterocycle biosynthetic process0.00015360.000000849Moderately InformativeDirect
Biological Process (BP)aromatic compound biosynthetic process0.000010170.0000002483Moderately InformativeDirect
Biological Process (BP)purine-containing compound metabolic process0.000000012430.0000000001774Moderately InformativeDirect
Biological Process (BP)organophosphate biosynthetic process0.000000000000057910Moderately InformativeDirect
Biological Process (BP)carbohydrate derivative metabolic process0.00002030.0000003564Moderately InformativeDirect
Biological Process (BP)organic cyclic compound biosynthetic process0.00044310.000005844Moderately InformativeDirect
Biological Process (BP)regulation of multicellular organismal process0.00024310.0156Moderately InformativeInherited
Biological Process (BP)positive regulation of cellular process0.00049750.2173Moderately InformativeInherited
Biological Process (BP)regulation of developmental process0.000038320.006674Moderately InformativeInherited
Biological Process (BP)cell communication0.30341Moderately InformativeInherited
Biological Process (BP)single organism signaling0.33370.9453Moderately InformativeInherited
Biological Process (BP)ribose phosphate biosynthetic process0.000000000063580.000000008184InformativeDirect
Biological Process (BP)purine-containing compound biosynthetic process0.000000000000037410.0000000000001015InformativeDirect
Biological Process (BP)glycosyl compound metabolic process0.0000000000085720InformativeDirect
Biological Process (BP)regulation of cell proliferation0.0068190.04974InformativeInherited
Biological Process (BP)phosphorylation0.33551InformativeInherited
Biological Process (BP)regulation of anatomical structure morphogenesis0.24060.1332InformativeInherited
Biological Process (BP)cell surface receptor signaling pathway0.002110.01714InformativeInherited
Biological Process (BP)nucleotide biosynthetic process0.0027070.02372InformativeInherited
Biological Process (BP)pyrimidine-containing compound biosynthetic process0.018620.0004687InformativeInherited
Biological Process (BP)nucleoside triphosphate biosynthetic process00Highly InformativeDirect
Biological Process (BP)nucleoside biosynthetic process00Highly InformativeDirect
Biological Process (BP)regulation of epithelial cell proliferation0.00000014220.00004225Highly InformativeDirect
Biological Process (BP)pyrimidine ribonucleotide metabolic process0.014070.0005891Highly InformativeInherited
Biological Process (BP)pyrimidine ribonucleoside metabolic process0.34040.2441Highly InformativeInherited
Biological Process (BP)pyrimidine nucleoside triphosphate metabolic process0.045610.003519Highly InformativeInherited
Biological Process (BP)pyrimidine nucleotide biosynthetic process0.23870.02144Highly InformativeInherited
Biological Process (BP)purine ribonucleoside metabolic process0.012260.009248Highly InformativeInherited
Molecular Function (MF)transferase activity00Least InformativeDirect
Molecular Function (MF)binding0.23311Least InformativeInherited
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups00Moderately InformativeDirect
Molecular Function (MF)carbohydrate derivative binding0.0032510.01065Moderately InformativeInherited
Molecular Function (MF)small molecule binding0.0052680.01163Moderately InformativeInherited
Molecular Function (MF)anion binding0.00046740.08851Moderately InformativeInherited
Molecular Function (MF)kinase activity00InformativeDirect
Molecular Function (MF)purine nucleotide binding0.00020760.001929InformativeInherited
Molecular Function (MF)ribonucleotide binding0.00030790.002177InformativeInherited
Molecular Function (MF)purine ribonucleoside triphosphate binding0.01650.01452InformativeInherited
Molecular Function (MF)ATP binding0.00000054380.0001443Highly InformativeDirect
Molecular Function (MF)phosphotransferase activity, phosphate group as acceptor00Highly InformativeDirect
Molecular Function (MF)nucleobase-containing compound kinase activity00Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.097880.4719Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.39590.03209Least InformativeInherited
Cellular Component (CC)cell projection0.000042480.000002131Moderately InformativeDirect
Cellular Component (CC)ruffle00.00000001442Highly InformativeDirect
Cellular Component (CC)cell-substrate adherens junction0.0000000000056570.00000222Highly InformativeDirect
Cellular Component (CC)lamellipodium0.0000000026560.0000148Highly InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) cellular aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) biosynthetic process 0.0008286 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) primary metabolic process 0.00000000004962 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.00001406 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) biological regulation 0.7547 Least Informative Inherited
Biological Process (BP) response to stimulus 0.9778 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) nucleoside phosphate metabolic process 0.0000002546 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0.000000849 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0.0000002483 Moderately Informative Direct
Biological Process (BP) purine-containing compound metabolic process 0.0000000001774 Moderately Informative Direct
Biological Process (BP) organophosphate biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.0000003564 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0.000005844 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 0.0156 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.2173 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.006674 Moderately Informative Inherited
Biological Process (BP) cell communication 1 Moderately Informative Inherited
Biological Process (BP) single organism signaling 0.9453 Moderately Informative Inherited
Biological Process (BP) response to oxidative stress 0.0002301 Informative Direct
Biological Process (BP) ribose phosphate biosynthetic process 0.000000008184 Informative Direct
Biological Process (BP) purine-containing compound biosynthetic process 0.0000000000001015 Informative Direct
Biological Process (BP) pyrimidine-containing compound biosynthetic process 0.0004687 Informative Direct
Biological Process (BP) glycosyl compound metabolic process 0 Informative Direct
Biological Process (BP) regulation of cell proliferation 0.04974 Informative Inherited
Biological Process (BP) phosphorylation 1 Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 0.1332 Informative Inherited
Biological Process (BP) cell surface receptor signaling pathway 0.01714 Informative Inherited
Biological Process (BP) nucleotide biosynthetic process 0.02372 Informative Inherited
Biological Process (BP) nucleoside triphosphate biosynthetic process 0 Highly Informative Direct
Biological Process (BP) nucleoside biosynthetic process 0 Highly Informative Direct
Biological Process (BP) pyrimidine ribonucleotide metabolic process 0.0005891 Highly Informative Direct
Biological Process (BP) regulation of epithelial cell proliferation 0.00004225 Highly Informative Direct
Biological Process (BP) pyrimidine ribonucleoside metabolic process 0.2441 Highly Informative Inherited
Biological Process (BP) pyrimidine nucleoside triphosphate metabolic process 0.003519 Highly Informative Inherited
Biological Process (BP) pyrimidine nucleotide biosynthetic process 0.02144 Highly Informative Inherited
Biological Process (BP) purine ribonucleoside metabolic process 0.009248 Highly Informative Inherited
Molecular Function (MF) transferase activity 0 Least Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0 Moderately Informative Direct
Molecular Function (MF) carbohydrate derivative binding 0.01065 Moderately Informative Inherited
Molecular Function (MF) small molecule binding 0.01163 Moderately Informative Inherited
Molecular Function (MF) anion binding 0.08851 Moderately Informative Inherited
Molecular Function (MF) kinase activity 0 Informative Direct
Molecular Function (MF) purine nucleotide binding 0.001929 Informative Inherited
Molecular Function (MF) ribonucleotide binding 0.002177 Informative Inherited
Molecular Function (MF) purine ribonucleoside triphosphate binding 0.01452 Informative Inherited
Molecular Function (MF) ATP binding 0.0001443 Highly Informative Direct
Molecular Function (MF) phosphotransferase activity, phosphate group as acceptor 0 Highly Informative Direct
Molecular Function (MF) nucleobase-containing compound kinase activity 0 Highly Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.6668 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.4719 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.03209 Least Informative Inherited
Cellular Component (CC) cytoskeleton 0.0002177 Moderately Informative Direct
Cellular Component (CC) cell projection 0.000002131 Moderately Informative Direct
Cellular Component (CC) cilium 0.0001186 Informative Direct
Cellular Component (CC) plasma membrane bounded cell projection part 0.856 Informative Inherited
Cellular Component (CC) ruffle 0.00000001442 Highly Informative Direct
Cellular Component (CC) cell-substrate adherens junction 0.00000222 Highly Informative Direct
Cellular Component (CC) lamellipodium 0.0000148 Highly Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Phosphotransferases with a phosphate group as acce0InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processNucleotide metabolism0Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionMagnesium0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationKinase0Moderately InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR001564 SSF54919 Protein matches
Abstract

Nucleoside diphosphate kinases (NDK) are enzymes required for the synthesis of nucleoside triphosphates (NTP) other than ATP. They provide NTPs for nucleic acid synthesis, CTP for lipid synthesis, UTP for polysaccharide synthesis and GTP for protein elongation, signal transduction and microtubule polymerization.

In eukaryotes, there seems to be a small family of NDK isozymes each of which acts in a different subcellular compartment and/or has a distinct biological function. Eukaryotic NDK isozymes are hexamers of two highly related chains (A and B) [PubMed1851158]. By random association (A6, A5B...AB5, B6), these two kinds of chain form isoenzymes differing in their isoelectric point.

NDK are proteins of 17 Kd that act via a ping-pong mechanism in which a histidine residue is phosphorylated, by transfer of the terminal phosphate group from ATP. In the presence of magnesium, the phosphoenzyme can transfer its phosphate group to any NDP, to produce an NTP.

NDK isozymes have been sequenced from prokaryotic and eukaryotic sources. It has also been shown [PubMed2175255] that the Drosophila awd (abnormal wing discs) protein, is a microtubule-associated NDK. Mammalian NDK is also known as metastasis inhibition factor nm23. The sequence of NDK has been highly conserved through evolution. There is a single histidine residue conserved in all known NDK isozymes, which is involved in the catalytic mechanism [PubMed1851158]. Our signature pattern contains this residue.


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 20 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a Nucleoside diphosphate kinase, NDK domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 20 hidden Markov models representing the Nucleoside diphosphate kinase, NDK superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]