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Conserved domains on  [gi|1088191043|gb|OHA50408|]
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MAG: arginine decarboxylase, pyruvoyl-dependent [Candidatus Terrybacteria bacterium RIFCSPHIGHO2_02_FULL_43_14]

Protein Classification

pyruvoyl-dependent arginine decarboxylase( domain architecture ID 10486916)

pyruvoyl-dependent arginine decarboxylase catalyzes the decarboxylation of L-arginine to produce agmatine

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PvlArgDC pfam01862
Pyruvoyl-dependent arginine decarboxylase (PvlArgDC); Methanococcus jannaschii contains ...
 6-183 5.53e-80

Pyruvoyl-dependent arginine decarboxylase (PvlArgDC); Methanococcus jannaschii contains homologs of most genes required for spermidine polyamine biosynthesis. Yet genomes from neither this organizm nor any other euryarchaeon have orthologues of the pyridoxal 5'-phosphate- dependent ornithine or arginine decarboxylase genes, required to produce putrescine. Instead,these organizms have a new class of arginine decarboxylase (PvlArgDC) formed by the self-cleavage of a proenzyme into a 5-kDa subunit and a 12-kDa subunit that contains a reactive pyruvoyl group. Although this extremely thermostable enzyme has no significant sequence similarity to previously characterized proteins, conserved active site residues are similar to those of the pyruvoyl-dependent histidine decarboxylase enzyme, and its subunits form a similar (alpha-beta)(3) complex. homologs of PvlArgDC are found in several bacterial genomes, including those of Chlamydia spp., which have no agmatine ureohydrolase enzyme to convert agmatine (decarboxylated arginine) into putrescine. In these intracellular pathogens, PvlArgDC may function analogously to pyruvoyl-dependent histidine decarboxylase; the cells are proposed to import arginine and export agmatine, increasing the pH and affecting the host cell's metabolism. Phylogenetic analysis of Pvl- ArgDC proteins suggests that this gene has been recruited from the euryarchaeal polyamine biosynthetic pathway to function as a degradative enzyme in bacteria.


:

Pssm-ID: 426480  Cd Length: 161  Bit Score: 235.15  E-value: 5.53e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088191043   6 VPARVFFTSGVGVHNEELAAFETALRDCGIAQFNLVHVSSIFPPGCRRIATSQGLKYLSPGEIVYCVMARNATNEPGRLV 85
Cdd:pfam01862   1 VPKKYFFTKGVGEHKTKLNSFDLALRDAGIENFNLVRVSSILPPGAEIVSVEEGLKLLPPGSIVFTVMARNTSNEPGRLI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088191043  86 SSAIGVALPAGDKQYGYLSEHHAFGqTDESAGEYAEDLAASMLASTLGIkfdpdeawdarrqafrMSGKIVRTSHVAQSA 165
Cdd:pfam01862  81 SAAVGVAIPKDESGYGYISEYHGFG-TEEEAGEYAEDLAAEMLATTRGL----------------RSGFIIETKEIEVAA 143

                         170
                  ....*....|....*...
gi 1088191043 166 RGDRRGRWTCVVSAAVFV 183
Cdd:pfam01862 144 VGHKVGKWGTVVAAAVFW 161
 
Name Accession Description Interval E-value
PvlArgDC pfam01862
Pyruvoyl-dependent arginine decarboxylase (PvlArgDC); Methanococcus jannaschii contains ...
 6-183 5.53e-80

Pyruvoyl-dependent arginine decarboxylase (PvlArgDC); Methanococcus jannaschii contains homologs of most genes required for spermidine polyamine biosynthesis. Yet genomes from neither this organizm nor any other euryarchaeon have orthologues of the pyridoxal 5'-phosphate- dependent ornithine or arginine decarboxylase genes, required to produce putrescine. Instead,these organizms have a new class of arginine decarboxylase (PvlArgDC) formed by the self-cleavage of a proenzyme into a 5-kDa subunit and a 12-kDa subunit that contains a reactive pyruvoyl group. Although this extremely thermostable enzyme has no significant sequence similarity to previously characterized proteins, conserved active site residues are similar to those of the pyruvoyl-dependent histidine decarboxylase enzyme, and its subunits form a similar (alpha-beta)(3) complex. homologs of PvlArgDC are found in several bacterial genomes, including those of Chlamydia spp., which have no agmatine ureohydrolase enzyme to convert agmatine (decarboxylated arginine) into putrescine. In these intracellular pathogens, PvlArgDC may function analogously to pyruvoyl-dependent histidine decarboxylase; the cells are proposed to import arginine and export agmatine, increasing the pH and affecting the host cell's metabolism. Phylogenetic analysis of Pvl- ArgDC proteins suggests that this gene has been recruited from the euryarchaeal polyamine biosynthetic pathway to function as a degradative enzyme in bacteria.


Pssm-ID: 426480  Cd Length: 161  Bit Score: 235.15  E-value: 5.53e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088191043   6 VPARVFFTSGVGVHNEELAAFETALRDCGIAQFNLVHVSSIFPPGCRRIATSQGLKYLSPGEIVYCVMARNATNEPGRLV 85
Cdd:pfam01862   1 VPKKYFFTKGVGEHKTKLNSFDLALRDAGIENFNLVRVSSILPPGAEIVSVEEGLKLLPPGSIVFTVMARNTSNEPGRLI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088191043  86 SSAIGVALPAGDKQYGYLSEHHAFGqTDESAGEYAEDLAASMLASTLGIkfdpdeawdarrqafrMSGKIVRTSHVAQSA 165
Cdd:pfam01862  81 SAAVGVAIPKDESGYGYISEYHGFG-TEEEAGEYAEDLAAEMLATTRGL----------------RSGFIIETKEIEVAA 143

                         170
                  ....*....|....*...
gi 1088191043 166 RGDRRGRWTCVVSAAVFV 183
Cdd:pfam01862 144 VGHKVGKWGTVVAAAVFW 161
PRK12398 PRK12398
pyruvoyl-dependent arginine decarboxylase; Provisional
 6-183 1.63e-76

pyruvoyl-dependent arginine decarboxylase; Provisional


Pssm-ID: 237089  Cd Length: 162  Bit Score: 226.54  E-value: 1.63e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088191043   6 VPARVFFTSGVGVHNEELAAFETALRDCGIAQFNLVHVSSIFPPGCRRIATSQGLKYLSPGEIVYCVMARNATNEPGRLV 85
Cdd:PRK12398    3 IPKKVFFTSGVGRHEEMLESFELALRDAGIEKFNLVTVSSILPPNCEIVSREEGLKELSPGEIVFCVMSRNSSNEPGRTI 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088191043  86 SSAIGVALPAGDKQYGYLSEHHAFGQTDESAGEYAEDLAASMLastlgikfdpdEAWdarrqafrMSGKIVRTSHVAQSA 165
Cdd:PRK12398   83 FASVGCAIPEDQSLNGYLSEYHGYGETEEDAGKYAEKLAREML-----------STW--------TNEEPLRTFNITRSA 143

                         170
                  ....*....|....*...
gi 1088191043 166 RGDRRGRWTCVVSAAVFV 183
Cdd:PRK12398  144 EVDEDGNWTTVVAAAVFI 161
PdaD COG1945
Pyruvoyl-dependent arginine decarboxylase [Amino acid transport and metabolism];
7-184 2.18e-69

Pyruvoyl-dependent arginine decarboxylase [Amino acid transport and metabolism];


Pssm-ID: 441548  Cd Length: 158  Bit Score: 208.10  E-value: 2.18e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088191043   7 PARVFFTSGVGVHNEELAAFETALRDCGIAQFNLVHVSSIFPPGCRRIATSQGLKYLSPGEIVYCVMARNATNEPGRLVS 86
Cdd:COG1945     1 PKKIFITKGVGEGPTELNAFDAALLDAGIGNYNLVRVSSILPPGAEIVPVEEGPDLLPPGAILPVVYARITSNEPGELIA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088191043  87 SAIGVALPAGDKQYGYLSEHHAFGqTDESAGEYAEDLAASMLAsTLGIkfdpdeawdarrqafrmsgKIVRTSHVAQSAR 166
Cdd:COG1945    81 AAVGVAIPKDPSGPGYISEHHGFG-TEEEAEEYAEDMAAEMLA-LRGW-------------------EIGETKVITVEAR 139

                         170
                  ....*....|....*...
gi 1088191043 167 GDRRGRWTCVVSAAVFVF 184
Cdd:COG1945   140 VEKDGCWTTAVAAAVLWY 157
TIGR00286 TIGR00286
arginine decarboxylase, pyruvoyl-dependent; The three copies present in Archeoglobus fulgidus, ...
 6-184 2.78e-39

arginine decarboxylase, pyruvoyl-dependent; The three copies present in Archeoglobus fulgidus, one of which is only half-length and excluded from the seed alignment, are very closely related and clearly arose by duplication after the separation from well-studied species. The other completed archaeal genomes each contain a single copy. The lone, weak (below trusted cutoff) hit to a non-archaeal sequence is to an uncharacterized protein of Chlamydia, with the greatest similarity in the amino-terminal half of the model. [Central intermediary metabolism, Polyamine biosynthesis, Energy metabolism, Amino acids and amines]


Pssm-ID: 211565  Cd Length: 152  Bit Score: 131.48  E-value: 2.78e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088191043   6 VPARVFFTSGVGVHNEELAAFETALRDCGIAQFNLVHVSSIFPPGCRRIAtsqgLKYLSPGEIVYCVMARNATNEPGRLV 85
Cdd:TIGR00286   2 LPNKVFFVSGVGEGETPLNAFDLALLDAGIGNVNLIRVSSIMPPECEIVE----LPKLPPGQIVFCVMSRMISNVPGETI 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088191043  86 SSAIGVALPAGDKQYGYLSEHHAFgQTDESAGEYAEDLAASMLaSTLGIKFDPDEAwdarrqafrmsgkiVRTSHVAQsa 165
Cdd:TIGR00286  78 SAAVGVAIPKDKSLNGYIMEYSGK-CSKEDAEKHAREMAKYML-KTRGWELARTFS--------------ITVEHTVE-- 139

                         170
                  ....*....|....*....
gi 1088191043 166 rgdrrgRWTCVVSAAVFVF 184
Cdd:TIGR00286 140 ------KCGTAVAAAVFVI 152
 
Name Accession Description Interval E-value
PvlArgDC pfam01862
Pyruvoyl-dependent arginine decarboxylase (PvlArgDC); Methanococcus jannaschii contains ...
 6-183 5.53e-80

Pyruvoyl-dependent arginine decarboxylase (PvlArgDC); Methanococcus jannaschii contains homologs of most genes required for spermidine polyamine biosynthesis. Yet genomes from neither this organizm nor any other euryarchaeon have orthologues of the pyridoxal 5'-phosphate- dependent ornithine or arginine decarboxylase genes, required to produce putrescine. Instead,these organizms have a new class of arginine decarboxylase (PvlArgDC) formed by the self-cleavage of a proenzyme into a 5-kDa subunit and a 12-kDa subunit that contains a reactive pyruvoyl group. Although this extremely thermostable enzyme has no significant sequence similarity to previously characterized proteins, conserved active site residues are similar to those of the pyruvoyl-dependent histidine decarboxylase enzyme, and its subunits form a similar (alpha-beta)(3) complex. homologs of PvlArgDC are found in several bacterial genomes, including those of Chlamydia spp., which have no agmatine ureohydrolase enzyme to convert agmatine (decarboxylated arginine) into putrescine. In these intracellular pathogens, PvlArgDC may function analogously to pyruvoyl-dependent histidine decarboxylase; the cells are proposed to import arginine and export agmatine, increasing the pH and affecting the host cell's metabolism. Phylogenetic analysis of Pvl- ArgDC proteins suggests that this gene has been recruited from the euryarchaeal polyamine biosynthetic pathway to function as a degradative enzyme in bacteria.


Pssm-ID: 426480  Cd Length: 161  Bit Score: 235.15  E-value: 5.53e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088191043   6 VPARVFFTSGVGVHNEELAAFETALRDCGIAQFNLVHVSSIFPPGCRRIATSQGLKYLSPGEIVYCVMARNATNEPGRLV 85
Cdd:pfam01862   1 VPKKYFFTKGVGEHKTKLNSFDLALRDAGIENFNLVRVSSILPPGAEIVSVEEGLKLLPPGSIVFTVMARNTSNEPGRLI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088191043  86 SSAIGVALPAGDKQYGYLSEHHAFGqTDESAGEYAEDLAASMLASTLGIkfdpdeawdarrqafrMSGKIVRTSHVAQSA 165
Cdd:pfam01862  81 SAAVGVAIPKDESGYGYISEYHGFG-TEEEAGEYAEDLAAEMLATTRGL----------------RSGFIIETKEIEVAA 143

                         170
                  ....*....|....*...
gi 1088191043 166 RGDRRGRWTCVVSAAVFV 183
Cdd:pfam01862 144 VGHKVGKWGTVVAAAVFW 161
PRK12398 PRK12398
pyruvoyl-dependent arginine decarboxylase; Provisional
 6-183 1.63e-76

pyruvoyl-dependent arginine decarboxylase; Provisional


Pssm-ID: 237089  Cd Length: 162  Bit Score: 226.54  E-value: 1.63e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088191043   6 VPARVFFTSGVGVHNEELAAFETALRDCGIAQFNLVHVSSIFPPGCRRIATSQGLKYLSPGEIVYCVMARNATNEPGRLV 85
Cdd:PRK12398    3 IPKKVFFTSGVGRHEEMLESFELALRDAGIEKFNLVTVSSILPPNCEIVSREEGLKELSPGEIVFCVMSRNSSNEPGRTI 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088191043  86 SSAIGVALPAGDKQYGYLSEHHAFGQTDESAGEYAEDLAASMLastlgikfdpdEAWdarrqafrMSGKIVRTSHVAQSA 165
Cdd:PRK12398   83 FASVGCAIPEDQSLNGYLSEYHGYGETEEDAGKYAEKLAREML-----------STW--------TNEEPLRTFNITRSA 143

                         170
                  ....*....|....*...
gi 1088191043 166 RGDRRGRWTCVVSAAVFV 183
Cdd:PRK12398  144 EVDEDGNWTTVVAAAVFI 161
PRK01285 PRK01285
pyruvoyl-dependent arginine decarboxylase; Reviewed
 6-184 2.20e-75

pyruvoyl-dependent arginine decarboxylase; Reviewed


Pssm-ID: 234933  Cd Length: 155  Bit Score: 223.20  E-value: 2.20e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088191043   6 VPARVFFTSGVGVHNEELAAFETALRDCGIAQFNLVHVSSIFPPGCRRIATSQGlkYLSPGEIVYCVMARNATNEPGRLV 85
Cdd:PRK01285    2 VPKKIFFTAGVGEGKTKLNAFDLALLDAGIGNVNLVRVSSILPPNCEIIPLEEK--LLPPGSLVPTVYARNSSNEPGRLI 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088191043  86 SSAIGVALPAGDKQYGYLSEHHAFGQTDEsageyAEDLAASMLastlgikfdpdeawdarRQAFRMSGKIVRTSHVAQSA 165
Cdd:PRK01285   80 AAAVGVAIPKDKELYGYISEHHGFGEKEE-----AEDLAATML-----------------EEGFKMRGKILDEIKITASE 137

                         170
                  ....*....|....*....
gi 1088191043 166 RGDrRGRWTCVVSAAVFVF 184
Cdd:PRK01285  138 HGV-EGIWTTVAAAAVWYP 155
PdaD COG1945
Pyruvoyl-dependent arginine decarboxylase [Amino acid transport and metabolism];
7-184 2.18e-69

Pyruvoyl-dependent arginine decarboxylase [Amino acid transport and metabolism];


Pssm-ID: 441548  Cd Length: 158  Bit Score: 208.10  E-value: 2.18e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088191043   7 PARVFFTSGVGVHNEELAAFETALRDCGIAQFNLVHVSSIFPPGCRRIATSQGLKYLSPGEIVYCVMARNATNEPGRLVS 86
Cdd:COG1945     1 PKKIFITKGVGEGPTELNAFDAALLDAGIGNYNLVRVSSILPPGAEIVPVEEGPDLLPPGAILPVVYARITSNEPGELIA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088191043  87 SAIGVALPAGDKQYGYLSEHHAFGqTDESAGEYAEDLAASMLAsTLGIkfdpdeawdarrqafrmsgKIVRTSHVAQSAR 166
Cdd:COG1945    81 AAVGVAIPKDPSGPGYISEHHGFG-TEEEAEEYAEDMAAEMLA-LRGW-------------------EIGETKVITVEAR 139

                         170
                  ....*....|....*...
gi 1088191043 167 GDRRGRWTCVVSAAVFVF 184
Cdd:COG1945   140 VEKDGCWTTAVAAAVLWY 157
TIGR00286 TIGR00286
arginine decarboxylase, pyruvoyl-dependent; The three copies present in Archeoglobus fulgidus, ...
 6-184 2.78e-39

arginine decarboxylase, pyruvoyl-dependent; The three copies present in Archeoglobus fulgidus, one of which is only half-length and excluded from the seed alignment, are very closely related and clearly arose by duplication after the separation from well-studied species. The other completed archaeal genomes each contain a single copy. The lone, weak (below trusted cutoff) hit to a non-archaeal sequence is to an uncharacterized protein of Chlamydia, with the greatest similarity in the amino-terminal half of the model. [Central intermediary metabolism, Polyamine biosynthesis, Energy metabolism, Amino acids and amines]


Pssm-ID: 211565  Cd Length: 152  Bit Score: 131.48  E-value: 2.78e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088191043   6 VPARVFFTSGVGVHNEELAAFETALRDCGIAQFNLVHVSSIFPPGCRRIAtsqgLKYLSPGEIVYCVMARNATNEPGRLV 85
Cdd:TIGR00286   2 LPNKVFFVSGVGEGETPLNAFDLALLDAGIGNVNLIRVSSIMPPECEIVE----LPKLPPGQIVFCVMSRMISNVPGETI 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088191043  86 SSAIGVALPAGDKQYGYLSEHHAFgQTDESAGEYAEDLAASMLaSTLGIKFDPDEAwdarrqafrmsgkiVRTSHVAQsa 165
Cdd:TIGR00286  78 SAAVGVAIPKDKSLNGYIMEYSGK-CSKEDAEKHAREMAKYML-KTRGWELARTFS--------------ITVEHTVE-- 139

                         170
                  ....*....|....*....
gi 1088191043 166 rgdrrgRWTCVVSAAVFVF 184
Cdd:TIGR00286 140 ------KCGTAVAAAVFVI 152
 
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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