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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 (2,878) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 5,297 17,917 34
Proteins 4,696 17,344 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 process0.000000019530.00008112Least InformativeDirect
Biological Process (BP)nitrogen compound metabolic process0.0000012310.0001951Least InformativeDirect
Biological Process (BP)biosynthetic process0.00012780.0003181Least InformativeDirect
Biological Process (BP)single-organism metabolic process0.000052240.00008478Least InformativeDirect
Biological Process (BP)heterocycle metabolic process0.000000017740.00005846Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process0.00000010710.00006452Least InformativeDirect
Biological Process (BP)multicellular organismal process0.14490.1391Least InformativeInherited
Biological Process (BP)regulation of cellular process0.0016290.00508Least InformativeInherited
Biological Process (BP)single-organism cellular process0.41710.7289Least InformativeInherited
Biological Process (BP)response to stimulus0.14710.1281Least InformativeInherited
Biological Process (BP)phosphate-containing compound metabolic process0.000000041350.000000398Moderately InformativeDirect
Biological Process (BP)heterocycle biosynthetic process0.0000057740.00001592Moderately InformativeDirect
Biological Process (BP)aromatic compound biosynthetic process0.0000013140.0000137Moderately InformativeDirect
Biological Process (BP)organophosphate metabolic process0.0000000012320.0000000008065Moderately InformativeDirect
Biological Process (BP)cellular nitrogen compound biosynthetic process0.0000036360.0000116Moderately InformativeDirect
Biological Process (BP)nucleobase-containing small molecule metabolic process0.000000000018730.0000000000003182Moderately InformativeDirect
Biological Process (BP)organic cyclic compound biosynthetic process0.000013280.00002498Moderately InformativeDirect
Biological Process (BP)positive regulation of cellular process0.00077370.5335Moderately InformativeInherited
Biological Process (BP)reproduction0.019440.05772Moderately InformativeInherited
Biological Process (BP)organonitrogen compound biosynthetic process0.062080.02614Moderately InformativeInherited
Biological Process (BP)carbohydrate derivative metabolic process0.0019430.000291Moderately InformativeInherited
Biological Process (BP)signal transduction0.1180.01527Moderately InformativeInherited
Biological Process (BP)nucleotide biosynthetic process0.00014270.00009238InformativeDirect
Biological Process (BP)purine ribonucleoside metabolic process0.000019570.00002909InformativeDirect
Biological Process (BP)ribose phosphate biosynthetic process0.00015140.0004361InformativeDirect
Biological Process (BP)multicellular organismal reproductive process0.00059530.0007337InformativeDirect
Biological Process (BP)purine-containing compound biosynthetic process0.0000046380.000001116InformativeDirect
Biological Process (BP)pyrimidine-containing compound metabolic process0.00047820.000002942InformativeDirect
Biological Process (BP)glycosyl compound biosynthetic process0.000032010.00000143InformativeDirect
Biological Process (BP)regulation of cell proliferation0.012890.1487InformativeInherited
Biological Process (BP)phosphorylation0.0048670.2365InformativeInherited
Biological Process (BP)nucleoside triphosphate metabolic process0.061390.04583InformativeInherited
Biological Process (BP)purine ribonucleotide metabolic process0.89970.9742InformativeInherited
Biological Process (BP)pyrimidine nucleotide metabolic process0.00027350.000009417Highly InformativeDirect
Biological Process (BP)nucleoside diphosphate metabolic process0.0000002230.000000001388Highly InformativeDirect
Biological Process (BP)purine nucleoside triphosphate biosynthetic process0.000000090690.00000001179Highly InformativeDirect
Biological Process (BP)ribonucleoside triphosphate biosynthetic process0.0000010640.0000005405Highly InformativeDirect
Biological Process (BP)pyrimidine ribonucleoside metabolic process0.000080150.0000002693Highly InformativeDirect
Biological Process (BP)positive regulation of epithelial cell proliferation0.000000010030.00000107Highly InformativeDirect
Biological Process (BP)guanosine-containing compound metabolic process0.00000067090.000000005013Highly InformativeDirect
Biological Process (BP)purine ribonucleoside triphosphate metabolic process0.861Highly InformativeInherited
Biological Process (BP)pyrimidine-containing compound biosynthetic process0.0018110.00007424Highly InformativeInherited
Molecular Function (MF)transferase activity0.00000000011460.00000000002124Least InformativeDirect
Molecular Function (MF)binding0.0064170.3065Least InformativeInherited
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups00Moderately InformativeDirect
Molecular Function (MF)anion binding0.000047180.1003Moderately InformativeInherited
Molecular Function (MF)nucleotide binding0.00002310.0003421InformativeDirect
Molecular Function (MF)kinase activity00InformativeDirect
Molecular Function (MF)purine ribonucleoside binding0.000004090.00003801InformativeDirect
Molecular Function (MF)purine ribonucleoside triphosphate binding0.0033620.002109InformativeInherited
Molecular Function (MF)ATP binding0.0000000020070.00000233Highly InformativeDirect
Molecular Function (MF)nucleobase-containing compound kinase activity00Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.12550.097Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.18810.0932Least InformativeInherited
Cellular Component (CC)cell projection0.000019770.00000004631Moderately InformativeDirect
Cellular Component (CC)cell leading edge0.000000000035940.00000002022InformativeDirect
Cellular Component (CC)cell junction0.0000020950.002302InformativeInherited
Cellular Component (CC)adherens junction10.000002322Highly InformativeInherited

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 0.00008112 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.0001951 Least Informative Direct
Biological Process (BP) biosynthetic process 0.0003181 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.00008478 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.00005846 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.00006452 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.03846 Least Informative Inherited
Biological Process (BP) localization 0.1225 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.1391 Least Informative Inherited
Biological Process (BP) developmental process 0.1073 Least Informative Inherited
Biological Process (BP) response to stimulus 0.1281 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.7289 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.00508 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.000000398 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0.00001592 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0.0000137 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 0.0000000008065 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.0000116 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.0000000000003182 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.000291 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0.00002498 Moderately Informative Direct
Biological Process (BP) regulation of phosphate metabolic process 0.04919 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.1971 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.5335 Moderately Informative Inherited
Biological Process (BP) reproduction 0.05772 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.2419 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound biosynthetic process 0.02614 Moderately Informative Inherited
Biological Process (BP) organ development 0.09326 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.02991 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.01527 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.0799 Moderately Informative Inherited
Biological Process (BP) response to oxidative stress 0.0007959 Informative Direct
Biological Process (BP) microtubule-based process 0.00000641 Informative Direct
Biological Process (BP) central nervous system development 0.0003056 Informative Direct
Biological Process (BP) nucleotide biosynthetic process 0.00009238 Informative Direct
Biological Process (BP) cellular membrane organization 0.0008667 Informative Direct
Biological Process (BP) purine ribonucleoside metabolic process 0.00002909 Informative Direct
Biological Process (BP) ribose phosphate biosynthetic process 0.0004361 Informative Direct
Biological Process (BP) multicellular organismal reproductive process 0.0007337 Informative Direct
Biological Process (BP) purine-containing compound biosynthetic process 0.000001116 Informative Direct
Biological Process (BP) pyrimidine-containing compound metabolic process 0.000002942 Informative Direct
Biological Process (BP) regulation of purine nucleotide metabolic process 0.0005196 Informative Direct
Biological Process (BP) glycosyl compound biosynthetic process 0.00000143 Informative Direct
Biological Process (BP) regulation of cell proliferation 0.1487 Informative Inherited
Biological Process (BP) phosphorylation 0.2365 Informative Inherited
Biological Process (BP) cell projection organization 0.003035 Informative Inherited
Biological Process (BP) nucleoside triphosphate metabolic process 0.04583 Informative Inherited
Biological Process (BP) purine ribonucleotide metabolic process 0.9742 Informative Inherited
Biological Process (BP) cellular component movement 0.002857 Informative Inherited
Biological Process (BP) pyrimidine nucleotide metabolic process 0.000009417 Highly Informative Direct
Biological Process (BP) microtubule-based movement 0.00000005072 Highly Informative Direct
Biological Process (BP) nucleoside diphosphate metabolic process 0.000000001388 Highly Informative Direct
Biological Process (BP) purine nucleoside triphosphate biosynthetic process 0.00000001179 Highly Informative Direct
Biological Process (BP) ribonucleoside triphosphate biosynthetic process 0.0000005405 Highly Informative Direct
Biological Process (BP) cytoskeleton-dependent intracellular transport 0.000001398 Highly Informative Direct
Biological Process (BP) cilium organization 0.0000000002574 Highly Informative Direct
Biological Process (BP) pyrimidine ribonucleoside metabolic process 0.0000002693 Highly Informative Direct
Biological Process (BP) positive regulation of epithelial cell proliferation 0.00000107 Highly Informative Direct
Biological Process (BP) pyrimidine-containing compound biosynthetic process 0.00007424 Highly Informative Direct
Biological Process (BP) guanosine-containing compound metabolic process 0.000000005013 Highly Informative Direct
Biological Process (BP) purine ribonucleoside triphosphate metabolic process 1 Highly Informative Inherited
Biological Process (BP) pattern specification process 0.001198 Highly Informative Inherited
Molecular Function (MF) transferase activity 0.00000000002124 Least Informative Direct
Molecular Function (MF) binding 0.3065 Least Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0 Moderately Informative Direct
Molecular Function (MF) anion binding 0.1003 Moderately Informative Inherited
Molecular Function (MF) nucleotide binding 0.0003421 Informative Direct
Molecular Function (MF) kinase activity 0 Informative Direct
Molecular Function (MF) purine ribonucleoside binding 0.00003801 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 0.002109 Informative Inherited
Molecular Function (MF) ATP binding 0.00000233 Highly Informative Direct
Molecular Function (MF) nucleobase-containing compound kinase activity 0 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 0.9309 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.5591 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.097 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.0932 Least Informative Inherited
Cellular Component (CC) cytoskeleton 0.0000005807 Moderately Informative Direct
Cellular Component (CC) cell projection 0.00000004631 Moderately Informative Direct
Cellular Component (CC) cell leading edge 0.00000002022 Informative Direct
Cellular Component (CC) microtubule cytoskeleton 0.01194 Informative Inherited
Cellular Component (CC) cell junction 0.002302 Informative Inherited
Cellular Component (CC) centrosome 0.00000009818 Highly Informative Direct
Cellular Component (CC) adherens junction 0.000002322 Highly Informative Direct
Cellular Component (CC) cilium part 0.00000001379 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

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorous-containing groups0Least InformativeDirect
Enzyme Commission (EC)Phosphotransferases with a phosphate group as acceptor0InformativeDirect

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
Cellular componentCell projection0.0001625Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionATP-binding0Moderately InformativeDirect
Molecular functionMagnesium0Moderately 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) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · 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) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]