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Conserved domains on  [gi|767987252|ref|XP_011520806|]
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nucleoside diphosphate kinase 3 isoform X3 [Homo sapiens]

Protein Classification

nucleoside-diphosphate kinase( domain architecture ID 1539)

nucleoside-diphosphate kinase catalyzes the exchange of phosphate groups between different nucleoside diphosphates

CATH:  3.30.70.141
EC:  2.7.4.6
Gene Ontology:  GO:0006241|GO:0004550|GO:0046872|GO:0005524|GO:0006228|GO:0006183

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NDPk super family cl00335
Nucleoside diphosphate kinases (NDP kinases, NDPks): NDP kinases, responsible for the ...
 22-60 8.72e-22

Nucleoside diphosphate kinases (NDP kinases, NDPks): NDP kinases, responsible for the synthesis of nucleoside triphosphates (NTPs), are involved in numerous regulatory processes associated with proliferation, development, and differentiation. They are vital for DNA/RNA synthesis, cell division, macromolecular metabolism and growth. The enzymes generate NTPs or their deoxy derivatives by terminal (gamma) phosphotransfer from an NTP such as ATP or GTP to any nucleoside diphosphate (NDP) or its deoxy derivative. The sequence of NDPk 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. The first confirmed metastasis suppressor gene was the NDP kinase protein encoded by the nm23 gene. Unicellular organisms generally possess only one gene encoding NDP kinase, while most multicellular organisms possess not only an ortholog that provides most of the NDP kinase enzymatic activity but also multiple divergent paralogous genes. The human genome codes for at least nine NDP kinases and can be classified into two groups, Groups I and II, according to their genomic architecture and distinct enzymatic activity. Group I isoforms (A-D) are well-conserved, catalytically active, and share 58-88% identity between each other, while Group II are more divergent, with only NDPk6 shown to be active. NDP kinases exist in two different quaternary structures; all known eukaryotic enzymes are hexamers, while some bacterial enzymes are tetramers, as in Myxococcus. The hexamer can be viewed as trimer of dimers, while tetramers are dimers of dimers, with the dimerization interface conserved.


The actual alignment was detected with superfamily member cd04413:

Pssm-ID: 469726  Cd Length: 130  Bit Score: 84.06  E-value: 8.72e-22
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 767987252  22 ERTFLAVKPDGVQRRLVGEIVRRFERKGFKLVALKLVQV 60
Cdd:cd04413    1 ERTLVIIKPDGVQRGLIGEIISRFERKGLKIVALKMLQL 39
 
Name Accession Description Interval E-value
NDPk_I cd04413
Nucleoside diphosphate kinase Group I (NDPk_I)-like: NDP kinase domains are present in a large ...
 22-60 8.72e-22

Nucleoside diphosphate kinase Group I (NDPk_I)-like: NDP kinase domains are present in a large family of structurally and functionally conserved proteins from bacteria to humans that generally catalyze the transfer of gamma-phosphates of a nucleoside triphosphate (NTP) donor onto a nucleoside diphosphate (NDP) acceptor through a phosphohistidine intermediate. The mammalian nm23/NDP kinase gene family can be divided into two distinct groups. The group I genes encode proteins that generally have highly homologous counterparts in other organisms and possess the classic enzymatic activity of a kinase. This group includes vertebrate NDP kinases A-D (Nm23- H1 to -H4), and its counterparts in bacteria, archea and other eukaryotes. NDP kinases exist in two different quaternary structures; all known eukaryotic enzymes are hexamers, while some bacterial enzymes are tetramers, as in Myxococcus. They possess the NDP kinase active site motif (NXXH[G/A]SD) and the nine residues that are most essential for catalysis.


Pssm-ID: 239876  Cd Length: 130  Bit Score: 84.06  E-value: 8.72e-22
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 767987252  22 ERTFLAVKPDGVQRRLVGEIVRRFERKGFKLVALKLVQV 60
Cdd:cd04413    1 ERTLVIIKPDGVQRGLIGEIISRFERKGLKIVALKMLQL 39
ndk PRK00668
mulitfunctional nucleoside diphosphate kinase/apyrimidinic endonuclease/3'-; Validated
 22-60 3.97e-21

mulitfunctional nucleoside diphosphate kinase/apyrimidinic endonuclease/3'-; Validated


Pssm-ID: 179085  Cd Length: 134  Bit Score: 82.46  E-value: 3.97e-21
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 767987252  22 ERTFLAVKPDGVQRRLVGEIVRRFERKGFKLVALKLVQV 60
Cdd:PRK00668   2 ERTFSIIKPDAVQRGLIGEIISRFEKKGLKIVALKMMQL 40
Ndk COG0105
Nucleoside diphosphate kinase [Nucleotide transport and metabolism]; Nucleoside diphosphate ...
 20-60 6.93e-21

Nucleoside diphosphate kinase [Nucleotide transport and metabolism]; Nucleoside diphosphate kinase is part of the Pathway/BioSystem: Pyrimidine biosynthesis


Pssm-ID: 439875  Cd Length: 140  Bit Score: 82.04  E-value: 6.93e-21
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 767987252  20 AHERTFLAVKPDGVQRRLVGEIVRRFERKGFKLVALKLVQV 60
Cdd:COG0105    1 AMERTLVIIKPDAVQRGLIGEIISRFERKGLKIVALKMLQL 41
NDK pfam00334
Nucleoside diphosphate kinase;
22-60 6.63e-20

Nucleoside diphosphate kinase;


Pssm-ID: 459766  Cd Length: 135  Bit Score: 79.07  E-value: 6.63e-20
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 767987252   22 ERTFLAVKPDGVQRRLVGEIVRRFERKGFKLVALKLVQV 60
Cdd:pfam00334   1 ERTLAIIKPDAVQRGLIGEIISRFERKGFKIVALKMLQL 39
NDK smart00562
Enzymes that catalyze nonsubstrate specific conversions of nucleoside diphosphates to ...
 22-60 8.89e-19

Enzymes that catalyze nonsubstrate specific conversions of nucleoside diphosphates to nucleoside triphosphates; These enzymes play important roles in bacterial growth, signal transduction and pathogenicity.


Pssm-ID: 197791  Cd Length: 135  Bit Score: 76.44  E-value: 8.89e-19
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 767987252    22 ERTFLAVKPDGVQRRLVGEIVRRFERKGFKLVALKLVQV 60
Cdd:smart00562   1 ERTLAIIKPDAVQRGLIGEIISRFERKGFKIVAMKMLQL 39
 
Name Accession Description Interval E-value
NDPk_I cd04413
Nucleoside diphosphate kinase Group I (NDPk_I)-like: NDP kinase domains are present in a large ...
 22-60 8.72e-22

Nucleoside diphosphate kinase Group I (NDPk_I)-like: NDP kinase domains are present in a large family of structurally and functionally conserved proteins from bacteria to humans that generally catalyze the transfer of gamma-phosphates of a nucleoside triphosphate (NTP) donor onto a nucleoside diphosphate (NDP) acceptor through a phosphohistidine intermediate. The mammalian nm23/NDP kinase gene family can be divided into two distinct groups. The group I genes encode proteins that generally have highly homologous counterparts in other organisms and possess the classic enzymatic activity of a kinase. This group includes vertebrate NDP kinases A-D (Nm23- H1 to -H4), and its counterparts in bacteria, archea and other eukaryotes. NDP kinases exist in two different quaternary structures; all known eukaryotic enzymes are hexamers, while some bacterial enzymes are tetramers, as in Myxococcus. They possess the NDP kinase active site motif (NXXH[G/A]SD) and the nine residues that are most essential for catalysis.


Pssm-ID: 239876  Cd Length: 130  Bit Score: 84.06  E-value: 8.72e-22
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 767987252  22 ERTFLAVKPDGVQRRLVGEIVRRFERKGFKLVALKLVQV 60
Cdd:cd04413    1 ERTLVIIKPDGVQRGLIGEIISRFERKGLKIVALKMLQL 39
ndk PRK00668
mulitfunctional nucleoside diphosphate kinase/apyrimidinic endonuclease/3'-; Validated
 22-60 3.97e-21

mulitfunctional nucleoside diphosphate kinase/apyrimidinic endonuclease/3'-; Validated


Pssm-ID: 179085  Cd Length: 134  Bit Score: 82.46  E-value: 3.97e-21
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 767987252  22 ERTFLAVKPDGVQRRLVGEIVRRFERKGFKLVALKLVQV 60
Cdd:PRK00668   2 ERTFSIIKPDAVQRGLIGEIISRFEKKGLKIVALKMMQL 40
Ndk COG0105
Nucleoside diphosphate kinase [Nucleotide transport and metabolism]; Nucleoside diphosphate ...
 20-60 6.93e-21

Nucleoside diphosphate kinase [Nucleotide transport and metabolism]; Nucleoside diphosphate kinase is part of the Pathway/BioSystem: Pyrimidine biosynthesis


Pssm-ID: 439875  Cd Length: 140  Bit Score: 82.04  E-value: 6.93e-21
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 767987252  20 AHERTFLAVKPDGVQRRLVGEIVRRFERKGFKLVALKLVQV 60
Cdd:COG0105    1 AMERTLVIIKPDAVQRGLIGEIISRFERKGLKIVALKMLQL 41
NDK pfam00334
Nucleoside diphosphate kinase;
22-60 6.63e-20

Nucleoside diphosphate kinase;


Pssm-ID: 459766  Cd Length: 135  Bit Score: 79.07  E-value: 6.63e-20
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 767987252   22 ERTFLAVKPDGVQRRLVGEIVRRFERKGFKLVALKLVQV 60
Cdd:pfam00334   1 ERTLAIIKPDAVQRGLIGEIISRFERKGFKIVALKMLQL 39
PTZ00093 PTZ00093
nucleoside diphosphate kinase, cytosolic; Provisional
 22-59 1.26e-19

nucleoside diphosphate kinase, cytosolic; Provisional


Pssm-ID: 173387  Cd Length: 149  Bit Score: 79.00  E-value: 1.26e-19
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 767987252  22 ERTFLAVKPDGVQRRLVGEIVRRFERKGFKLVALKLVQ 59
Cdd:PTZ00093   3 ERTFIMVKPDGVQRGLVGEIIKRFEKKGYKLVALKMLQ 40
NDK smart00562
Enzymes that catalyze nonsubstrate specific conversions of nucleoside diphosphates to ...
 22-60 8.89e-19

Enzymes that catalyze nonsubstrate specific conversions of nucleoside diphosphates to nucleoside triphosphates; These enzymes play important roles in bacterial growth, signal transduction and pathogenicity.


Pssm-ID: 197791  Cd Length: 135  Bit Score: 76.44  E-value: 8.89e-19
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 767987252    22 ERTFLAVKPDGVQRRLVGEIVRRFERKGFKLVALKLVQV 60
Cdd:smart00562   1 ERTLAIIKPDAVQRGLIGEIISRFERKGFKIVAMKMLQL 39
PLN02619 PLN02619
nucleoside-diphosphate kinase
 22-58 2.51e-16

nucleoside-diphosphate kinase


Pssm-ID: 178228  Cd Length: 238  Bit Score: 72.19  E-value: 2.51e-16
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 767987252  22 ERTFLAVKPDGVQRRLVGEIVRRFERKGFKLVALKLV 58
Cdd:PLN02619  89 ERTFIAIKPDGVQRGLISEIISRFERKGFKLVAIKVV 125
PRK14544 PRK14544
nucleoside diphosphate kinase; Provisional
 22-59 5.09e-13

nucleoside diphosphate kinase; Provisional


Pssm-ID: 173010 [Multi-domain]  Cd Length: 183  Bit Score: 62.52  E-value: 5.09e-13
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 767987252  22 ERTFLAVKPDGVQRRLVGEIVRRFERKGFKLVALKLVQ 59
Cdd:PRK14544   4 ERTLVILKPDAVKRGLVGEIISRFEKAGLKIVAMKMVK 41
PRK14540 PRK14540
nucleoside diphosphate kinase; Provisional
 22-60 2.99e-12

nucleoside diphosphate kinase; Provisional


Pssm-ID: 184733  Cd Length: 134  Bit Score: 59.45  E-value: 2.99e-12
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 767987252  22 ERTFLAVKPDGVQRRLVGEIVRRFERKGFKLVALKLVQV 60
Cdd:PRK14540   3 ERTFVALKPDAVERKLIGKIIQRFENKGFEIVEMKMLKL 41
NDPk cd00595
Nucleoside diphosphate kinases (NDP kinases, NDPks): NDP kinases, responsible for the ...
 22-58 7.17e-11

Nucleoside diphosphate kinases (NDP kinases, NDPks): NDP kinases, responsible for the synthesis of nucleoside triphosphates (NTPs), are involved in numerous regulatory processes associated with proliferation, development, and differentiation. They are vital for DNA/RNA synthesis, cell division, macromolecular metabolism and growth. The enzymes generate NTPs or their deoxy derivatives by terminal (gamma) phosphotransfer from an NTP such as ATP or GTP to any nucleoside diphosphate (NDP) or its deoxy derivative. The sequence of NDPk 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. The first confirmed metastasis suppressor gene was the NDP kinase protein encoded by the nm23 gene. Unicellular organisms generally possess only one gene encoding NDP kinase, while most multicellular organisms possess not only an ortholog that provides most of the NDP kinase enzymatic activity but also multiple divergent paralogous genes. The human genome codes for at least nine NDP kinases and can be classified into two groups, Groups I and II, according to their genomic architecture and distinct enzymatic activity. Group I isoforms (A-D) are well-conserved, catalytically active, and share 58-88% identity between each other, while Group II are more divergent, with only NDPk6 shown to be active. NDP kinases exist in two different quaternary structures; all known eukaryotic enzymes are hexamers, while some bacterial enzymes are tetramers, as in Myxococcus. The hexamer can be viewed as trimer of dimers, while tetramers are dimers of dimers, with the dimerization interface conserved.


Pssm-ID: 238335  Cd Length: 133  Bit Score: 55.82  E-value: 7.17e-11
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 767987252  22 ERTFLAVKPDGVQRRLVGEIVRRFERKGFKLVALKLV 58
Cdd:cd00595    1 ERTLALIKPDAVAEGLLGEIIMRIEDAGFEIVAMKEL 37
PRK14543 PRK14543
nucleoside diphosphate kinase; Provisional
 22-60 2.96e-09

nucleoside diphosphate kinase; Provisional


Pssm-ID: 237749  Cd Length: 169  Bit Score: 52.20  E-value: 2.96e-09
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 767987252  22 ERTFLAVKPDGVQRRLVGEIVRRFERKGFKLVALKLVQV 60
Cdd:PRK14543   6 QKTLCIIKPDGVRRGLIGNVVSRFERVGLKIVAAKMLLV 44
PRK14542 PRK14542
nucleoside diphosphate kinase; Provisional
 22-60 3.49e-08

nucleoside diphosphate kinase; Provisional


Pssm-ID: 173008 [Multi-domain]  Cd Length: 137  Bit Score: 48.90  E-value: 3.49e-08
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 767987252  22 ERTFLAVKPDGVQRRLVGEIVRRFERKGFKLVALKLVQV 60
Cdd:PRK14542   2 SRTFIMIKPDGVKNKHVGNILQRIEKEGFKILGLKYLKL 40
PRK14545 PRK14545
nucleoside diphosphate kinase; Provisional
 20-63 7.47e-07

nucleoside diphosphate kinase; Provisional


Pssm-ID: 184734  Cd Length: 139  Bit Score: 45.28  E-value: 7.47e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 767987252  20 AHERTFLAVKPDGVQRRLVGEIVRRFERKGFKLVALKLVQVGAR 63
Cdd:PRK14545   2 AGNRTFTMIKPDAVENGHIGGILDMITAAGFRIVAMKLTQLTVA 45
PRK14541 PRK14541
nucleoside diphosphate kinase; Provisional
 22-60 1.94e-06

nucleoside diphosphate kinase; Provisional


Pssm-ID: 173007  Cd Length: 140  Bit Score: 44.17  E-value: 1.94e-06
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 767987252  22 ERTFLAVKPDGVQRRLVGEIVRRFERKGFKLVALKLVQV 60
Cdd:PRK14541   2 ERTLTILKPDCVRKQLIGAVIDKIERAGFRVVAMKKTRL 40
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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