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 (2,877) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 5,296 17,917 34
Proteins 4,695 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 process1.807e-088.075e-05Least InformativeDirect
Biological Process (BP)nitrogen compound metabolic process1.159e-060.0001943Least InformativeDirect
Biological Process (BP)biosynthetic process0.00012820.0003156Least InformativeDirect
Biological Process (BP)single-organism metabolic process5.118e-058.88e-05Least InformativeDirect
Biological Process (BP)heterocycle metabolic process1.642e-085.837e-05Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process1.004e-076.423e-05Least InformativeDirect
Biological Process (BP)multicellular organismal process0.14410.1383Least InformativeInherited
Biological Process (BP)regulation of cellular process0.0015070.004755Least InformativeInherited
Biological Process (BP)single-organism cellular process0.41720.725Least InformativeInherited
Biological Process (BP)response to stimulus0.14530.1258Least InformativeInherited
Biological Process (BP)phosphate-containing compound metabolic process3.816e-084.065e-07Moderately InformativeDirect
Biological Process (BP)heterocycle biosynthetic process4.935e-061.153e-05Moderately InformativeDirect
Biological Process (BP)aromatic compound biosynthetic process1.082e-069.887e-06Moderately InformativeDirect
Biological Process (BP)organophosphate metabolic process1.08e-097.953e-10Moderately InformativeDirect
Biological Process (BP)cellular nitrogen compound biosynthetic process3.001e-068.271e-06Moderately InformativeDirect
Biological Process (BP)nucleobase-containing small molecule metabolic process1.507e-113.027e-13Moderately InformativeDirect
Biological Process (BP)organic cyclic compound biosynthetic process1.145e-051.895e-05Moderately InformativeDirect
Biological Process (BP)positive regulation of cellular process0.00069390.5197Moderately InformativeInherited
Biological Process (BP)reproduction0.019350.05721Moderately InformativeInherited
Biological Process (BP)organonitrogen compound biosynthetic process0.061920.02577Moderately InformativeInherited
Biological Process (BP)carbohydrate derivative metabolic process0.001820.0002853Moderately InformativeInherited
Biological Process (BP)signal transduction0.12180.01599Moderately InformativeInherited
Biological Process (BP)nucleotide biosynthetic process0.00016629.343e-05InformativeDirect
Biological Process (BP)regulation of apoptotic process5.877e-050.0009771InformativeDirect
Biological Process (BP)purine ribonucleoside metabolic process1.661e-052.877e-05InformativeDirect
Biological Process (BP)ribose phosphate biosynthetic process0.0001560.0004388InformativeDirect
Biological Process (BP)multicellular organismal reproductive process0.00059760.0007141InformativeDirect
Biological Process (BP)purine-containing compound biosynthetic process5.003e-061.24e-06InformativeDirect
Biological Process (BP)pyrimidine-containing compound metabolic process0.00048862.952e-06InformativeDirect
Biological Process (BP)glycosyl compound biosynthetic process3.312e-051.455e-06InformativeDirect
Biological Process (BP)regulation of cell proliferation0.013220.148InformativeInherited
Biological Process (BP)phosphorylation0.0050070.2356InformativeInherited
Biological Process (BP)nucleoside triphosphate metabolic process0.054660.04555InformativeInherited
Biological Process (BP)purine ribonucleotide metabolic process0.88950.9726InformativeInherited
Biological Process (BP)pyrimidine nucleotide metabolic process0.00029629.588e-06Highly InformativeDirect
Biological Process (BP)nucleoside diphosphate metabolic process2.568e-071.419e-09Highly InformativeDirect
Biological Process (BP)purine ribonucleotide biosynthetic process2.131e-054.426e-06Highly InformativeDirect
Biological Process (BP)purine ribonucleoside triphosphate biosynthetic process2.789e-081.062e-09Highly InformativeDirect
Biological Process (BP)pyrimidine ribonucleoside metabolic process8.944e-052.738e-07Highly InformativeDirect
Biological Process (BP)positive regulation of epithelial cell proliferation1.006e-081.078e-06Highly InformativeDirect
Biological Process (BP)guanosine-containing compound metabolic process4.807e-074.052e-09Highly InformativeDirect
Biological Process (BP)pyrimidine-containing compound biosynthetic process0.0019038.218e-05Highly InformativeInherited
Molecular Function (MF)transferase activity1.145e-102.133e-11Least InformativeDirect
Molecular Function (MF)binding0.0063160.2994Least InformativeInherited
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups00Moderately InformativeDirect
Molecular Function (MF)anion binding4.736e-050.09913Moderately InformativeInherited
Molecular Function (MF)nucleotide binding2.306e-050.0003346InformativeDirect
Molecular Function (MF)kinase activity00InformativeDirect
Molecular Function (MF)purine ribonucleoside binding4.126e-063.811e-05InformativeDirect
Molecular Function (MF)purine ribonucleoside triphosphate binding0.0033840.002188InformativeInherited
Molecular Function (MF)ATP binding2.027e-092.328e-06Highly InformativeDirect
Molecular Function (MF)nucleobase-containing compound kinase activity00Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.12430.09591Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.18560.09197Least InformativeInherited
Cellular Component (CC)cell projection1.75e-054.027e-08Moderately InformativeDirect
Cellular Component (CC)cell leading edge3.776e-112.048e-08InformativeDirect
Cellular Component (CC)cell junction1.985e-060.002311InformativeInherited
Cellular Component (CC)adherens junction12.342e-06Highly 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 8.075e-05 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.0001943 Least Informative Direct
Biological Process (BP) biosynthetic process 0.0003156 Least Informative Direct
Biological Process (BP) single-organism metabolic process 8.88e-05 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 5.837e-05 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 6.423e-05 Least Informative Direct
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.03689 Least Informative Inherited
Biological Process (BP) localization 0.1191 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.1383 Least Informative Inherited
Biological Process (BP) developmental process 0.1071 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.004755 Least Informative Inherited
Biological Process (BP) response to stimulus 0.1258 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.725 Least Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 4.065e-07 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 1.153e-05 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 9.887e-06 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 7.953e-10 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 8.271e-06 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 3.027e-13 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.0002853 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 1.895e-05 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.0777 Moderately Informative Inherited
Biological Process (BP) regulation of phosphate metabolic process 0.04844 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.1999 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.5197 Moderately Informative Inherited
Biological Process (BP) reproduction 0.05721 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.2404 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound biosynthetic process 0.02577 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.09707 Moderately Informative Inherited
Biological Process (BP) organ development 0.09322 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.02947 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.01599 Moderately Informative Inherited
Biological Process (BP) response to oxidative stress 0.0007536 Informative Direct
Biological Process (BP) microtubule-based process 6.547e-06 Informative Direct
Biological Process (BP) central nervous system development 0.0002974 Informative Direct
Biological Process (BP) nucleotide biosynthetic process 9.343e-05 Informative Direct
Biological Process (BP) cellular membrane organization 0.0008571 Informative Direct
Biological Process (BP) regulation of apoptotic process 0.0009771 Informative Direct
Biological Process (BP) purine ribonucleoside metabolic process 2.877e-05 Informative Direct
Biological Process (BP) ribose phosphate biosynthetic process 0.0004388 Informative Direct
Biological Process (BP) multicellular organismal reproductive process 0.0007141 Informative Direct
Biological Process (BP) purine-containing compound biosynthetic process 1.24e-06 Informative Direct
Biological Process (BP) pyrimidine-containing compound metabolic process 2.952e-06 Informative Direct
Biological Process (BP) regulation of purine nucleotide metabolic process 0.0005906 Informative Direct
Biological Process (BP) glycosyl compound biosynthetic process 1.455e-06 Informative Direct
Biological Process (BP) regulation of cell proliferation 0.148 Informative Inherited
Biological Process (BP) phosphorylation 0.2356 Informative Inherited
Biological Process (BP) cell projection organization 0.00303 Informative Inherited
Biological Process (BP) nucleoside triphosphate metabolic process 0.04555 Informative Inherited
Biological Process (BP) purine ribonucleotide metabolic process 0.9726 Informative Inherited
Biological Process (BP) cellular component movement 0.002916 Informative Inherited
Biological Process (BP) pyrimidine nucleotide metabolic process 9.588e-06 Highly Informative Direct
Biological Process (BP) microtubule-based movement 5.08e-08 Highly Informative Direct
Biological Process (BP) nucleoside diphosphate metabolic process 1.419e-09 Highly Informative Direct
Biological Process (BP) purine ribonucleotide biosynthetic process 4.426e-06 Highly Informative Direct
Biological Process (BP) purine ribonucleoside triphosphate biosynthetic process 1.062e-09 Highly Informative Direct
Biological Process (BP) cilium organization 1.992e-10 Highly Informative Direct
Biological Process (BP) pyrimidine ribonucleoside metabolic process 2.738e-07 Highly Informative Direct
Biological Process (BP) positive regulation of epithelial cell proliferation 1.078e-06 Highly Informative Direct
Biological Process (BP) pyrimidine-containing compound biosynthetic process 8.218e-05 Highly Informative Direct
Biological Process (BP) guanosine-containing compound metabolic process 4.052e-09 Highly Informative Direct
Biological Process (BP) pattern specification process 0.001214 Highly Informative Inherited
Molecular Function (MF) transferase activity 2.133e-11 Least Informative Direct
Molecular Function (MF) binding 0.2994 Least Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0 Moderately Informative Direct
Molecular Function (MF) anion binding 0.09913 Moderately Informative Inherited
Molecular Function (MF) nucleotide binding 0.0003346 Informative Direct
Molecular Function (MF) kinase activity 0 Informative Direct
Molecular Function (MF) purine ribonucleoside binding 3.811e-05 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 0.002188 Informative Inherited
Molecular Function (MF) ATP binding 2.328e-06 Highly Informative Direct
Molecular Function (MF) nucleobase-containing compound kinase activity 0 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 0.9316 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.5627 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.09591 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.09197 Least Informative Inherited
Cellular Component (CC) cytoskeleton 5.717e-07 Moderately Informative Direct
Cellular Component (CC) cell projection 4.027e-08 Moderately Informative Direct
Cellular Component (CC) cell leading edge 2.048e-08 Informative Direct
Cellular Component (CC) microtubule cytoskeleton 0.01232 Informative Inherited
Cellular Component (CC) cell junction 0.002311 Informative Inherited
Cellular Component (CC) centrosome 9.824e-08 Highly Informative Direct
Cellular Component (CC) adherens junction 2.342e-06 Highly Informative Direct
Cellular Component (CC) cilium part 1.257e-08 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 projection0.0001527Moderately 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 ]