SUPERFAMILY 1.75 HMM library and genome assignments server

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 (2,879) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 5,315 17,917 34
Proteins 4,711 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 process0.000000026370.00008338Least InformativeDirect
Biological Process (BP)nitrogen compound metabolic process0.0000015310.0001944Least InformativeDirect
Biological Process (BP)biosynthetic process0.00010840.0002656Least InformativeDirect
Biological Process (BP)heterocycle metabolic process0.000000023920.00006003Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process0.00000013780.00006727Least InformativeDirect
Biological Process (BP)single-organism metabolic process0.01160.02568Least InformativeInherited
Biological Process (BP)positive regulation of biological process0.0048120.1638Least InformativeInherited
Biological Process (BP)regulation of cellular process0.0020180.005771Least InformativeInherited
Biological Process (BP)single-organism cellular process0.010730.03624Least InformativeInherited
Biological Process (BP)response to stimulus0.14650.1305Least InformativeInherited
Biological Process (BP)phosphate-containing compound metabolic process0.000000075650.0000008483Moderately InformativeDirect
Biological Process (BP)heterocycle biosynthetic process0.0000057160.00001516Moderately InformativeDirect
Biological Process (BP)aromatic compound biosynthetic process0.0000013320.00001307Moderately InformativeDirect
Biological Process (BP)organophosphate metabolic process0.0000000016870.00000000108Moderately InformativeDirect
Biological Process (BP)cellular nitrogen compound biosynthetic process0.0000035250.00001066Moderately InformativeDirect
Biological Process (BP)nucleobase-containing small molecule metabolic process0.0000000000034480.0000000000002211Moderately InformativeDirect
Biological Process (BP)organic cyclic compound biosynthetic process0.000012830.00002386Moderately InformativeDirect
Biological Process (BP)carbohydrate derivative metabolic process0.0023160.0003739Moderately InformativeInherited
Biological Process (BP)organonitrogen compound biosynthetic process0.060050.0244Moderately InformativeInherited
Biological Process (BP)positive regulation of cellular process0.0013240.09318Moderately InformativeInherited
Biological Process (BP)signal transduction0.10650.01519Moderately InformativeInherited
Biological Process (BP)nucleotide biosynthetic process0.000078230.00005293InformativeDirect
Biological Process (BP)purine ribonucleoside metabolic process0.000032880.00004983InformativeDirect
Biological Process (BP)ribose phosphate biosynthetic process0.00011880.0003434InformativeDirect
Biological Process (BP)purine-containing compound biosynthetic process0.0000039630.0000009525InformativeDirect
Biological Process (BP)pyrimidine-containing compound metabolic process0.00048850.000003InformativeDirect
Biological Process (BP)glycosyl compound biosynthetic process0.000028410.000001259InformativeDirect
Biological Process (BP)regulation of cell proliferation0.011960.147InformativeInherited
Biological Process (BP)phosphorylation0.012180.3424InformativeInherited
Biological Process (BP)purine ribonucleotide metabolic process0.92740.9974InformativeInherited
Biological Process (BP)nucleoside triphosphate metabolic process0.0890.0665InformativeInherited
Biological Process (BP)pyrimidine nucleotide metabolic process0.00020560.000006941Highly InformativeDirect
Biological Process (BP)nucleoside diphosphate metabolic process0.00000014110.0000000009087Highly InformativeDirect
Biological Process (BP)purine ribonucleoside triphosphate biosynthetic process0.0000000097150.0000000004952Highly InformativeDirect
Biological Process (BP)pyrimidine ribonucleoside metabolic process0.000055420.0000001752Highly InformativeDirect
Biological Process (BP)positive regulation of epithelial cell proliferation0.0000000099680.000001103Highly InformativeDirect
Biological Process (BP)guanosine-containing compound metabolic process0.00000066480.000000004928Highly InformativeDirect
Molecular Function (MF)transferase activity0.00000000034670.0000000001986Least InformativeDirect
Molecular Function (MF)binding0.0068060.3214Least InformativeInherited
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups00Moderately InformativeDirect
Molecular Function (MF)small molecule binding0.00038440.0002787Moderately InformativeDirect
Molecular Function (MF)carbohydrate derivative binding0.00052390.0008036Moderately InformativeDirect
Molecular Function (MF)anion binding0.000047590.1005Moderately InformativeInherited
Molecular Function (MF)kinase activity00InformativeDirect
Molecular Function (MF)protein complex binding0.00053180.0009597InformativeDirect
Molecular Function (MF)purine ribonucleoside binding0.0000041010.00003807InformativeDirect
Molecular Function (MF)nucleotide binding0.14250.2386InformativeInherited
Molecular Function (MF)purine ribonucleoside triphosphate binding0.0034050.00213InformativeInherited
Molecular Function (MF)ATP binding0.0000000020090.000002338Highly InformativeDirect
Molecular Function (MF)nucleobase-containing compound kinase activity00Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.09481Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.12040.05099Least InformativeInherited
Cellular Component (CC)cell projection0.000022980.00000006651Moderately InformativeDirect
Cellular Component (CC)cell leading edge0.000000000034840.00000001968InformativeDirect
Cellular Component (CC)cell junction0.0000020330.002271InformativeInherited
Cellular Component (CC)adherens junction10.000002288Highly 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 0.00008338 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.0001944 Least Informative Direct
Biological Process (BP) biosynthetic process 0.0002656 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.00006003 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.00006727 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.02568 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 0.1305 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.005771 Least Informative Inherited
Biological Process (BP) positive regulation of biological process 0.1638 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.04664 Least Informative Inherited
Biological Process (BP) localization 0.1398 Least Informative Inherited
Biological Process (BP) developmental process 0.1089 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.03624 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.1061 Least Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.0000008483 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0.00001516 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0.00001307 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 0.00000000108 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.00001066 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.0000000000002211 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.0003739 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0.00002386 Moderately Informative Direct
Biological Process (BP) regulation of phosphorus metabolic process 0.03827 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.1746 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.2457 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound biosynthetic process 0.0244 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.08496 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.09318 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.009432 Moderately Informative Inherited
Biological Process (BP) single-organism organelle organization 0.02384 Moderately Informative Inherited
Biological Process (BP) organ development 0.08479 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.03264 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.01519 Moderately Informative Inherited
Biological Process (BP) response to oxidative stress 0.0007927 Informative Direct
Biological Process (BP) microtubule-based process 0.00004248 Informative Direct
Biological Process (BP) central nervous system development 0.0003404 Informative Direct
Biological Process (BP) nucleotide biosynthetic process 0.00005293 Informative Direct
Biological Process (BP) purine ribonucleoside metabolic process 0.00004983 Informative Direct
Biological Process (BP) ribose phosphate biosynthetic process 0.0003434 Informative Direct
Biological Process (BP) purine-containing compound biosynthetic process 0.0000009525 Informative Direct
Biological Process (BP) pyrimidine-containing compound metabolic process 0.000003 Informative Direct
Biological Process (BP) regulation of purine nucleotide metabolic process 0.0005938 Informative Direct
Biological Process (BP) glycosyl compound biosynthetic process 0.000001259 Informative Direct
Biological Process (BP) positive regulation of phosphate metabolic process 0.004646 Informative Inherited
Biological Process (BP) single-organism membrane organization 0.003916 Informative Inherited
Biological Process (BP) regulation of cell proliferation 0.147 Informative Inherited
Biological Process (BP) phosphorylation 0.3424 Informative Inherited
Biological Process (BP) purine ribonucleotide metabolic process 0.9974 Informative Inherited
Biological Process (BP) cell projection organization 0.002901 Informative Inherited
Biological Process (BP) single-organism cellular localization 0.005056 Informative Inherited
Biological Process (BP) cellular component movement 0.0125 Informative Inherited
Biological Process (BP) single-organism intracellular transport 0.01123 Informative Inherited
Biological Process (BP) nucleoside triphosphate metabolic process 0.0665 Informative Inherited
Biological Process (BP) pyrimidine nucleotide metabolic process 0.000006941 Highly Informative Direct
Biological Process (BP) microtubule-based movement 0.00000005039 Highly Informative Direct
Biological Process (BP) nucleoside diphosphate metabolic process 0.0000000009087 Highly Informative Direct
Biological Process (BP) purine ribonucleoside triphosphate biosynthetic process 0.0000000004952 Highly Informative Direct
Biological Process (BP) cilium organization 0.00000000004836 Highly Informative Direct
Biological Process (BP) pyrimidine ribonucleoside metabolic process 0.0000001752 Highly Informative Direct
Biological Process (BP) positive regulation of epithelial cell proliferation 0.000001103 Highly Informative Direct
Biological Process (BP) protein localization to membrane 0.00002533 Highly Informative Direct
Biological Process (BP) guanosine-containing compound metabolic process 0.000000004928 Highly Informative Direct
Biological Process (BP) pattern specification process 0.001547 Highly Informative Inherited
Molecular Function (MF) transferase activity 0.0000000001986 Least Informative Direct
Molecular Function (MF) binding 0.3214 Least Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0 Moderately Informative Direct
Molecular Function (MF) small molecule binding 0.0002787 Moderately Informative Direct
Molecular Function (MF) carbohydrate derivative binding 0.0008036 Moderately Informative Direct
Molecular Function (MF) anion binding 0.1005 Moderately Informative Inherited
Molecular Function (MF) kinase activity 0 Informative Direct
Molecular Function (MF) protein complex binding 0.0009597 Informative Direct
Molecular Function (MF) purine ribonucleoside binding 0.00003807 Informative Direct
Molecular Function (MF) nucleotide binding 0.2386 Informative Inherited
Molecular Function (MF) purine ribonucleoside triphosphate binding 0.00213 Informative Inherited
Molecular Function (MF) ATP binding 0.000002338 Highly Informative Direct
Molecular Function (MF) nucleobase-containing compound kinase activity 0 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 0.8147 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.6184 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.05099 Least Informative Inherited
Cellular Component (CC) cytoskeleton 0.0000008377 Moderately Informative Direct
Cellular Component (CC) cell projection 0.00000006651 Moderately Informative Direct
Cellular Component (CC) cell leading edge 0.00000001968 Informative Direct
Cellular Component (CC) microtubule cytoskeleton 0.009546 Informative Inherited
Cellular Component (CC) cell junction 0.002271 Informative Inherited
Cellular Component (CC) microtubule organizing center 0.0002038 Highly Informative Direct
Cellular Component (CC) adherens junction 0.000002288 Highly Informative Direct
Cellular Component (CC) ciliary part 0.0000001409 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 ]