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Conserved domains on  [gi|1233717755|gb|OZG56872|]
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nucleotidyltransferase [Aeriscardovia aeriphila]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SMODS super family cl39525
Second Messenger Oligonucleotide or Dinucleotide Synthetase domain; Nucleotide synthetase ...
 2-115 2.18e-29

Second Messenger Oligonucleotide or Dinucleotide Synthetase domain; Nucleotide synthetase enzyme of the DNA polymerase beta superfamily. Experimental studies have demonstrated cGAMP synthetase activity in the Vibrio cholerae DncV protein, a member of the SMODS family. The diversity inherent to the SMODS family suggests members of the family could generate a range of nucleotides, cyclic and/or linear. The nucleotide second messengers generated by the SMODS domains are predicted to activate effectors in a class of conflict systems reliant on the production and sensing of the nucleotide second messengers.


The actual alignment was detected with superfamily member pfam18144:

Pssm-ID: 477034  Cd Length: 164  Bit Score: 107.73  E-value: 2.18e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1233717755   2 YVGSYGRGTAI-STSDIDILLELPKNEYYHYSSLTGNGQSRLLQTVKKSVLSRYPRTEVHGDGQVVVVVFsDGMRFELLP 80
Cdd:pfam18144  51 LVGSYARGTIIrPVSDLDMLFRLDADILVVYDPYDGWGPSDYLQKLKRAIEKTYSTSEIRQDRCVIVVYF-NHIKFDVVP 129

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1233717755  81 AFETSSGEYEYPDTHmGGNWKSTNPKAEQEALKRK 115
Cdd:pfam18144 130 AFKNRDGSYTIPDRN-NGEWKKTNPREETDWLREK 163
 
Name Accession Description Interval E-value
SMODS pfam18144
Second Messenger Oligonucleotide or Dinucleotide Synthetase domain; Nucleotide synthetase ...
 2-115 2.18e-29

Second Messenger Oligonucleotide or Dinucleotide Synthetase domain; Nucleotide synthetase enzyme of the DNA polymerase beta superfamily. Experimental studies have demonstrated cGAMP synthetase activity in the Vibrio cholerae DncV protein, a member of the SMODS family. The diversity inherent to the SMODS family suggests members of the family could generate a range of nucleotides, cyclic and/or linear. The nucleotide second messengers generated by the SMODS domains are predicted to activate effectors in a class of conflict systems reliant on the production and sensing of the nucleotide second messengers.


Pssm-ID: 436305  Cd Length: 164  Bit Score: 107.73  E-value: 2.18e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1233717755   2 YVGSYGRGTAI-STSDIDILLELPKNEYYHYSSLTGNGQSRLLQTVKKSVLSRYPRTEVHGDGQVVVVVFsDGMRFELLP 80
Cdd:pfam18144  51 LVGSYARGTIIrPVSDLDMLFRLDADILVVYDPYDGWGPSDYLQKLKRAIEKTYSTSEIRQDRCVIVVYF-NHIKFDVVP 129

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1233717755  81 AFETSSGEYEYPDTHmGGNWKSTNPKAEQEALKRK 115
Cdd:pfam18144 130 AFKNRDGSYTIPDRN-NGEWKKTNPREETDWLREK 163
NT_2-5OAS_ClassI-CCAase cd05400
Nucleotidyltransferase (NT) domain of 2'5'-oligoadenylate (2-5A)synthetase (2-5OAS) and class ...
 3-114 2.03e-20

Nucleotidyltransferase (NT) domain of 2'5'-oligoadenylate (2-5A)synthetase (2-5OAS) and class I CCA-adding enzyme; In vertebrates, 2-5OASs are induced by interferon during the innate immune response to protect against RNA virus infections. In the presence of an RNA activator, 2-5OASs catalyze the oligomerization of ATP into 2-5A. 2-5A activates endoribonuclease L, which leads to degradation of the viral RNA. 2-5OASs are also implicated in cell growth control, differentiation, and apoptosis. This family includes human OAS1, -2, -3, and OASL. CCA-adding enzymes add the sequence [cytidine(C)-cytidine-adenosine (A)], one nucleotide at a time, onto the 3' end of tRNA, in a template-independent reaction. This class I group includes the archaeal Sulfolobus shibatae and Archeoglobus fulgidus CCA-adding enzymes. It belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These carboxylate residues are conserved in this family.


Pssm-ID: 143390 [Multi-domain]  Cd Length: 143  Bit Score: 83.60  E-value: 2.03e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1233717755   3 VGSYGRGTAI-STSDIDILLELPKNEYYhysslTGNGQSRLLQTVKKSVLSRYP-RTEVHGDGQVVVVVFSD-GMRFELL 79
Cdd:cd05400    33 QGSYARGTALrGDSDIDLVVVLPDDTSF-----AEYGPAELLDELGEALKEYYGaNEEVKAQHRSVTVKFKGqGFHVDVV 107

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1233717755  80 PAFETSSGEYEYP-DTHMGGNWKSTNPKAEQEALKR 114
Cdd:cd05400   108 PAFEADSGSKYGSvPDRDGGSWVDRNPKHHAELLRR 143
MJ0435 COG1669
Predicted nucleotidyltransferase MJ0435 [General function prediction only];
4-25 3.10e-03

Predicted nucleotidyltransferase MJ0435 [General function prediction only];


Pssm-ID: 441275  Cd Length: 96  Bit Score: 36.05  E-value: 3.10e-03
                          10        20
                  ....*....|....*....|..
gi 1233717755   4 GSYGRGTAISTSDIDILLELPK 25
Cdd:COG1669    30 GSVARGEAREDSDIDLLVEFDE 51
 
Name Accession Description Interval E-value
SMODS pfam18144
Second Messenger Oligonucleotide or Dinucleotide Synthetase domain; Nucleotide synthetase ...
 2-115 2.18e-29

Second Messenger Oligonucleotide or Dinucleotide Synthetase domain; Nucleotide synthetase enzyme of the DNA polymerase beta superfamily. Experimental studies have demonstrated cGAMP synthetase activity in the Vibrio cholerae DncV protein, a member of the SMODS family. The diversity inherent to the SMODS family suggests members of the family could generate a range of nucleotides, cyclic and/or linear. The nucleotide second messengers generated by the SMODS domains are predicted to activate effectors in a class of conflict systems reliant on the production and sensing of the nucleotide second messengers.


Pssm-ID: 436305  Cd Length: 164  Bit Score: 107.73  E-value: 2.18e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1233717755   2 YVGSYGRGTAI-STSDIDILLELPKNEYYHYSSLTGNGQSRLLQTVKKSVLSRYPRTEVHGDGQVVVVVFsDGMRFELLP 80
Cdd:pfam18144  51 LVGSYARGTIIrPVSDLDMLFRLDADILVVYDPYDGWGPSDYLQKLKRAIEKTYSTSEIRQDRCVIVVYF-NHIKFDVVP 129

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1233717755  81 AFETSSGEYEYPDTHmGGNWKSTNPKAEQEALKRK 115
Cdd:pfam18144 130 AFKNRDGSYTIPDRN-NGEWKKTNPREETDWLREK 163
NT_2-5OAS_ClassI-CCAase cd05400
Nucleotidyltransferase (NT) domain of 2'5'-oligoadenylate (2-5A)synthetase (2-5OAS) and class ...
 3-114 2.03e-20

Nucleotidyltransferase (NT) domain of 2'5'-oligoadenylate (2-5A)synthetase (2-5OAS) and class I CCA-adding enzyme; In vertebrates, 2-5OASs are induced by interferon during the innate immune response to protect against RNA virus infections. In the presence of an RNA activator, 2-5OASs catalyze the oligomerization of ATP into 2-5A. 2-5A activates endoribonuclease L, which leads to degradation of the viral RNA. 2-5OASs are also implicated in cell growth control, differentiation, and apoptosis. This family includes human OAS1, -2, -3, and OASL. CCA-adding enzymes add the sequence [cytidine(C)-cytidine-adenosine (A)], one nucleotide at a time, onto the 3' end of tRNA, in a template-independent reaction. This class I group includes the archaeal Sulfolobus shibatae and Archeoglobus fulgidus CCA-adding enzymes. It belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These carboxylate residues are conserved in this family.


Pssm-ID: 143390 [Multi-domain]  Cd Length: 143  Bit Score: 83.60  E-value: 2.03e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1233717755   3 VGSYGRGTAI-STSDIDILLELPKNEYYhysslTGNGQSRLLQTVKKSVLSRYP-RTEVHGDGQVVVVVFSD-GMRFELL 79
Cdd:cd05400    33 QGSYARGTALrGDSDIDLVVVLPDDTSF-----AEYGPAELLDELGEALKEYYGaNEEVKAQHRSVTVKFKGqGFHVDVV 107

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1233717755  80 PAFETSSGEYEYP-DTHMGGNWKSTNPKAEQEALKR 114
Cdd:cd05400   108 PAFEADSGSKYGSvPDRDGGSWVDRNPKHHAELLRR 143
NTP_transf_2 pfam01909
Nucleotidyltransferase domain; Members of this family belong to a large family of ...
 3-29 1.59e-04

Nucleotidyltransferase domain; Members of this family belong to a large family of nucleotidyltransferases. This family includes kanamycin nucleotidyltransferase (KNTase) which is a plasmid-coded enzyme responsible for some types of bacterial resistance to aminoglycosides. KNTase in-activates antibiotics by catalysing the addition of a nucleotidyl group onto the drug.


Pssm-ID: 396474  Cd Length: 91  Bit Score: 39.32  E-value: 1.59e-04
                          10        20
                  ....*....|....*....|....*..
gi 1233717755   3 VGSYGRGTAISTSDIDILLELPKNEYY 29
Cdd:pfam01909  20 FGSYARGTALPGSDIDLLVVFPEPVEE 46
NT_KNTase_like cd05403
Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, ...
 4-29 7.19e-04

Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins; S. aureus KNTase is a plasmid encoded enzyme which confers resistance to a wide range of aminoglycoside antibiotics which have a 4'- or 4''-hydroxyl group in the equatorial position, such as kanamycin A. This enzyme transfers a nucleoside monophosphate group from a nucleotide (ATP,GTP, or UTP) to the 4'-hydroxyl group of kanamycin A. This enzyme is a homodimer, having two NT active sites. The nucleotide and antibiotic binding sites of each active site include residues from each monomer. Included in this subgroup is Escherichia coli AadA5 which confers resistance to the antibiotic spectinomycin and is a putative aminoglycoside-3'-adenylyltransferase. It is part of the aadA5 cassette of a class 1 integron. This subgroup also includes Haemophilus influenzae HI0073 which forms a 2:2 heterotetramer with an unrelated protein HI0074. Structurally HI0074 is related to the substrate-binding domain of S. aureus KNTase. The genes encoding HI0073 and HI0074 form an operon. Little is known about the substrate specificity or function of two-component NTs. The characterized members of this subgroup may not be representive of the function of this subgroup. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, co-ordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These carboxylate residues are conserved in this subgroup.


Pssm-ID: 143393  Cd Length: 93  Bit Score: 37.78  E-value: 7.19e-04
                          10        20
                  ....*....|....*....|....*.
gi 1233717755   4 GSYGRGTAISTSDIDILLELPKNEYY 29
Cdd:cd05403    25 GSYARGDARPDSDIDLLVIFDDPLDP 50
MJ0435 COG1669
Predicted nucleotidyltransferase MJ0435 [General function prediction only];
4-25 3.10e-03

Predicted nucleotidyltransferase MJ0435 [General function prediction only];


Pssm-ID: 441275  Cd Length: 96  Bit Score: 36.05  E-value: 3.10e-03
                          10        20
                  ....*....|....*....|..
gi 1233717755   4 GSYGRGTAISTSDIDILLELPK 25
Cdd:COG1669    30 GSVARGEAREDSDIDLLVEFDE 51
 
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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