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Conserved domains on  [gi|446569383|ref|WP_000646729|]
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MULTISPECIES: nucleoside deaminase [Acinetobacter]

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 ...
 1-133 5.44e-57

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: 174.92  E-value: 5.44e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446569383   1 MKANQEFLRQAIELAYNNIEKGGRPFGAVIVKDGKVIASGVNQILTTNDPTAHAELLAIRAASQVLGTANLEGCSVFASG 80
Cdd:COG0590    1 MEDDEEFMRRALELARKAVAEGEVPVGAVLVKDGEIIARGHNRVETLNDPTAHAEILAIRAAARKLGNWRLSGCTLYVTL 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 446569383  81 HPCPMCMAAMRLAGIKTVNYAYSNEDGAPFGLstaeIYADLVKPFAEQSMKIE 133
Cdd:COG0590   81 EPCPMCAGAIVWARIGRVVYGASDPKAGAAGS----IYDLLADPRLNHRVEVV 129
 
Name Accession Description Interval E-value
TadA COG0590
tRNA(Arg) A34 adenosine deaminase TadA [Translation, ribosomal structure and biogenesis]; tRNA ...
 1-133 5.44e-57

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: 174.92  E-value: 5.44e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446569383   1 MKANQEFLRQAIELAYNNIEKGGRPFGAVIVKDGKVIASGVNQILTTNDPTAHAELLAIRAASQVLGTANLEGCSVFASG 80
Cdd:COG0590    1 MEDDEEFMRRALELARKAVAEGEVPVGAVLVKDGEIIARGHNRVETLNDPTAHAEILAIRAAARKLGNWRLSGCTLYVTL 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 446569383  81 HPCPMCMAAMRLAGIKTVNYAYSNEDGAPFGLstaeIYADLVKPFAEQSMKIE 133
Cdd:COG0590   81 EPCPMCAGAIVWARIGRVVYGASDPKAGAAGS----IYDLLADPRLNHRVEVV 129
nucleoside_deaminase cd01285
Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn ...
 8-111 1.23e-40

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: 132.36  E-value: 1.23e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446569383   8 LRQAIELAYNNIEKGGRPFGAVIV-KDGKVIASGVNQILTTNDPTAHAELLAIRAASQVLGTANLEGCSVFASGHPCPMC 86
Cdd:cd01285    1 MRLAIELARKALAEGEVPFGAVIVdDDGKVIARGHNRVEQDGDPTAHAEIVAIRNAARRLGSYLLSGCTLYTTLEPCPMC 80

                         90       100
                 ....*....|....*....|....*
gi 446569383  87 MAAMRLAGIKTVNYAYSNEDGAPFG 111
Cdd:cd01285   81 AGALLWARIKRVVYGASDPKLGGIG 105
MafB19-deam pfam14437
MafB19-like deaminase; A member of the nucleic acid/nucleotide deaminase superfamily ...
 5-111 2.30e-26

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: 97.21  E-value: 2.30e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446569383    5 QEFLRQAIELAYNNIEKGGRPFGAVIVKDGKVIASGVNQILTTNDPTAHAELLAIRAASQVLGTANLEGCSVFASGHPCP 84
Cdd:pfam14437   4 EKWFRKALGLAEKAYDAGEVPIGAVIVKDGKVIARGYNRKELNADTTAHAEILAIQQAAKKLGSWRLDDATLYVTLEPCP 83

                          90       100
                  ....*....|....*....|....*..
gi 446569383   85 MCMAAMRLAGIKTVNYAYSNEDGAPFG 111
Cdd:pfam14437  84 MCAGAIVQAGLKSLVYGAGNPKGGAVG 110
PRK10860 PRK10860
tRNA-specific adenosine deaminase; Provisional
 7-105 1.62e-19

tRNA-specific adenosine deaminase; Provisional


Pssm-ID: 182786 [Multi-domain]  Cd Length: 172  Bit Score: 80.24  E-value: 1.62e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446569383   7 FLRQAIELAYNNIEKGGRPFGAVIVKDGKVIASGVNQILTTNDPTAHAELLAIRAASQVLGTANLEGCSVFASGHPCPMC 86
Cdd:PRK10860  16 WMRHALTLAKRAWDEREVPVGAVLVHNNRVIGEGWNRPIGRHDPTAHAEIMALRQGGLVLQNYRLLDATLYVTLEPCVMC 95

                         90
                 ....*....|....*....
gi 446569383  87 MAAMRLAGIKTVNYAYSNE 105
Cdd:PRK10860  96 AGAMVHSRIGRLVFGARDA 114
 
Name Accession Description Interval E-value
TadA COG0590
tRNA(Arg) A34 adenosine deaminase TadA [Translation, ribosomal structure and biogenesis]; tRNA ...
 1-133 5.44e-57

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: 174.92  E-value: 5.44e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446569383   1 MKANQEFLRQAIELAYNNIEKGGRPFGAVIVKDGKVIASGVNQILTTNDPTAHAELLAIRAASQVLGTANLEGCSVFASG 80
Cdd:COG0590    1 MEDDEEFMRRALELARKAVAEGEVPVGAVLVKDGEIIARGHNRVETLNDPTAHAEILAIRAAARKLGNWRLSGCTLYVTL 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 446569383  81 HPCPMCMAAMRLAGIKTVNYAYSNEDGAPFGLstaeIYADLVKPFAEQSMKIE 133
Cdd:COG0590   81 EPCPMCAGAIVWARIGRVVYGASDPKAGAAGS----IYDLLADPRLNHRVEVV 129
nucleoside_deaminase cd01285
Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn ...
 8-111 1.23e-40

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: 132.36  E-value: 1.23e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446569383   8 LRQAIELAYNNIEKGGRPFGAVIV-KDGKVIASGVNQILTTNDPTAHAELLAIRAASQVLGTANLEGCSVFASGHPCPMC 86
Cdd:cd01285    1 MRLAIELARKALAEGEVPFGAVIVdDDGKVIARGHNRVEQDGDPTAHAEIVAIRNAARRLGSYLLSGCTLYTTLEPCPMC 80

                         90       100
                 ....*....|....*....|....*
gi 446569383  87 MAAMRLAGIKTVNYAYSNEDGAPFG 111
Cdd:cd01285   81 AGALLWARIKRVVYGASDPKLGGIG 105
MafB19-deam pfam14437
MafB19-like deaminase; A member of the nucleic acid/nucleotide deaminase superfamily ...
 5-111 2.30e-26

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: 97.21  E-value: 2.30e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446569383    5 QEFLRQAIELAYNNIEKGGRPFGAVIVKDGKVIASGVNQILTTNDPTAHAELLAIRAASQVLGTANLEGCSVFASGHPCP 84
Cdd:pfam14437   4 EKWFRKALGLAEKAYDAGEVPIGAVIVKDGKVIARGYNRKELNADTTAHAEILAIQQAAKKLGSWRLDDATLYVTLEPCP 83

                          90       100
                  ....*....|....*....|....*..
gi 446569383   85 MCMAAMRLAGIKTVNYAYSNEDGAPFG 111
Cdd:pfam14437  84 MCAGAIVQAGLKSLVYGAGNPKGGAVG 110
dCMP_cyt_deam_1 pfam00383
Cytidine and deoxycytidylate deaminase zinc-binding region;
5-101 5.24e-26

Cytidine and deoxycytidylate deaminase zinc-binding region;


Pssm-ID: 395307 [Multi-domain]  Cd Length: 100  Bit Score: 94.68  E-value: 5.24e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446569383    5 QEFLRQAIELAYNNIEKGGRPFGAVIVK-DGKVIASGVNQILTTNDPTAHAELLAIRAASQVLGTANLEGCSVFASGHPC 83
Cdd:pfam00383   3 EYFMRLALKAAKRAYPYSNFPVGAVIVKkDGEIIATGYNGENAGYDPTIHAERNAIRQAGKRGEGVRLEGATLYVTLEPC 82

                          90
                  ....*....|....*...
gi 446569383   84 PMCMAAMRLAGIKTVNYA 101
Cdd:pfam00383  83 GMCAQAIIESGIKRVVFG 100
PRK10860 PRK10860
tRNA-specific adenosine deaminase; Provisional
 7-105 1.62e-19

tRNA-specific adenosine deaminase; Provisional


Pssm-ID: 182786 [Multi-domain]  Cd Length: 172  Bit Score: 80.24  E-value: 1.62e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446569383   7 FLRQAIELAYNNIEKGGRPFGAVIVKDGKVIASGVNQILTTNDPTAHAELLAIRAASQVLGTANLEGCSVFASGHPCPMC 86
Cdd:PRK10860  16 WMRHALTLAKRAWDEREVPVGAVLVHNNRVIGEGWNRPIGRHDPTAHAEIMALRQGGLVLQNYRLLDATLYVTLEPCVMC 95

                         90
                 ....*....|....*....
gi 446569383  87 MAAMRLAGIKTVNYAYSNE 105
Cdd:PRK10860  96 AGAMVHSRIGRLVFGARDA 114
deoxycytidylate_deaminase cd01286
Deoxycytidylate deaminase domain. Deoxycytidylate deaminase catalyzes the deamination of dCMP ...
 24-111 1.31e-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: 55.74  E-value: 1.31e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446569383  24 RPFGAVIVKDGKVIASGVNQ----------ILTTNDP-----------TAHAELLAIRAASQVlgTANLEGCSVFASGHP 82
Cdd:cd01286   20 RQVGAVIVKDKRIISTGYNGspsglphcaeVGCERDDlpsgedqkccrTVHAEQNAILQAARH--GVSLEGATLYVTLFP 97

                         90       100
                 ....*....|....*....|....*....
gi 446569383  83 CPMCMAAMRLAGIKTVNYAYSNEDGAPFG 111
Cdd:cd01286   98 CIECAKLIIQAGIKKVVYAEPYDDDDPAA 126
RibD1 COG0117
Riboflavin biosynthesis protein RibD, pyrimidine deaminase domain [Coenzyme transport and ...
 5-101 4.99e-09

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: 53.52  E-value: 4.99e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446569383   5 QEFLRQAIELAYNniekgGRPF-------GAVIVKDGKVIASGVNQilttnDP-TAHAELLAIRAASQVL--GTA--NLE 72
Cdd:COG0117    1 ERYMRRALELARR-----GLGTtspnplvGCVIVKDGRIVGEGYHQ-----RAgGPHAEVNALAQAGEAArgATLyvTLE 70

                         90       100       110
                 ....*....|....*....|....*....|.
gi 446569383  73 GCSVFASGHPCpmcmaAMRL--AGIKTVNYA 101
Cdd:COG0117   71 PCSHHGRTPPC-----ADALieAGIKRVVIA 96
Riboflavin_deaminase-reductase cd01284
Riboflavin-specific deaminase. Riboflavin biosynthesis protein RibD ...
 8-101 1.24e-08

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: 50.31  E-value: 1.24e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446569383   8 LRQAIELAynniEKG-GR-----PFGAVIVKD-GKVIASGVnqilTTNDPTAHAELLAIRAASQVL---GTA--NLEGCS 75
Cdd:cd01284    1 MRRALELA----EKGrGLtspnpPVGCVIVDDdGEIVGEGY----HRKAGGPHAEVNALASAGEKLargATLyvTLEPCS 72

                         90       100
                 ....*....|....*....|....*.
gi 446569383  76 VFASGHPCPMCMAAmrlAGIKTVNYA 101
Cdd:cd01284   73 HHGKTPPCVDAIIE---AGIKRVVVG 95
cd PHA02588
deoxycytidylate deaminase; Provisional
 27-101 8.66e-06

deoxycytidylate deaminase; Provisional


Pssm-ID: 222894 [Multi-domain]  Cd Length: 168  Bit Score: 43.59  E-value: 8.66e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446569383  27 GAVIVKDGKVIASGVN--------------QILTTNDPTA------------------HAELLAIRAASQvlGTANLEGC 74
Cdd:PHA02588  25 GAVIEKNGRIISTGYNgtpaggvnccdhanEQGWLDDEGKlkkehrpehsawsskneiHAELNAILFAAR--NGISIEGA 102

                         90       100
                 ....*....|....*....|....*..
gi 446569383  75 SVFASGHPCPMCMAAMRLAGIKTVNYA 101
Cdd:PHA02588 103 TMYVTASPCPDCAKAIAQSGIKKLVYC 129
cytidine_deaminase-like cd00786
Cytidine and deoxycytidylate deaminase zinc-binding region. The family contains cytidine ...
 22-98 2.79e-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: 41.00  E-value: 2.79e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446569383  22 GGRPFGAVIV--KDGKVIASGVNQILTTNDPTAHAELLAIRAASQvlgTANLEGCSVFASGHPCPMCMAAMRLAGIKTV 98
Cdd:cd00786   16 SNFQVGACLVnkKDGGKVGRGCNIENAAYSMCNHAERTALFNAGS---EGDTKGQMLYVALSPCGACAQLIIELGIKDV 91
PLN02807 PLN02807
diaminohydroxyphosphoribosylaminopyrimidine deaminase
 7-98 1.32e-04

diaminohydroxyphosphoribosylaminopyrimidine deaminase


Pssm-ID: 215433 [Multi-domain]  Cd Length: 380  Bit Score: 40.91  E-value: 1.32e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446569383   7 FLRQAIELAYNNIEKGG-RPF-GAVIVKDGKVIASGVNqilttndPTA---HAELLAIRAASQVlgtanLEGCSVFASGH 81
Cdd:PLN02807  35 YMRRCVELARKAIGCTSpNPMvGCVIVKDGRIVGEGFH-------PKAgqpHAEVFALRDAGDL-----AENATAYVSLE 102

                         90       100
                 ....*....|....*....|...
gi 446569383  82 PC------PMCMAAMRLAGIKTV 98
Cdd:PLN02807 103 PCnhygrtPPCTEALIKAKVKRV 125
 
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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