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Conserved domains on  [gi|2107977422|gb|UCD46233|]
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nucleoside deaminase [Candidatus Bathyarchaeota archaeon]

Protein Classification

nucleoside deaminase( domain architecture ID 10001752)

nucleoside deaminase such as adenosine, guanine, or cytosine deaminase is a Zn-dependent enzyme which catalyzes the deamination of nucleosides. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on the substrate. The functional enzyme is a homodimer

EC:  3.5.4.-
Gene Ontology:  GO:0008270|GO:0019239|GO:0009116
PubMed:  38524700
SCOP:  3001838

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TadA COG0590
tRNA(Arg) A34 adenosine deaminase TadA [Translation, ribosomal structure and biogenesis]; tRNA ...
 1-152 4.22e-38

tRNA(Arg) A34 adenosine deaminase TadA [Translation, ribosomal structure and biogenesis]; tRNA(Arg) A34 adenosine deaminase TadA is part of the Pathway/BioSystem: Pyrimidine salvagetRNA modification


:

Pssm-ID: 440355 [Multi-domain]  Cd Length: 148  Bit Score: 127.54  E-value: 4.22e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2107977422   1 MACEEARWSVEVGGGPFGAVLlqIDDGT--GEAirfwrdHNHVVEHSDPTAHAEISVIRSACHELGVHDLgeirgseskl 78
Cdd:COG0590    10 RALELARKAVAEGEVPVGAVL--VKDGEiiARG------HNRVETLNDPTAHAEILAIRAAARKLGNWRL---------- 71

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2107977422  79 pqegeiSHCEIYSSCEPCPMCYSAISWARIPVLVFSATRFEASDERvgflddHIYEELRKDYPRRKIRVYQALC 152
Cdd:COG0590    72 ------SGCTLYVTLEPCPMCAGAIVWARIGRVVYGASDPKAGAAG------SIYDLLADPRLNHRVEVVGGVL 133
 
Name Accession Description Interval E-value
TadA COG0590
tRNA(Arg) A34 adenosine deaminase TadA [Translation, ribosomal structure and biogenesis]; tRNA ...
 1-152 4.22e-38

tRNA(Arg) A34 adenosine deaminase TadA [Translation, ribosomal structure and biogenesis]; tRNA(Arg) A34 adenosine deaminase TadA is part of the Pathway/BioSystem: Pyrimidine salvagetRNA modification


Pssm-ID: 440355 [Multi-domain]  Cd Length: 148  Bit Score: 127.54  E-value: 4.22e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2107977422   1 MACEEARWSVEVGGGPFGAVLlqIDDGT--GEAirfwrdHNHVVEHSDPTAHAEISVIRSACHELGVHDLgeirgseskl 78
Cdd:COG0590    10 RALELARKAVAEGEVPVGAVL--VKDGEiiARG------HNRVETLNDPTAHAEILAIRAAARKLGNWRL---------- 71

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2107977422  79 pqegeiSHCEIYSSCEPCPMCYSAISWARIPVLVFSATRFEASDERvgflddHIYEELRKDYPRRKIRVYQALC 152
Cdd:COG0590    72 ------SGCTLYVTLEPCPMCAGAIVWARIGRVVYGASDPKAGAAG------SIYDLLADPRLNHRVEVVGGVL 133
nucleoside_deaminase cd01285
Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn ...
 1-132 3.58e-29

Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn dependent and catalyze the deamination of nucleosides. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on the substrate. The functional enzyme is a homodimer. Cytosine deaminase catalyzes the deamination of cytosine to uracil and ammonia and is a member of the pyrimidine salvage pathway. Cytosine deaminase is found in bacteria and fungi but is not present in mammals; for this reason, the enzyme is currently of interest for antimicrobial drug design and gene therapy applications against tumors. Some members of this family are tRNA-specific adenosine deaminases that generate inosine at the first position of their anticodon (position 34) of specific tRNAs; this modification is thought to enlarge the codon recognition capacity during protein synthesis. Other members of the family are guanine deaminases which deaminate guanine to xanthine as part of the utilization of guanine as a nitrogen source.


Pssm-ID: 238612 [Multi-domain]  Cd Length: 109  Bit Score: 103.47  E-value: 3.58e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2107977422   1 MACEEARWSVEVGGGPFGAVLLqidDGTGEAIRfwRDHNHVVEHSDPTAHAEISVIRSACHELGVHDLgeirgsesklpq 80
Cdd:cd01285     3 LAIELARKALAEGEVPFGAVIV---DDDGKVIA--RGHNRVEQDGDPTAHAEIVAIRNAARRLGSYLL------------ 65

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2107977422  81 egeiSHCEIYSSCEPCPMCYSAISWARIPVLVFSatrfeASDERVGFLDDHI 132
Cdd:cd01285    66 ----SGCTLYTTLEPCPMCAGALLWARIKRVVYG-----ASDPKLGGIGFLI 108
dCMP_cyt_deam_1 pfam00383
Cytidine and deoxycytidylate deaminase zinc-binding region;
1-114 7.32e-19

Cytidine and deoxycytidylate deaminase zinc-binding region;


Pssm-ID: 395307 [Multi-domain]  Cd Length: 100  Bit Score: 76.57  E-value: 7.32e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2107977422   1 MACEEARWSVEVGGGPFGAVLLQIDD---GTGeairfwrdHNHVVEHSDPTAHAEISVIRSAChelgvhdlgeirgsesK 77
Cdd:pfam00383   8 LALKAAKRAYPYSNFPVGAVIVKKDGeiiATG--------YNGENAGYDPTIHAERNAIRQAG----------------K 63

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2107977422  78 LPQEGEISHCEIYSSCEPCPMCYSAISWARIPVLVFS 114
Cdd:pfam00383  64 RGEGVRLEGATLYVTLEPCGMCAQAIIESGIKRVVFG 100
PRK10860 PRK10860
tRNA-specific adenosine deaminase; Provisional
 2-126 4.30e-08

tRNA-specific adenosine deaminase; Provisional


Pssm-ID: 182786 [Multi-domain]  Cd Length: 172  Bit Score: 50.19  E-value: 4.30e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2107977422   2 ACEEARWSVEVGGGPFGAVLLQIDDGTGEAirfWrdhNHVVEHSDPTAHAEISVIRSACHELgvhdlgeirgsesklpQE 81
Cdd:PRK10860   20 ALTLAKRAWDEREVPVGAVLVHNNRVIGEG---W---NRPIGRHDPTAHAEIMALRQGGLVL----------------QN 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2107977422  82 GEISHCEIYSSCEPCPMCYSAISWARIPVLVFSatrfeASDERVG 126
Cdd:PRK10860   78 YRLLDATLYVTLEPCVMCAGAMVHSRIGRLVFG-----ARDAKTG 117
 
Name Accession Description Interval E-value
TadA COG0590
tRNA(Arg) A34 adenosine deaminase TadA [Translation, ribosomal structure and biogenesis]; tRNA ...
 1-152 4.22e-38

tRNA(Arg) A34 adenosine deaminase TadA [Translation, ribosomal structure and biogenesis]; tRNA(Arg) A34 adenosine deaminase TadA is part of the Pathway/BioSystem: Pyrimidine salvagetRNA modification


Pssm-ID: 440355 [Multi-domain]  Cd Length: 148  Bit Score: 127.54  E-value: 4.22e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2107977422   1 MACEEARWSVEVGGGPFGAVLlqIDDGT--GEAirfwrdHNHVVEHSDPTAHAEISVIRSACHELGVHDLgeirgseskl 78
Cdd:COG0590    10 RALELARKAVAEGEVPVGAVL--VKDGEiiARG------HNRVETLNDPTAHAEILAIRAAARKLGNWRL---------- 71

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2107977422  79 pqegeiSHCEIYSSCEPCPMCYSAISWARIPVLVFSATRFEASDERvgflddHIYEELRKDYPRRKIRVYQALC 152
Cdd:COG0590    72 ------SGCTLYVTLEPCPMCAGAIVWARIGRVVYGASDPKAGAAG------SIYDLLADPRLNHRVEVVGGVL 133
nucleoside_deaminase cd01285
Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn ...
 1-132 3.58e-29

Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn dependent and catalyze the deamination of nucleosides. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on the substrate. The functional enzyme is a homodimer. Cytosine deaminase catalyzes the deamination of cytosine to uracil and ammonia and is a member of the pyrimidine salvage pathway. Cytosine deaminase is found in bacteria and fungi but is not present in mammals; for this reason, the enzyme is currently of interest for antimicrobial drug design and gene therapy applications against tumors. Some members of this family are tRNA-specific adenosine deaminases that generate inosine at the first position of their anticodon (position 34) of specific tRNAs; this modification is thought to enlarge the codon recognition capacity during protein synthesis. Other members of the family are guanine deaminases which deaminate guanine to xanthine as part of the utilization of guanine as a nitrogen source.


Pssm-ID: 238612 [Multi-domain]  Cd Length: 109  Bit Score: 103.47  E-value: 3.58e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2107977422   1 MACEEARWSVEVGGGPFGAVLLqidDGTGEAIRfwRDHNHVVEHSDPTAHAEISVIRSACHELGVHDLgeirgsesklpq 80
Cdd:cd01285     3 LAIELARKALAEGEVPFGAVIV---DDDGKVIA--RGHNRVEQDGDPTAHAEIVAIRNAARRLGSYLL------------ 65

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2107977422  81 egeiSHCEIYSSCEPCPMCYSAISWARIPVLVFSatrfeASDERVGFLDDHI 132
Cdd:cd01285    66 ----SGCTLYTTLEPCPMCAGALLWARIKRVVYG-----ASDPKLGGIGFLI 108
dCMP_cyt_deam_1 pfam00383
Cytidine and deoxycytidylate deaminase zinc-binding region;
1-114 7.32e-19

Cytidine and deoxycytidylate deaminase zinc-binding region;


Pssm-ID: 395307 [Multi-domain]  Cd Length: 100  Bit Score: 76.57  E-value: 7.32e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2107977422   1 MACEEARWSVEVGGGPFGAVLLQIDD---GTGeairfwrdHNHVVEHSDPTAHAEISVIRSAChelgvhdlgeirgsesK 77
Cdd:pfam00383   8 LALKAAKRAYPYSNFPVGAVIVKKDGeiiATG--------YNGENAGYDPTIHAERNAIRQAG----------------K 63

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2107977422  78 LPQEGEISHCEIYSSCEPCPMCYSAISWARIPVLVFS 114
Cdd:pfam00383  64 RGEGVRLEGATLYVTLEPCGMCAQAIIESGIKRVVFG 100
MafB19-deam pfam14437
MafB19-like deaminase; A member of the nucleic acid/nucleotide deaminase superfamily ...
 1-164 4.40e-11

MafB19-like deaminase; A member of the nucleic acid/nucleotide deaminase superfamily prototyped by Neisseria MafB19. Members of this family are present in a wide phyletic range of bacteria and are predicted to function as toxins in bacterial polymorphic toxin systems.


Pssm-ID: 433953 [Multi-domain]  Cd Length: 144  Bit Score: 57.53  E-value: 4.40e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2107977422   1 MACEEARWSVEVGGGPFGAVLLQiddgtgEAIRFWRDHNHVVEHSDPTAHAEISVIRSACHELGvhdlgeirgseSKLPQ 80
Cdd:pfam14437   9 KALGLAEKAYDAGEVPIGAVIVK------DGKVIARGYNRKELNADTTAHAEILAIQQAAKKLG-----------SWRLD 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2107977422  81 EgeishCEIYSSCEPCPMCYSAISWARIPVLVFSatrfeASDERVGFLDDHIyEELRKDYPRRKIRVYQALCPGTLDAFE 160
Cdd:pfam14437  72 D-----ATLYVTLEPCPMCAGAIVQAGLKSLVYG-----AGNPKGGAVGSVL-NKLVIVLWNHRVELVEEDCSEILKGFF 140


                  ....
gi 2107977422 161 LWKK 164
Cdd:pfam14437 141 KKLR 144
PRK10860 PRK10860
tRNA-specific adenosine deaminase; Provisional
 2-126 4.30e-08

tRNA-specific adenosine deaminase; Provisional


Pssm-ID: 182786 [Multi-domain]  Cd Length: 172  Bit Score: 50.19  E-value: 4.30e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2107977422   2 ACEEARWSVEVGGGPFGAVLLQIDDGTGEAirfWrdhNHVVEHSDPTAHAEISVIRSACHELgvhdlgeirgsesklpQE 81
Cdd:PRK10860   20 ALTLAKRAWDEREVPVGAVLVHNNRVIGEG---W---NRPIGRHDPTAHAEIMALRQGGLVL----------------QN 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2107977422  82 GEISHCEIYSSCEPCPMCYSAISWARIPVLVFSatrfeASDERVG 126
Cdd:PRK10860   78 YRLLDATLYVTLEPCVMCAGAMVHSRIGRLVFG-----ARDAKTG 117
 
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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