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749  structures 7752  species 0  interactions 16155  sequences 145  architectures

Family: NDK (PF00334)

Summary: Nucleoside diphosphate kinase

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Nucleoside diphosphate kinase Provide feedback

No Pfam abstract.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR034907

Nucleoside diphosphate kinases ( EC ) (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 polymerisation.

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 [ PUBMED:2175255 ] 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 [ PUBMED:1851158 ].

The enzyme is a hexamer composed by identical subunits with a novel mononucleotide binding fold. Each subunit contains an alpha/beta domain with a four stranded, anti-parallel beta-sheet [ PUBMED:556853 ].

This alpha/beta domain is also found at the C terminus of retinitis pigmentosa 2 protein (XRP2/RP2) [ PUBMED:16472755 ]. XRP2, a GTPase-activating protein, is required for maintenance of rod and cone photoreceptor cells in the retina [ PUBMED:26034134 ].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(125)
Full
(16155)
Representative proteomes UniProt
(53649)
RP15
(2805)
RP35
(7335)
RP55
(14734)
RP75
(22415)
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HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(125)
Full
(16155)
Representative proteomes UniProt
(53649)
RP15
(2805)
RP35
(7335)
RP55
(14734)
RP75
(22415)
Alignment:
Format:
Order:
Sequence:
Gaps:
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Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(125)
Full
(16155)
Representative proteomes UniProt
(53649)
RP15
(2805)
RP35
(7335)
RP55
(14734)
RP75
(22415)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Prosite
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD
Number in seed: 125
Number in full: 16155
Average length of the domain: 129.80 aa
Average identity of full alignment: 38 %
Average coverage of the sequence by the domain: 69.51 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.0 27.0
Noise cut-off 26.9 26.9
Model length: 135
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the NDK domain has been found. There are 749 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0G2L2L7 View 3D Structure Click here
A0A0R0FJJ3 View 3D Structure Click here
A0A0R0GQL8 View 3D Structure Click here
A0A0R0HT11 View 3D Structure Click here
A0A0R4IS05 View 3D Structure Click here
A0A1D6EH51 View 3D Structure Click here
A0A1D6IBV3 View 3D Structure Click here
A0A1D6IW63 View 3D Structure Click here
A0A1D6IZB9 View 3D Structure Click here
A0A1D6MEM8 View 3D Structure Click here
A0A1D6Q3H8 View 3D Structure Click here
A0A1L1SUL6 View 3D Structure Click here
A0A1L8EYB2 View 3D Structure Click here
A0KJ40 View 3D Structure Click here
A1AU17 View 3D Structure Click here
A1B2U9 View 3D Structure Click here
A1BIX9 View 3D Structure Click here
A1K3Y5 View 3D Structure Click here
A1S552 View 3D Structure Click here
A1SMD1 View 3D Structure Click here
A1SZU8 View 3D Structure Click here
A1TC25 View 3D Structure Click here
A1TM23 View 3D Structure Click here
A1US76 View 3D Structure Click here
A1VNF0 View 3D Structure Click here
A1W573 View 3D Structure Click here
A1WE20 View 3D Structure Click here
A1WXZ4 View 3D Structure Click here
A2BK98 View 3D Structure Click here
A2SHB9 View 3D Structure Click here
A2STK8 View 3D Structure Click here
A3DDC2 View 3D Structure Click here
A3DMR9 View 3D Structure Click here
A3MZ69 View 3D Structure Click here
A3PA97 View 3D Structure Click here
A3QFC8 View 3D Structure Click here
A4F9J8 View 3D Structure Click here
A4G4J8 View 3D Structure Click here
A4IA74 View 3D Structure Click here
A4IBS5 View 3D Structure Click here