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Conserved domains on  [gi|1940424044|ref|WP_196824398|]
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nucleotidyltransferase family protein [Corynebacterium aquatimens]

Protein Classification

nucleotidyltransferase family protein( domain architecture ID 10004143)

nucleotidyltransferase family protein such as Thermococcus cleftensis protein adenylyltransferase MntA, the antitoxin component of a type VII toxin-antitoxin (TA) that neutralizes the toxic effect of cognate toxin HepT by AMPylation

CATH:  3.30.460.10
EC:  2.7.7.-
Gene Ontology:  GO:0016779|GO:0046872
PubMed:  10075991
SCOP:  4001404

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
MJ0435 COG1669
Predicted nucleotidyltransferase MJ0435 [General function prediction only];
13-107 1.85e-12

Predicted nucleotidyltransferase MJ0435 [General function prediction only];


:

Pssm-ID: 441275  Cd Length: 96  Bit Score: 58.00  E-value: 1.85e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1940424044  13 LRELVQARRADFYELLGRYCATNPRLFGSVATGTAGENSDIDILVDMDPVDGniLMRAAGLMEETRELFRSEsIDIFPAQ 92
Cdd:COG1669     3 REEILEILREVIEELAERYGVSRLGLFGSVARGEAREDSDIDLLVEFDEPTS--LFDLFELEEELEELLGRK-VDLVTLD 79

                          90
                  ....*....|....*..
gi 1940424044  93 LLKFPISE--LEETILI 107
Cdd:COG1669    80 GLSPRLREriLKEGVLL 96
 
Name Accession Description Interval E-value
MJ0435 COG1669
Predicted nucleotidyltransferase MJ0435 [General function prediction only];
13-107 1.85e-12

Predicted nucleotidyltransferase MJ0435 [General function prediction only];


Pssm-ID: 441275  Cd Length: 96  Bit Score: 58.00  E-value: 1.85e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1940424044  13 LRELVQARRADFYELLGRYCATNPRLFGSVATGTAGENSDIDILVDMDPVDGniLMRAAGLMEETRELFRSEsIDIFPAQ 92
Cdd:COG1669     3 REEILEILREVIEELAERYGVSRLGLFGSVARGEAREDSDIDLLVEFDEPTS--LFDLFELEEELEELLGRK-VDLVTLD 79

                          90
                  ....*....|....*..
gi 1940424044  93 LLKFPISE--LEETILI 107
Cdd:COG1669    80 GLSPRLREriLKEGVLL 96
NTP_transf_2 pfam01909
Nucleotidyltransferase domain; Members of this family belong to a large family of ...
 38-107 2.17e-09

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: 50.11  E-value: 2.17e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1940424044  38 LFGSVATGTAGENSDIDILVDMD-PVDGNILMRAAGLMEETRELFRSEsIDIFPAQLLKFP---ISELEETILI 107
Cdd:pfam01909  19 LFGSYARGTALPGSDIDLLVVFPePVEEERLLKLAKIIKELEELLGLE-VDLVTREKIEFPlvkIDILEERILL 91
NT_KNTase_like cd05403
Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, ...
 38-103 2.59e-08

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: 47.41  E-value: 2.59e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1940424044  38 LFGSVATGTAGENSDIDILVDMDPVDGniLMRAAGLMEETRELFRsESIDIFPAQLLKFPISELEE 103
Cdd:cd05403    23 LFGSYARGDARPDSDIDLLVIFDDPLD--PLELARLLEELELLLG-RPVDLVVLNALELELLLRIL 85
 
Name Accession Description Interval E-value
MJ0435 COG1669
Predicted nucleotidyltransferase MJ0435 [General function prediction only];
13-107 1.85e-12

Predicted nucleotidyltransferase MJ0435 [General function prediction only];


Pssm-ID: 441275  Cd Length: 96  Bit Score: 58.00  E-value: 1.85e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1940424044  13 LRELVQARRADFYELLGRYCATNPRLFGSVATGTAGENSDIDILVDMDPVDGniLMRAAGLMEETRELFRSEsIDIFPAQ 92
Cdd:COG1669     3 REEILEILREVIEELAERYGVSRLGLFGSVARGEAREDSDIDLLVEFDEPTS--LFDLFELEEELEELLGRK-VDLVTLD 79

                          90
                  ....*....|....*..
gi 1940424044  93 LLKFPISE--LEETILI 107
Cdd:COG1669    80 GLSPRLREriLKEGVLL 96
NTP_transf_2 pfam01909
Nucleotidyltransferase domain; Members of this family belong to a large family of ...
 38-107 2.17e-09

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: 50.11  E-value: 2.17e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1940424044  38 LFGSVATGTAGENSDIDILVDMD-PVDGNILMRAAGLMEETRELFRSEsIDIFPAQLLKFP---ISELEETILI 107
Cdd:pfam01909  19 LFGSYARGTALPGSDIDLLVVFPePVEEERLLKLAKIIKELEELLGLE-VDLVTREKIEFPlvkIDILEERILL 91
NT_KNTase_like cd05403
Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, ...
 38-103 2.59e-08

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: 47.41  E-value: 2.59e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1940424044  38 LFGSVATGTAGENSDIDILVDMDPVDGniLMRAAGLMEETRELFRsESIDIFPAQLLKFPISELEE 103
Cdd:cd05403    23 LFGSYARGDARPDSDIDLLVIFDDPLD--PLELARLLEELELLLG-RPVDLVVLNALELELLLRIL 85
MJ0604 COG1708
Predicted nucleotidyltransferase, MJ0604 family [General function prediction only];
38-57 1.24e-05

Predicted nucleotidyltransferase, MJ0604 family [General function prediction only];


Pssm-ID: 441314  Cd Length: 95  Bit Score: 40.40  E-value: 1.24e-05
                          10        20
                  ....*....|....*....|
gi 1940424044  38 LFGSVATGTAGENSDIDILV 57
Cdd:COG1708    27 LFGSYARGDARPDSDIDLLV 46
Polbeta pfam18765
Polymerase beta, Nucleotidyltransferase; A member of the nucleotidyltransferase fold found in ...
 38-63 1.42e-05

Polymerase beta, Nucleotidyltransferase; A member of the nucleotidyltransferase fold found in polymorphic toxins (NTox45) and polyvalent proteins.


Pssm-ID: 465859  Cd Length: 93  Bit Score: 40.20  E-value: 1.42e-05
                          10        20
                  ....*....|....*....|....*.
gi 1940424044  38 LFGSVATGTAGENSDIDILVDMDPVD 63
Cdd:pfam18765  18 LFGSRAKGDAREDSDIDLAVLYDEKL 43
NT_PAP_TUTase cd05402
Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases; ...
 37-67 1.95e-04

Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases; Poly(A) polymerases (PAPs) catalyze mRNA poly(A) tail synthesis, and terminal uridylyl transferases (TUTases) uridylate RNA. PAPs in this subgroup include human PAP alpha, mouse testis-specific cytoplasmic PAP beta, human nuclear PAP gamma, Saccharomyces cerevisiae PAP1, TRF4 and-5, Schizosaccharomyces pombe caffeine-induced death proteins -1, and -14, Caenorhabditis elegans Germ Line Development-2, and Chlamydomonas reinhardtii MUT68. This family also includes human U6 snRNA-specific TUTase1, and Trypanosoma brucei 3'-TUTase-1,-2, and 4. This family 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. For the majority of proteins in this family, these carboxylate residues are conserved.


Pssm-ID: 143392 [Multi-domain]  Cd Length: 114  Bit Score: 37.54  E-value: 1.95e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1940424044  37 RLFGSVATGTAGENSDIDILVDMDPVDGNIL 67
Cdd:cd05402    23 YPFGSYVTGLGLPGSDIDLCLLGPNHRVDRE 53
SMODS pfam18144
Second Messenger Oligonucleotide or Dinucleotide Synthetase domain; Nucleotide synthetase ...
 21-83 6.24e-03

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: 34.16  E-value: 6.24e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1940424044  21 RADFYELLGRYcaTNPRLFGSVATGTA---------GENSDIDILVDMDPVDGNilmRAAGLMEETRELFRS 83
Cdd:pfam18144  36 NTDFWDFGSKT--SESFLVGSYARGTIirpvsdldmLFRLDADILVVYDPYDGW---GPSDYLQKLKRAIEK 102
 
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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