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Conserved domains on  [gi|15241124|ref|NP_198157|]
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Cytidine/deoxycytidylate deaminase family protein [Arabidopsis thaliana]

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 ...
 28-139 5.33e-50

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: 158.36  E-value: 5.33e-50
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15241124  28 DSDHKFLTQAVEEAYKGVDCGdGGPFGAVIVHNNEVVASCHNMVLKYTDPTAHAEVTAIREACKKLNKIELSECEIYASC 107
Cdd:COG0590   2 EDDEEFMRRALELARKAVAEG-EVPVGAVLVKDGEIIARGHNRVETLNDPTAHAEILAIRAAARKLGNWRLSGCTLYVTL 80

                        90       100       110
                ....*....|....*....|....*....|..
gi 15241124 108 EPCPMCFGAIHLSRLKRLVYGAKAEAAIAIGF 139
Cdd:COG0590  81 EPCPMCAGAIVWARIGRVVYGASDPKAGAAGS 112
 
Name Accession Description Interval E-value
TadA COG0590
tRNA(Arg) A34 adenosine deaminase TadA [Translation, ribosomal structure and biogenesis]; tRNA ...
 28-139 5.33e-50

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: 158.36  E-value: 5.33e-50
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15241124  28 DSDHKFLTQAVEEAYKGVDCGdGGPFGAVIVHNNEVVASCHNMVLKYTDPTAHAEVTAIREACKKLNKIELSECEIYASC 107
Cdd:COG0590   2 EDDEEFMRRALELARKAVAEG-EVPVGAVLVKDGEIIARGHNRVETLNDPTAHAEILAIRAAARKLGNWRLSGCTLYVTL 80

                        90       100       110
                ....*....|....*....|....*....|..
gi 15241124 108 EPCPMCFGAIHLSRLKRLVYGAKAEAAIAIGF 139
Cdd:COG0590  81 EPCPMCAGAIVWARIGRVVYGASDPKAGAAGS 112
nucleoside_deaminase cd01285
Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn ...
 34-141 2.11e-44

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: 142.76  E-value: 2.11e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15241124  34 LTQAVEEAYKGVDcGDGGPFGAVIVHNN-EVVASCHNMVLKYTDPTAHAEVTAIREACKKLNKIELSECEIYASCEPCPM 112
Cdd:cd01285   1 MRLAIELARKALA-EGEVPFGAVIVDDDgKVIARGHNRVEQDGDPTAHAEIVAIRNAARRLGSYLLSGCTLYTTLEPCPM 79

                        90       100
                ....*....|....*....|....*....
gi 15241124 113 CFGAIHLSRLKRLVYGAKAEAAIAIGFDD 141
Cdd:cd01285  80 CAGALLWARIKRVVYGASDPKLGGIGFLI 108
dCMP_cyt_deam_1 pfam00383
Cytidine and deoxycytidylate deaminase zinc-binding region;
30-128 1.00e-30

Cytidine and deoxycytidylate deaminase zinc-binding region;


Pssm-ID: 395307 [Multi-domain]  Cd Length: 100  Bit Score: 107.77  E-value: 1.00e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15241124    30 DHKFLTQAVEEAYKGVDCGdGGPFGAVIVH-NNEVVASCHNMVLKYTDPTAHAEVTAIREACKKLNKIELSECEIYASCE 108
Cdd:pfam00383   2 DEYFMRLALKAAKRAYPYS-NFPVGAVIVKkDGEIIATGYNGENAGYDPTIHAERNAIRQAGKRGEGVRLEGATLYVTLE 80

                          90       100
                  ....*....|....*....|
gi 15241124   109 PCPMCFGAIHLSRLKRLVYG 128
Cdd:pfam00383  81 PCGMCAQAIIESGIKRVVFG 100
PRK10860 PRK10860
tRNA-specific adenosine deaminase; Provisional
 29-138 7.50e-22

tRNA-specific adenosine deaminase; Provisional


Pssm-ID: 182786 [Multi-domain]  Cd Length: 172  Bit Score: 87.17  E-value: 7.50e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15241124   29 SDHKFLTQAVEEAYKGVDCGDGgPFGAVIVHNNEVVASCHNMVLKYTDPTAHAEVTAIREACKKLNKIELSECEIYASCE 108
Cdd:PRK10860  12 SHEYWMRHALTLAKRAWDEREV-PVGAVLVHNNRVIGEGWNRPIGRHDPTAHAEIMALRQGGLVLQNYRLLDATLYVTLE 90

                         90       100       110
                 ....*....|....*....|....*....|
gi 15241124  109 PCPMCFGAIHLSRLKRLVYGAKAEAAIAIG 138
Cdd:PRK10860  91 PCVMCAGAMVHSRIGRLVFGARDAKTGAAG 120
 
Name Accession Description Interval E-value
TadA COG0590
tRNA(Arg) A34 adenosine deaminase TadA [Translation, ribosomal structure and biogenesis]; tRNA ...
 28-139 5.33e-50

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: 158.36  E-value: 5.33e-50
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15241124  28 DSDHKFLTQAVEEAYKGVDCGdGGPFGAVIVHNNEVVASCHNMVLKYTDPTAHAEVTAIREACKKLNKIELSECEIYASC 107
Cdd:COG0590   2 EDDEEFMRRALELARKAVAEG-EVPVGAVLVKDGEIIARGHNRVETLNDPTAHAEILAIRAAARKLGNWRLSGCTLYVTL 80

                        90       100       110
                ....*....|....*....|....*....|..
gi 15241124 108 EPCPMCFGAIHLSRLKRLVYGAKAEAAIAIGF 139
Cdd:COG0590  81 EPCPMCAGAIVWARIGRVVYGASDPKAGAAGS 112
nucleoside_deaminase cd01285
Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn ...
 34-141 2.11e-44

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: 142.76  E-value: 2.11e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15241124  34 LTQAVEEAYKGVDcGDGGPFGAVIVHNN-EVVASCHNMVLKYTDPTAHAEVTAIREACKKLNKIELSECEIYASCEPCPM 112
Cdd:cd01285   1 MRLAIELARKALA-EGEVPFGAVIVDDDgKVIARGHNRVEQDGDPTAHAEIVAIRNAARRLGSYLLSGCTLYTTLEPCPM 79

                        90       100
                ....*....|....*....|....*....
gi 15241124 113 CFGAIHLSRLKRLVYGAKAEAAIAIGFDD 141
Cdd:cd01285  80 CAGALLWARIKRVVYGASDPKLGGIGFLI 108
dCMP_cyt_deam_1 pfam00383
Cytidine and deoxycytidylate deaminase zinc-binding region;
30-128 1.00e-30

Cytidine and deoxycytidylate deaminase zinc-binding region;


Pssm-ID: 395307 [Multi-domain]  Cd Length: 100  Bit Score: 107.77  E-value: 1.00e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15241124    30 DHKFLTQAVEEAYKGVDCGdGGPFGAVIVH-NNEVVASCHNMVLKYTDPTAHAEVTAIREACKKLNKIELSECEIYASCE 108
Cdd:pfam00383   2 DEYFMRLALKAAKRAYPYS-NFPVGAVIVKkDGEIIATGYNGENAGYDPTIHAERNAIRQAGKRGEGVRLEGATLYVTLE 80

                          90       100
                  ....*....|....*....|
gi 15241124   109 PCPMCFGAIHLSRLKRLVYG 128
Cdd:pfam00383  81 PCGMCAQAIIESGIKRVVFG 100
MafB19-deam pfam14437
MafB19-like deaminase; A member of the nucleic acid/nucleotide deaminase superfamily ...
 29-138 7.71e-25

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: 94.13  E-value: 7.71e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15241124    29 SDHKFLTQAVEEAYKGVDCgDGGPFGAVIVHNNEVVASCHNMVLKYTDPTAHAEVTAIREACKKLNKIELSECEIYASCE 108
Cdd:pfam14437   2 NHEKWFRKALGLAEKAYDA-GEVPIGAVIVKDGKVIARGYNRKELNADTTAHAEILAIQQAAKKLGSWRLDDATLYVTLE 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 15241124   109 PCPMCFGAIHLSRLKRLVYGAKAEAAIAIG 138
Cdd:pfam14437  81 PCPMCAGAIVQAGLKSLVYGAGNPKGGAVG 110
PRK10860 PRK10860
tRNA-specific adenosine deaminase; Provisional
 29-138 7.50e-22

tRNA-specific adenosine deaminase; Provisional


Pssm-ID: 182786 [Multi-domain]  Cd Length: 172  Bit Score: 87.17  E-value: 7.50e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15241124   29 SDHKFLTQAVEEAYKGVDCGDGgPFGAVIVHNNEVVASCHNMVLKYTDPTAHAEVTAIREACKKLNKIELSECEIYASCE 108
Cdd:PRK10860  12 SHEYWMRHALTLAKRAWDEREV-PVGAVLVHNNRVIGEGWNRPIGRHDPTAHAEIMALRQGGLVLQNYRLLDATLYVTLE 90

                         90       100       110
                 ....*....|....*....|....*....|
gi 15241124  109 PCPMCFGAIHLSRLKRLVYGAKAEAAIAIG 138
Cdd:PRK10860  91 PCVMCAGAMVHSRIGRLVFGARDAKTGAAG 120
Riboflavin_deaminase-reductase cd01284
Riboflavin-specific deaminase. Riboflavin biosynthesis protein RibD ...
 37-130 1.08e-06

Riboflavin-specific deaminase. Riboflavin biosynthesis protein RibD (Diaminohydroxyphosphoribosylaminopyrimidine deaminase) catalyzes the deamination of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate, which is an intermediate step in the biosynthesis of riboflavin.The ribG gene of Bacillus subtilis and the ribD gene of E. coli are bifunctional and contain this deaminase domain and a reductase domain which catalyzes the subsequent reduction of the ribosyl side chain.


Pssm-ID: 238611 [Multi-domain]  Cd Length: 115  Bit Score: 45.30  E-value: 1.08e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15241124  37 AVEEAYKGVD-CGDGGPFGAVIVHNN-EVVAschnmvLKYT--DPTAHAEVTAIREACKKLnkieLSECEIYASCEPC-- 110
Cdd:cd01284   4 ALELAEKGRGlTSPNPPVGCVIVDDDgEIVG------EGYHrkAGGPHAEVNALASAGEKL----ARGATLYVTLEPCsh 73

                        90       100
                ....*....|....*....|....
gi 15241124 111 ----PMCFGAIHLSRLKRLVYGAK 130
Cdd:cd01284  74 hgktPPCVDAIIEAGIKRVVVGVR 97
PLN02807 PLN02807
diaminohydroxyphosphoribosylaminopyrimidine deaminase
 24-128 2.92e-06

diaminohydroxyphosphoribosylaminopyrimidine deaminase


Pssm-ID: 215433 [Multi-domain]  Cd Length: 380  Bit Score: 46.30  E-value: 2.92e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15241124   24 QAVHDSDHKFLTQAVEEAYKGVDCGDGGPF-GAVIVHNNEVVASCHNmvlkytdPTA---HAEVTAIREACkklnkiELS 99
Cdd:PLN02807  26 RAAGDDDSFYMRRCVELARKAIGCTSPNPMvGCVIVKDGRIVGEGFH-------PKAgqpHAEVFALRDAG------DLA 92

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 15241124  100 E-CEIYASCEPC------PMCFGAIHLSRLKRLVYG 128
Cdd:PLN02807  93 EnATAYVSLEPCnhygrtPPCTEALIKAKVKRVVVG 128
cytidine_deaminase-like cd00786
Cytidine and deoxycytidylate deaminase zinc-binding region. The family contains cytidine ...
 34-124 8.77e-05

Cytidine and deoxycytidylate deaminase zinc-binding region. The family contains cytidine deaminases, nucleoside deaminases, deoxycytidylate deaminases and riboflavin deaminases. Also included are the apoBec family of mRNA editing enzymes. All members are Zn dependent. 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.


Pssm-ID: 238406 [Multi-domain]  Cd Length: 96  Bit Score: 39.84  E-value: 8.77e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15241124  34 LTQAVEEAYKGVDCGDGGPFGAVIVHN---NEVVASCHNMVLKYTdPTAHAEVTAIrEACKKLNKIElsECEIYASCEPC 110
Cdd:cd00786   1 MTEALKAADLGYAKESNFQVGACLVNKkdgGKVGRGCNIENAAYS-MCNHAERTAL-FNAGSEGDTK--GQMLYVALSPC 76

                        90
                ....*....|....
gi 15241124 111 PMCFGAIHLSRLKR 124
Cdd:cd00786  77 GACAQLIIELGIKD 90
cd PHA02588
deoxycytidylate deaminase; Provisional
 80-130 8.56e-04

deoxycytidylate deaminase; Provisional


Pssm-ID: 222894 [Multi-domain]  Cd Length: 168  Bit Score: 38.20  E-value: 8.56e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 15241124   80 HAEVTAIREACKKLNKIElsECEIYASCEPCPMCFGAIHLSRLKRLVYGAK 130
Cdd:PHA02588  83 HAELNAILFAARNGISIE--GATMYVTASPCPDCAKAIAQSGIKKLVYCEK 131
 
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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