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Conserved domains on  [gi|17554608|ref|NP_498663|]
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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 ...
 2-122 2.16e-60

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: 183.40  E-value: 2.16e-60
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17554608   2 EFMKLAIEEAKKGMEKGdGGPFGAVIVKDGKVIGSGHNMVLVTKDPTAHAEVTAIRNTCKNVDNFDLSGCQLYTSCYPCP 81
Cdd:COG0590   6 EFMRRALELARKAVAEG-EVPVGAVLVKDGEIIARGHNRVETLNDPTAHAEILAIRAAARKLGNWRLSGCTLYVTLEPCP 84

                        90       100       110       120
                ....*....|....*....|....*....|....*....|.
gi 17554608  82 MCMGAALWSRVDAIYYGATSQDAANIGFGDHEFHEFLQNPK 122
Cdd:COG0590  85 MCAGAIVWARIGRVVYGASDPKAGAAGSIYDLLADPRLNHR 125
 
Name Accession Description Interval E-value
TadA COG0590
tRNA(Arg) A34 adenosine deaminase TadA [Translation, ribosomal structure and biogenesis]; tRNA ...
 2-122 2.16e-60

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: 183.40  E-value: 2.16e-60
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17554608   2 EFMKLAIEEAKKGMEKGdGGPFGAVIVKDGKVIGSGHNMVLVTKDPTAHAEVTAIRNTCKNVDNFDLSGCQLYTSCYPCP 81
Cdd:COG0590   6 EFMRRALELARKAVAEG-EVPVGAVLVKDGEIIARGHNRVETLNDPTAHAEILAIRAAARKLGNWRLSGCTLYVTLEPCP 84

                        90       100       110       120
                ....*....|....*....|....*....|....*....|.
gi 17554608  82 MCMGAALWSRVDAIYYGATSQDAANIGFGDHEFHEFLQNPK 122
Cdd:COG0590  85 MCAGAIVWARIGRVVYGASDPKAGAAGSIYDLLADPRLNHR 125
nucleoside_deaminase cd01285
Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn ...
 4-112 4.79e-53

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: 163.56  E-value: 4.79e-53
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17554608   4 MKLAIEEAKKGMEKGdGGPFGAVIV-KDGKVIGSGHNMVLVTKDPTAHAEVTAIRNTCKNVDNFDLSGCQLYTSCYPCPM 82
Cdd:cd01285   1 MRLAIELARKALAEG-EVPFGAVIVdDDGKVIARGHNRVEQDGDPTAHAEIVAIRNAARRLGSYLLSGCTLYTTLEPCPM 79

                        90       100       110
                ....*....|....*....|....*....|
gi 17554608  83 CMGAALWSRVDAIYYGATSQDAANIGFGDH 112
Cdd:cd01285  80 CAGALLWARIKRVVYGASDPKLGGIGFLIE 109
dCMP_cyt_deam_1 pfam00383
Cytidine and deoxycytidylate deaminase zinc-binding region;
2-98 3.72e-33

Cytidine and deoxycytidylate deaminase zinc-binding region;


Pssm-ID: 395307 [Multi-domain]  Cd Length: 100  Bit Score: 112.78  E-value: 3.72e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17554608     2 EFMKLAIEEAKKGmEKGDGGPFGAVIVK-DGKVIGSGHNMVLVTKDPTAHAEVTAIRNTCKNVDNFDLSGCQLYTSCYPC 80
Cdd:pfam00383   4 YFMRLALKAAKRA-YPYSNFPVGAVIVKkDGEIIATGYNGENAGYDPTIHAERNAIRQAGKRGEGVRLEGATLYVTLEPC 82

                          90
                  ....*....|....*...
gi 17554608    81 PMCMGAALWSRVDAIYYG 98
Cdd:pfam00383  83 GMCAQAIIESGIKRVVFG 100
PRK10860 PRK10860
tRNA-specific adenosine deaminase; Provisional
 3-99 8.25e-21

tRNA-specific adenosine deaminase; Provisional


Pssm-ID: 182786 [Multi-domain]  Cd Length: 172  Bit Score: 83.32  E-value: 8.25e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17554608    3 FMKLAIEEAKKGMEKGDGgPFGAVIVKDGKVIGSGHNMVLVTKDPTAHAEVTAIRNTCKNVDNFDLSGCQLYTSCYPCPM 82
Cdd:PRK10860  16 WMRHALTLAKRAWDEREV-PVGAVLVHNNRVIGEGWNRPIGRHDPTAHAEIMALRQGGLVLQNYRLLDATLYVTLEPCVM 94

                         90
                 ....*....|....*..
gi 17554608   83 CMGAALWSRVDAIYYGA 99
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 ...
 2-122 2.16e-60

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: 183.40  E-value: 2.16e-60
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17554608   2 EFMKLAIEEAKKGMEKGdGGPFGAVIVKDGKVIGSGHNMVLVTKDPTAHAEVTAIRNTCKNVDNFDLSGCQLYTSCYPCP 81
Cdd:COG0590   6 EFMRRALELARKAVAEG-EVPVGAVLVKDGEIIARGHNRVETLNDPTAHAEILAIRAAARKLGNWRLSGCTLYVTLEPCP 84

                        90       100       110       120
                ....*....|....*....|....*....|....*....|.
gi 17554608  82 MCMGAALWSRVDAIYYGATSQDAANIGFGDHEFHEFLQNPK 122
Cdd:COG0590  85 MCAGAIVWARIGRVVYGASDPKAGAAGSIYDLLADPRLNHR 125
nucleoside_deaminase cd01285
Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn ...
 4-112 4.79e-53

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: 163.56  E-value: 4.79e-53
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17554608   4 MKLAIEEAKKGMEKGdGGPFGAVIV-KDGKVIGSGHNMVLVTKDPTAHAEVTAIRNTCKNVDNFDLSGCQLYTSCYPCPM 82
Cdd:cd01285   1 MRLAIELARKALAEG-EVPFGAVIVdDDGKVIARGHNRVEQDGDPTAHAEIVAIRNAARRLGSYLLSGCTLYTTLEPCPM 79

                        90       100       110
                ....*....|....*....|....*....|
gi 17554608  83 CMGAALWSRVDAIYYGATSQDAANIGFGDH 112
Cdd:cd01285  80 CAGALLWARIKRVVYGASDPKLGGIGFLIE 109
dCMP_cyt_deam_1 pfam00383
Cytidine and deoxycytidylate deaminase zinc-binding region;
2-98 3.72e-33

Cytidine and deoxycytidylate deaminase zinc-binding region;


Pssm-ID: 395307 [Multi-domain]  Cd Length: 100  Bit Score: 112.78  E-value: 3.72e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17554608     2 EFMKLAIEEAKKGmEKGDGGPFGAVIVK-DGKVIGSGHNMVLVTKDPTAHAEVTAIRNTCKNVDNFDLSGCQLYTSCYPC 80
Cdd:pfam00383   4 YFMRLALKAAKRA-YPYSNFPVGAVIVKkDGEIIATGYNGENAGYDPTIHAERNAIRQAGKRGEGVRLEGATLYVTLEPC 82

                          90
                  ....*....|....*...
gi 17554608    81 PMCMGAALWSRVDAIYYG 98
Cdd:pfam00383  83 GMCAQAIIESGIKRVVFG 100
MafB19-deam pfam14437
MafB19-like deaminase; A member of the nucleic acid/nucleotide deaminase superfamily ...
 2-108 7.21e-23

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: 87.96  E-value: 7.21e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17554608     2 EFMKLAIEEAKKGMEKgDGGPFGAVIVKDGKVIGSGHNMVLVTKDPTAHAEVTAIRNTCKNVDNFDLSGCQLYTSCYPCP 81
Cdd:pfam14437   5 KWFRKALGLAEKAYDA-GEVPIGAVIVKDGKVIARGYNRKELNADTTAHAEILAIQQAAKKLGSWRLDDATLYVTLEPCP 83

                          90       100
                  ....*....|....*....|....*..
gi 17554608    82 MCMGAALWSRVDAIYYGATSQDAANIG 108
Cdd:pfam14437  84 MCAGAIVQAGLKSLVYGAGNPKGGAVG 110
PRK10860 PRK10860
tRNA-specific adenosine deaminase; Provisional
 3-99 8.25e-21

tRNA-specific adenosine deaminase; Provisional


Pssm-ID: 182786 [Multi-domain]  Cd Length: 172  Bit Score: 83.32  E-value: 8.25e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17554608    3 FMKLAIEEAKKGMEKGDGgPFGAVIVKDGKVIGSGHNMVLVTKDPTAHAEVTAIRNTCKNVDNFDLSGCQLYTSCYPCPM 82
Cdd:PRK10860  16 WMRHALTLAKRAWDEREV-PVGAVLVHNNRVIGEGWNRPIGRHDPTAHAEIMALRQGGLVLQNYRLLDATLYVTLEPCVM 94

                         90
                 ....*....|....*..
gi 17554608   83 CMGAALWSRVDAIYYGA 99
Cdd:PRK10860  95 CAGAMVHSRIGRLVFGA 111
RibD1 COG0117
Riboflavin biosynthesis protein RibD, pyrimidine deaminase domain [Coenzyme transport and ...
 2-80 1.72e-12

Riboflavin biosynthesis protein RibD, pyrimidine deaminase domain [Coenzyme transport and metabolism]; Riboflavin biosynthesis protein RibD, pyrimidine deaminase domain is part of the Pathway/BioSystem: Riboflavin/FAD biosynthesis


Pssm-ID: 439887 [Multi-domain]  Cd Length: 311  Bit Score: 63.15  E-value: 1.72e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17554608   2 EFMKLAIEEAKKGMekGDGGP---FGAVIVKDGKVIGSGHnmvlvTKDP-TAHAEVTAIRNtCKNvdnfDLSGCQLYTSC 77
Cdd:COG0117   2 RYMRRALELARRGL--GTTSPnplVGCVIVKDGRIVGEGY-----HQRAgGPHAEVNALAQ-AGE----AARGATLYVTL 69


                ...
gi 17554608  78 YPC 80
Cdd:COG0117  70 EPC 72
cytidine_deaminase-like cd00786
Cytidine and deoxycytidylate deaminase zinc-binding region. The family contains cytidine ...
 4-86 2.07e-12

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: 59.49  E-value: 2.07e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17554608   4 MKLAIEEAKKGMEKGDGGPFGAVIV--KDGKVIGSGHNMVLVTKDPTAHAEVTAIRNtCKNVDnfDLSGCQLYTSCYPCP 81
Cdd:cd00786   1 MTEALKAADLGYAKESNFQVGACLVnkKDGGKVGRGCNIENAAYSMCNHAERTALFN-AGSEG--DTKGQMLYVALSPCG 77


                ....*
gi 17554608  82 MCMGA 86
Cdd:cd00786  78 ACAQL 82
Riboflavin_deaminase-reductase cd01284
Riboflavin-specific deaminase. Riboflavin biosynthesis protein RibD ...
 4-98 4.32e-11

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: 56.47  E-value: 4.32e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17554608   4 MKLAIEEAKKGMEKGDGGP-FGAVIVKD-GKVIGSGHNMvlvtKDPTAHAEVTAIRntckNVDNFDLSGCQLYTSCYPC- 80
Cdd:cd01284   1 MRRALELAEKGRGLTSPNPpVGCVIVDDdGEIVGEGYHR----KAGGPHAEVNALA----SAGEKLARGATLYVTLEPCs 72

                        90       100
                ....*....|....*....|...
gi 17554608  81 -----PMCMGAALWSRVDAIYYG 98
Cdd:cd01284  73 hhgktPPCVDAIIEAGIKRVVVG 95
deoxycytidylate_deaminase cd01286
Deoxycytidylate deaminase domain. Deoxycytidylate deaminase catalyzes the deamination of dCMP ...
 24-97 5.59e-10

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: 53.82  E-value: 5.59e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17554608  24 GAVIVKDGKVIGSGHN------------MVLVTKDP---------TAHAEVTAIRNTCKNvdNFDLSGCQLYTSCYPCPM 82
Cdd:cd01286  23 GAVIVKDKRIISTGYNgspsglphcaevGCERDDLPsgedqkccrTVHAEQNAILQAARH--GVSLEGATLYVTLFPCIE 100

                        90
                ....*....|....*
gi 17554608  83 CMGAALWSRVDAIYY 97
Cdd:cd01286 101 CAKLIIQAGIKKVVY 115
ComEB COG2131
Deoxycytidylate deaminase [Nucleotide transport and metabolism];
3-97 2.36e-07

Deoxycytidylate deaminase [Nucleotide transport and metabolism];


Pssm-ID: 441734 [Multi-domain]  Cd Length: 154  Bit Score: 47.14  E-value: 2.36e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17554608   3 FMKLAIEEAKKGmeKGDGGPFGAVIVKDGKVIGSGHN----------------MVLVTKDP-------TAHAEVTAIRNT 59
Cdd:COG2131  12 FMEIAKLVALRS--TCLRRQVGAVIVKDKRILATGYNgapsglphcdevgclrEKLGIPSGergeccrTVHAEQNAILQA 89

                        90       100       110
                ....*....|....*....|....*....|....*...
gi 17554608  60 CKNvdNFDLSGCQLYTSCYPCPMCMGAALWSRVDAIYY 97
Cdd:COG2131  90 ARH--GVSTEGATLYVTHFPCLECAKMIIQAGIKRVVY 125
PLN02807 PLN02807
diaminohydroxyphosphoribosylaminopyrimidine deaminase
 3-100 8.03e-06

diaminohydroxyphosphoribosylaminopyrimidine deaminase


Pssm-ID: 215433 [Multi-domain]  Cd Length: 380  Bit Score: 44.38  E-value: 8.03e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17554608    3 FMKLAIEEAKKGMEKGDGGPF-GAVIVKDGKVIGSGHNmvlvtkdPTA---HAEVTAIRntcknvDNFDLS-GCQLYTSC 77
Cdd:PLN02807  35 YMRRCVELARKAIGCTSPNPMvGCVIVKDGRIVGEGFH-------PKAgqpHAEVFALR------DAGDLAeNATAYVSL 101

                         90       100
                 ....*....|....*....|....*....
gi 17554608   78 YPC------PMCMGAALWSRVDAIYYGAT 100
Cdd:PLN02807 102 EPCnhygrtPPCTEALIKAKVKRVVVGMV 130
 
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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