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Conserved domains on  [gi|2711983584|ref|WP_339394149|]
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RNA pyrophosphohydrolase, partial [Brevibacterium metallidurans]

Protein Classification

RNA pyrophosphohydrolase( domain architecture ID 10011496)

RNA pyrophosphohydrolase initiates mRNA decay by removing pyrophosphate from the 5' end of triphosphorylated RNA

EC:  3.6.1.-
Gene Ontology:  GO:0005737|GO:0034353|GO:0006402
PubMed:  14739989|16378245

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK00714 PRK00714
RNA pyrophosphohydrolase; Reviewed
 1-98 2.04e-59

RNA pyrophosphohydrolase; Reviewed


:

Pssm-ID: 234820 [Multi-domain]  Cd Length: 156  Bit Score: 179.58  E-value: 2.04e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2711983584   1 GLSRKDVRILASTRNWLRYKLPKRLVRWdTKPVCIGQKQKWFLLQLVGSDTAINMQTSSTPEFDGWRWVSYWYPVRQVVS 80
Cdd:PRK00714   60 GLRPEDVEILAETRDWLRYDLPKRLVRR-SKGVYRGQKQKWFLLRLTGDDSEINLNTTSHPEFDAWRWVSYWYPLDQVVP 138

                          90
                  ....*....|....*...
gi 2711983584  81 FKRDVYRRVMKEFAGVTM 98
Cdd:PRK00714  139 FKRDVYRRVLKEFARLLM 156
 
Name Accession Description Interval E-value
PRK00714 PRK00714
RNA pyrophosphohydrolase; Reviewed
 1-98 2.04e-59

RNA pyrophosphohydrolase; Reviewed


Pssm-ID: 234820 [Multi-domain]  Cd Length: 156  Bit Score: 179.58  E-value: 2.04e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2711983584   1 GLSRKDVRILASTRNWLRYKLPKRLVRWdTKPVCIGQKQKWFLLQLVGSDTAINMQTSSTPEFDGWRWVSYWYPVRQVVS 80
Cdd:PRK00714   60 GLRPEDVEILAETRDWLRYDLPKRLVRR-SKGVYRGQKQKWFLLRLTGDDSEINLNTTSHPEFDAWRWVSYWYPLDQVVP 138

                          90
                  ....*....|....*...
gi 2711983584  81 FKRDVYRRVMKEFAGVTM 98
Cdd:PRK00714  139 FKRDVYRRVLKEFARLLM 156
NUDIX_Ap4A_hydrolase_plant_like cd03671
plant diadenosine tetraphosphate (Ap4A) hydrolase and similar proteins; Diadenosine ...
 1-93 3.81e-44

plant diadenosine tetraphosphate (Ap4A) hydrolase and similar proteins; Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the NUDIX hydrolase superfamily. Members of this family are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where plant enzymes fall into one group (represented by this subfamily) and fungi/animals/archaea enzymes fall into another. Bacterial enzymes are found in both subfamilies. Ap4A is a potential by-product of aminoacyl tRNA synthesis, and accumulation of Ap4A has been implicated in a range of biological events, such as DNA replication, cellular differentiation, heat shock, metabolic stress, and apoptosis. Ap4A hydrolase cleaves Ap4A asymmetrically into ATP and AMP. It is important in the invasive properties of bacteria and thus presents a potential target for the inhibition of such invasive bacteria. Besides the signature NUDIX motif (G[X5]E[X7]REUXEEXGU where U is Ile, Leu, or Val), Ap4A hydrolase is structurally similar to the other members of the NUDIX hydrolase superfamily with some degree of variations. Several regions in the sequences are poorly defined and substrate and metal binding sites are only predicted based on kinetic studies.


Pssm-ID: 467539 [Multi-domain]  Cd Length: 147  Bit Score: 140.78  E-value: 3.81e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2711983584   1 GLSRKDVRILASTRNWLRYKLPKRLVRWDTKPVCIGQKQKWFLLQLVGSDTAINMQTSSTPEFDGWRWVSYWYPVRQVVS 80
Cdd:cd03671    55 GLSPEDVEIIAETPDWLTYDLPEDLIRKGWGGKYRGQKQKWFLFRFTGDDSEINLDTHEHPEFDAWRWVDLEELPDLVVP 134

                          90
                  ....*....|...
gi 2711983584  81 FKRDVYRRVMKEF 93
Cdd:cd03671   135 FKRDVYRQVLKEF 147
MutT COG0494
8-oxo-dGTP pyrophosphatase MutT and related house-cleaning NTP pyrophosphohydrolases, NUDIX ...
 1-94 6.80e-08

8-oxo-dGTP pyrophosphatase MutT and related house-cleaning NTP pyrophosphohydrolases, NUDIX family [Defense mechanisms];


Pssm-ID: 440260 [Multi-domain]  Cd Length: 143  Bit Score: 47.72  E-value: 6.80e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2711983584   1 GLSRKDVRILASTrnwlryklpkrlvrwdTKPVCIGQKQKWFLLQLVGSDTAINMqtSSTPEFDGWRWVSYWYPVRQVVS 80
Cdd:COG0494    68 GLTAEDLELLGEL----------------PSPGYTDEKVHVFLARGLGPGEEVGL--DDEDEFIEVRWVPLDEALALVTA 129

                          90
                  ....*....|....
gi 2711983584  81 FKRdvyRRVMKEFA 94
Cdd:COG0494   130 GEI---AKTLAALA 140
 
Name Accession Description Interval E-value
PRK00714 PRK00714
RNA pyrophosphohydrolase; Reviewed
 1-98 2.04e-59

RNA pyrophosphohydrolase; Reviewed


Pssm-ID: 234820 [Multi-domain]  Cd Length: 156  Bit Score: 179.58  E-value: 2.04e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2711983584   1 GLSRKDVRILASTRNWLRYKLPKRLVRWdTKPVCIGQKQKWFLLQLVGSDTAINMQTSSTPEFDGWRWVSYWYPVRQVVS 80
Cdd:PRK00714   60 GLRPEDVEILAETRDWLRYDLPKRLVRR-SKGVYRGQKQKWFLLRLTGDDSEINLNTTSHPEFDAWRWVSYWYPLDQVVP 138

                          90
                  ....*....|....*...
gi 2711983584  81 FKRDVYRRVMKEFAGVTM 98
Cdd:PRK00714  139 FKRDVYRRVLKEFARLLM 156
NUDIX_Ap4A_hydrolase_plant_like cd03671
plant diadenosine tetraphosphate (Ap4A) hydrolase and similar proteins; Diadenosine ...
 1-93 3.81e-44

plant diadenosine tetraphosphate (Ap4A) hydrolase and similar proteins; Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the NUDIX hydrolase superfamily. Members of this family are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where plant enzymes fall into one group (represented by this subfamily) and fungi/animals/archaea enzymes fall into another. Bacterial enzymes are found in both subfamilies. Ap4A is a potential by-product of aminoacyl tRNA synthesis, and accumulation of Ap4A has been implicated in a range of biological events, such as DNA replication, cellular differentiation, heat shock, metabolic stress, and apoptosis. Ap4A hydrolase cleaves Ap4A asymmetrically into ATP and AMP. It is important in the invasive properties of bacteria and thus presents a potential target for the inhibition of such invasive bacteria. Besides the signature NUDIX motif (G[X5]E[X7]REUXEEXGU where U is Ile, Leu, or Val), Ap4A hydrolase is structurally similar to the other members of the NUDIX hydrolase superfamily with some degree of variations. Several regions in the sequences are poorly defined and substrate and metal binding sites are only predicted based on kinetic studies.


Pssm-ID: 467539 [Multi-domain]  Cd Length: 147  Bit Score: 140.78  E-value: 3.81e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2711983584   1 GLSRKDVRILASTRNWLRYKLPKRLVRWDTKPVCIGQKQKWFLLQLVGSDTAINMQTSSTPEFDGWRWVSYWYPVRQVVS 80
Cdd:cd03671    55 GLSPEDVEIIAETPDWLTYDLPEDLIRKGWGGKYRGQKQKWFLFRFTGDDSEINLDTHEHPEFDAWRWVDLEELPDLVVP 134

                          90
                  ....*....|...
gi 2711983584  81 FKRDVYRRVMKEF 93
Cdd:cd03671   135 FKRDVYRQVLKEF 147
MutT COG0494
8-oxo-dGTP pyrophosphatase MutT and related house-cleaning NTP pyrophosphohydrolases, NUDIX ...
 1-94 6.80e-08

8-oxo-dGTP pyrophosphatase MutT and related house-cleaning NTP pyrophosphohydrolases, NUDIX family [Defense mechanisms];


Pssm-ID: 440260 [Multi-domain]  Cd Length: 143  Bit Score: 47.72  E-value: 6.80e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2711983584   1 GLSRKDVRILASTrnwlryklpkrlvrwdTKPVCIGQKQKWFLLQLVGSDTAINMqtSSTPEFDGWRWVSYWYPVRQVVS 80
Cdd:COG0494    68 GLTAEDLELLGEL----------------PSPGYTDEKVHVFLARGLGPGEEVGL--DDEDEFIEVRWVPLDEALALVTA 129

                          90
                  ....*....|....
gi 2711983584  81 FKRdvyRRVMKEFA 94
Cdd:COG0494   130 GEI---AKTLAALA 140
 
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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