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Conserved domains on  [gi|17555996|ref|NP_499418|]
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CMP/dCMP-type deaminase domain-containing protein [Caenorhabditis elegans]

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 ...
 14-136 1.45e-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: 159.13  E-value: 1.45e-50
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17555996  14 HAEHMAEAVAEACRGVECGdGGPFGAVVVDsNGKVVAKGHNMVLVTKDPTMHAEMTAIKNACKALGTFDLSGHILYTSCY 93
Cdd:COG0590   4 DEEFMRRALELARKAVAEG-EVPVGAVLVK-DGEIIARGHNRVETLNDPTAHAEILAIRAAARKLGNWRLSGCTLYVTLE 81

                        90       100       110       120
                ....*....|....*....|....*....|....*....|...
gi 17555996  94 PCPMCMGGCLWARFDAIYYGATAQQAAEIGFddkaFHDFLKDP 136
Cdd:COG0590  82 PCPMCAGAIVWARIGRVVYGASDPKAGAAGS----IYDLLADP 120
 
Name Accession Description Interval E-value
TadA COG0590
tRNA(Arg) A34 adenosine deaminase TadA [Translation, ribosomal structure and biogenesis]; tRNA ...
 14-136 1.45e-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: 159.13  E-value: 1.45e-50
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17555996  14 HAEHMAEAVAEACRGVECGdGGPFGAVVVDsNGKVVAKGHNMVLVTKDPTMHAEMTAIKNACKALGTFDLSGHILYTSCY 93
Cdd:COG0590   4 DEEFMRRALELARKAVAEG-EVPVGAVLVK-DGEIIARGHNRVETLNDPTAHAEILAIRAAARKLGNWRLSGCTLYVTLE 81

                        90       100       110       120
                ....*....|....*....|....*....|....*....|...
gi 17555996  94 PCPMCMGGCLWARFDAIYYGATAQQAAEIGFddkaFHDFLKDP 136
Cdd:COG0590  82 PCPMCAGAIVWARIGRVVYGASDPKAGAAGS----IYDLLADP 120
nucleoside_deaminase cd01285
Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn ...
 18-126 2.03e-48

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: 152.39  E-value: 2.03e-48
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17555996  18 MAEAVAEACRGVEcGDGGPFGAVVVDSNGKVVAKGHNMVLVTKDPTMHAEMTAIKNACKALGTFDLSGHILYTSCYPCPM 97
Cdd:cd01285   1 MRLAIELARKALA-EGEVPFGAVIVDDDGKVIARGHNRVEQDGDPTAHAEIVAIRNAARRLGSYLLSGCTLYTTLEPCPM 79

                        90       100
                ....*....|....*....|....*....
gi 17555996  98 CMGGCLWARFDAIYYGATAQQAAEIGFDD 126
Cdd:cd01285  80 CAGALLWARIKRVVYGASDPKLGGIGFLI 108
dCMP_cyt_deam_1 pfam00383
Cytidine and deoxycytidylate deaminase zinc-binding region;
14-113 2.47e-28

Cytidine and deoxycytidylate deaminase zinc-binding region;


Pssm-ID: 395307 [Multi-domain]  Cd Length: 100  Bit Score: 100.84  E-value: 2.47e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17555996    14 HAEHMAEAVAEACRGVECGdGGPFGAVVVDSNGKVVAKGHNMVLVTKDPTMHAEMTAIKNACKALGTFDLSGHILYTSCY 93
Cdd:pfam00383   2 DEYFMRLALKAAKRAYPYS-NFPVGAVIVKKDGEIIATGYNGENAGYDPTIHAERNAIRQAGKRGEGVRLEGATLYVTLE 80

                          90       100
                  ....*....|....*....|
gi 17555996    94 PCPMCMGGCLWARFDAIYYG 113
Cdd:pfam00383  81 PCGMCAQAIIESGIKRVVFG 100
PRK10860 PRK10860
tRNA-specific adenosine deaminase; Provisional
 18-114 2.58e-11

tRNA-specific adenosine deaminase; Provisional


Pssm-ID: 182786 [Multi-domain]  Cd Length: 172  Bit Score: 58.66  E-value: 2.58e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17555996   18 MAEAVAEACRGVECGDGgPFGAVVVdSNGKVVAKGHNMVLVTKDPTMHAEMTAIKNACKALGTFDLSGHILYTSCYPCPM 97
Cdd:PRK10860  17 MRHALTLAKRAWDEREV-PVGAVLV-HNNRVIGEGWNRPIGRHDPTAHAEIMALRQGGLVLQNYRLLDATLYVTLEPCVM 94

                         90
                 ....*....|....*..
gi 17555996   98 CMGGCLWARFDAIYYGA 114
Cdd:PRK10860  95 CAGAMVHSRIGRLVFGA 111
 
Name Accession Description Interval E-value
TadA COG0590
tRNA(Arg) A34 adenosine deaminase TadA [Translation, ribosomal structure and biogenesis]; tRNA ...
 14-136 1.45e-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: 159.13  E-value: 1.45e-50
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17555996  14 HAEHMAEAVAEACRGVECGdGGPFGAVVVDsNGKVVAKGHNMVLVTKDPTMHAEMTAIKNACKALGTFDLSGHILYTSCY 93
Cdd:COG0590   4 DEEFMRRALELARKAVAEG-EVPVGAVLVK-DGEIIARGHNRVETLNDPTAHAEILAIRAAARKLGNWRLSGCTLYVTLE 81

                        90       100       110       120
                ....*....|....*....|....*....|....*....|...
gi 17555996  94 PCPMCMGGCLWARFDAIYYGATAQQAAEIGFddkaFHDFLKDP 136
Cdd:COG0590  82 PCPMCAGAIVWARIGRVVYGASDPKAGAAGS----IYDLLADP 120
nucleoside_deaminase cd01285
Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn ...
 18-126 2.03e-48

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: 152.39  E-value: 2.03e-48
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17555996  18 MAEAVAEACRGVEcGDGGPFGAVVVDSNGKVVAKGHNMVLVTKDPTMHAEMTAIKNACKALGTFDLSGHILYTSCYPCPM 97
Cdd:cd01285   1 MRLAIELARKALA-EGEVPFGAVIVDDDGKVIARGHNRVEQDGDPTAHAEIVAIRNAARRLGSYLLSGCTLYTTLEPCPM 79

                        90       100
                ....*....|....*....|....*....
gi 17555996  98 CMGGCLWARFDAIYYGATAQQAAEIGFDD 126
Cdd:cd01285  80 CAGALLWARIKRVVYGASDPKLGGIGFLI 108
dCMP_cyt_deam_1 pfam00383
Cytidine and deoxycytidylate deaminase zinc-binding region;
14-113 2.47e-28

Cytidine and deoxycytidylate deaminase zinc-binding region;


Pssm-ID: 395307 [Multi-domain]  Cd Length: 100  Bit Score: 100.84  E-value: 2.47e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17555996    14 HAEHMAEAVAEACRGVECGdGGPFGAVVVDSNGKVVAKGHNMVLVTKDPTMHAEMTAIKNACKALGTFDLSGHILYTSCY 93
Cdd:pfam00383   2 DEYFMRLALKAAKRAYPYS-NFPVGAVIVKKDGEIIATGYNGENAGYDPTIHAERNAIRQAGKRGEGVRLEGATLYVTLE 80

                          90       100
                  ....*....|....*....|
gi 17555996    94 PCPMCMGGCLWARFDAIYYG 113
Cdd:pfam00383  81 PCGMCAQAIIESGIKRVVFG 100
MafB19-deam pfam14437
MafB19-like deaminase; A member of the nucleic acid/nucleotide deaminase superfamily ...
 14-114 8.51e-17

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: 72.56  E-value: 8.51e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17555996    14 HAEHMAEAVAEACRGVECgDGGPFGAVVVDsNGKVVAKGHNMVLVTKDPTMHAEMTAIKNACKALGTFDLSGHILYTSCY 93
Cdd:pfam14437   3 HEKWFRKALGLAEKAYDA-GEVPIGAVIVK-DGKVIARGYNRKELNADTTAHAEILAIQQAAKKLGSWRLDDATLYVTLE 80

                          90       100
                  ....*....|....*....|.
gi 17555996    94 PCPMCMGGCLWARFDAIYYGA 114
Cdd:pfam14437  81 PCPMCAGAIVQAGLKSLVYGA 101
PRK10860 PRK10860
tRNA-specific adenosine deaminase; Provisional
 18-114 2.58e-11

tRNA-specific adenosine deaminase; Provisional


Pssm-ID: 182786 [Multi-domain]  Cd Length: 172  Bit Score: 58.66  E-value: 2.58e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17555996   18 MAEAVAEACRGVECGDGgPFGAVVVdSNGKVVAKGHNMVLVTKDPTMHAEMTAIKNACKALGTFDLSGHILYTSCYPCPM 97
Cdd:PRK10860  17 MRHALTLAKRAWDEREV-PVGAVLV-HNNRVIGEGWNRPIGRHDPTAHAEIMALRQGGLVLQNYRLLDATLYVTLEPCVM 94

                         90
                 ....*....|....*..
gi 17555996   98 CMGGCLWARFDAIYYGA 114
Cdd:PRK10860  95 CAGAMVHSRIGRLVFGA 111
Riboflavin_deaminase-reductase cd01284
Riboflavin-specific deaminase. Riboflavin biosynthesis protein RibD ...
 17-95 1.99e-07

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: 47.23  E-value: 1.99e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 17555996  17 HMAEAVAEACRGvECGDGGPFGAVVVDSNGKVVAKGHNMvlvtKDPTMHAEMTAIKNAckalGTFDLSGHILYTSCYPC 95
Cdd:cd01284   2 RRALELAEKGRG-LTSPNPPVGCVIVDDDGEIVGEGYHR----KAGGPHAEVNALASA----GEKLARGATLYVTLEPC 71
cytidine_deaminase-like cd00786
Cytidine and deoxycytidylate deaminase zinc-binding region. The family contains cytidine ...
 18-100 9.67e-07

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: 44.85  E-value: 9.67e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17555996  18 MAEAVAEACRGVECGDGGPFGAVVV-DSNGKVVAKGHNMVLVTKDPTMHAEMTAIKNaCKALGtfDLSGHILYTSCYPCP 96
Cdd:cd00786   1 MTEALKAADLGYAKESNFQVGACLVnKKDGGKVGRGCNIENAAYSMCNHAERTALFN-AGSEG--DTKGQMLYVALSPCG 77


                ....
gi 17555996  97 MCMG 100
Cdd:cd00786  78 ACAQ 81
deoxycytidylate_deaminase cd01286
Deoxycytidylate deaminase domain. Deoxycytidylate deaminase catalyzes the deamination of dCMP ...
 38-99 9.22e-05

Deoxycytidylate deaminase domain. Deoxycytidylate deaminase catalyzes the deamination of dCMP to dUMP, providing the nucleotide substrate for thymidylate synthase. The enzyme binds Zn++, which is required for catalytic activity. The activity of the enzyme is allosterically regulated by the ratio of dCTP to dTTP not only in eukaryotic cells but also in T-even phage-infected Escherichia coli, with dCTP acting as an activator and dTTP as an inhibitor.


Pssm-ID: 238613 [Multi-domain]  Cd Length: 131  Bit Score: 40.34  E-value: 9.22e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17555996  38 GAVVVDsNGKVVAKGHN------------MVLVTKDP---------TMHAEMTAIKNACKaLGTfDLSGHILYTSCYPCP 96
Cdd:cd01286  23 GAVIVK-DKRIISTGYNgspsglphcaevGCERDDLPsgedqkccrTVHAEQNAILQAAR-HGV-SLEGATLYVTLFPCI 99


                ...
gi 17555996  97 MCM 99
Cdd:cd01286 100 ECA 102
cytidine_deaminase cd01283
Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the ...
 36-98 3.89e-03

Cytidine deaminase zinc-binding domain. These enzymes 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. Cytidine deaminases catalyze the deamination of cytidine to uridine and are important in the pyrimadine salvage pathway in many cell types, from bacteria to humans. This family also includes the apoBec proteins, which are a mammal specific expansion of RNA editing enzymes, and the closely related phorbolins, and the AID (activation-induced) enzymes.


Pssm-ID: 238610 [Multi-domain]  Cd Length: 112  Bit Score: 35.39  E-value: 3.89e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17555996  36 PFGAVVVDSNGKVVAkGHNMVLVTKDPTMHAEMTAIKNACKALGTFDLsgHILYTS-----CYPCPMC 98
Cdd:cd01283  19 TVGAALLTKDGRIFT-GVNVENASYGLTLCAERTAIGKAVSEGLRRYL--VTWAVSdeggvWSPCGAC 83
 
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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