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Conserved domains on  [gi|2395585017|gb|WAK44282|]
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ribonucleotide reductase of class III (anaerobic), activating protein [Escherichia virus CAM-21]

Protein Classification

anaerobic ribonucleoside-triphosphate reductase-activating protein( domain architecture ID 11494355)

anaerobic ribonucleoside-triphosphate reductase-activating protein NrdG, the small component of class III ribonucleotide reductase, generates an organic free radical with S-adenosylmethionine and reduced flavodoxin as cosubstrates, resulting in 5'-deoxy-adenosine

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NrdG TIGR02491
anaerobic ribonucleoside-triphosphate reductase activating protein; This enzyme is a member of ...
 2-149 1.63e-72

anaerobic ribonucleoside-triphosphate reductase activating protein; This enzyme is a member of the radical-SAM family (pfam04055) and utilizes S-adenosyl methionine, an iron-sulfur cluster and a reductant (dihydroflavodoxin) to produce a glycine-centered radical in the class III (anaerobic) ribonucleotide triphosphate reductase (NrdD, TIGR02487). The two components form an alpha-2/beta-2 heterodimer. [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism, Protein fate, Protein modification and repair]


:

Pssm-ID: 274161 [Multi-domain]  Cd Length: 154  Bit Score: 214.52  E-value: 1.63e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395585017   2 NYDRFYPCDFVNGPGCRTVLFVTGCLHKCEGCYNKSTWNARNGVPFTGETLEQLIECLN-NDYIEGLTITGGDPLYPDNR 80
Cdd:TIGR02491   1 NYMNIKPDDIVNGEGIRVSLFVAGCKHHCEGCFNKETWNFNGGKEFTEALEKEIIRDLNdNPLIDGLTLSGGDPLYPRNV 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2395585017  81 DVIHSVVQTIKNLYPNKSIWLWTGYKFEDI----KQLEMLKYVDVIIDGKYEKNLPTKKL-WRGSDNQRLWSNT 149
Cdd:TIGR02491  81 EELIELVKKIKAEFPEKDIWLWTGYTWEEIledeKHLEVLKYIDVLVDGKFELSKKDLKLkFRGSSNQRIIDLK 154
 
Name Accession Description Interval E-value
NrdG TIGR02491
anaerobic ribonucleoside-triphosphate reductase activating protein; This enzyme is a member of ...
 2-149 1.63e-72

anaerobic ribonucleoside-triphosphate reductase activating protein; This enzyme is a member of the radical-SAM family (pfam04055) and utilizes S-adenosyl methionine, an iron-sulfur cluster and a reductant (dihydroflavodoxin) to produce a glycine-centered radical in the class III (anaerobic) ribonucleotide triphosphate reductase (NrdD, TIGR02487). The two components form an alpha-2/beta-2 heterodimer. [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism, Protein fate, Protein modification and repair]


Pssm-ID: 274161 [Multi-domain]  Cd Length: 154  Bit Score: 214.52  E-value: 1.63e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395585017   2 NYDRFYPCDFVNGPGCRTVLFVTGCLHKCEGCYNKSTWNARNGVPFTGETLEQLIECLN-NDYIEGLTITGGDPLYPDNR 80
Cdd:TIGR02491   1 NYMNIKPDDIVNGEGIRVSLFVAGCKHHCEGCFNKETWNFNGGKEFTEALEKEIIRDLNdNPLIDGLTLSGGDPLYPRNV 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2395585017  81 DVIHSVVQTIKNLYPNKSIWLWTGYKFEDI----KQLEMLKYVDVIIDGKYEKNLPTKKL-WRGSDNQRLWSNT 149
Cdd:TIGR02491  81 EELIELVKKIKAEFPEKDIWLWTGYTWEEIledeKHLEVLKYIDVLVDGKFELSKKDLKLkFRGSSNQRIIDLK 154
Fer4_12 pfam13353
4Fe-4S single cluster domain; This family includes proteins containing domains which bind to ...
 12-146 6.91e-64

4Fe-4S single cluster domain; This family includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. The structure of the domain is an alpha-antiparallel beta sandwich.


Pssm-ID: 433138 [Multi-domain]  Cd Length: 137  Bit Score: 192.00  E-value: 6.91e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395585017  12 VNGPGCRTVLFVTGCLHKCEGCYNKSTWNARNGVPFTGETLEQLIECLNNDYIEGLTITGGDPLYpdNRDVIHSVVQTIK 91
Cdd:pfam13353   1 VNGPGVRCSLFVSGCNHHCKGCFNPETWDFKYGKPFTEELEDEIIEDLAKPYIQGLTLSGGEPLL--NAEALLELVKRVR 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2395585017  92 NLYPNKSIWLWTGYKFEDI---KQLEMLKYVDVIIDGKYEKNLPTKKL-WRGSDNQRLW 146
Cdd:pfam13353  79 EECPEKDIWLWTGYTFEELqskDQLELLKLIDVLVDGKFEQSLKDPSLrFRGSSNQRII 137
nrdG PRK11121
anaerobic ribonucleoside-triphosphate reductase-activating protein;
1-143 2.98e-61

anaerobic ribonucleoside-triphosphate reductase-activating protein;


Pssm-ID: 236853  Cd Length: 154  Bit Score: 185.97  E-value: 2.98e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395585017   1 MNYDRFYPCDFVNGPGCRTVLFVTGCLHKCEGCYNKSTWNARNGVPFTGETLEQLIECLNNDYI--EGLTITGGDPLYPD 78
Cdd:PRK11121    1 MNYHQYYPVDVVNGPGTRCTLFVSGCVHQCPGCYNKSTWRLNSGHPFTKEMEDQIIADLNDTRIkrQGLSLSGGDPLHPQ 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2395585017  79 NRDVIHSVVQTIKNLYPNKSIWLWTGYKFEDI--KQLEMLKYVDVIIDGKYEKNLPTKKL-WRGSDNQ 143
Cdd:PRK11121   81 NVPDILKLVQRVKAECPGKDIWVWTGYKLDELnaAQRQVVDLIDVLVDGKFVQDLADPSLiWRGSSNQ 148
PflA COG1180
Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, ...
 5-124 4.30e-08

Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440793 [Multi-domain]  Cd Length: 242  Bit Score: 50.57  E-value: 4.30e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395585017   5 RFY---PCDFVNGPG-CRTVLFVTGCLHKCEGCYNKSTWNARNGVPFTGETLEQLIECLNNDYI-----EGLTITGGDPL 75
Cdd:COG1180     6 RIYgisPFSTVDGPGsIRLSVFTQGCNLRCPYCHNPEISQGRPDAAGRELSPEELVEEALKDRGfldscGGVTFSGGEPT 85

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395585017  76 -YPDN-RDV--------IHSVVQTikNLYPNKSIWlwtgykfedikqLEMLKYVD-VIID 124
Cdd:COG1180    86 lQPEFlLDLaklakelgLHTALDT--NGYIPEEAL------------EELLPYLDaVNID 131
Radical_SAM cd01335
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
 20-83 4.52e-05

Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster. Mechanistically, they share the transfer of a single electron from the iron-sulfur cluster to SAM, which leads to its reductive cleavage to methionine and a 5'-deoxyadenosyl radical, which, in turn, abstracts a hydrogen from the appropriately positioned carbon atom. Depending on the enzyme, SAM is consumed during this process or it is restored and reused. Radical SAM enzymes catalyze steps in metabolism, DNA repair, the biosynthesis of vitamins and coenzymes, and the biosynthesis of many antibiotics. Examples are biotin synthase (BioB), lipoyl synthase (LipA), pyruvate formate-lyase (PFL), coproporphyrinogen oxidase (HemN), lysine 2,3-aminomutase (LAM), anaerobic ribonucleotide reductase (ARR), and MoaA, an enzyme of the biosynthesis of molybdopterin.


Pssm-ID: 100105 [Multi-domain]  Cd Length: 204  Bit Score: 41.55  E-value: 4.52e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2395585017  20 VLFVTGCLHKCEGCYNKSTWNARNGVPFTGETLEQLIECLNNDYIEGLTITGGDPL-YPDNRDVI 83
Cdd:cd01335     1 LELTRGCNLNCGFCSNPASKGRGPESPPEIEEILDIVLEAKERGVEVVILTGGEPLlYPELAELL 65
 
Name Accession Description Interval E-value
NrdG TIGR02491
anaerobic ribonucleoside-triphosphate reductase activating protein; This enzyme is a member of ...
 2-149 1.63e-72

anaerobic ribonucleoside-triphosphate reductase activating protein; This enzyme is a member of the radical-SAM family (pfam04055) and utilizes S-adenosyl methionine, an iron-sulfur cluster and a reductant (dihydroflavodoxin) to produce a glycine-centered radical in the class III (anaerobic) ribonucleotide triphosphate reductase (NrdD, TIGR02487). The two components form an alpha-2/beta-2 heterodimer. [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism, Protein fate, Protein modification and repair]


Pssm-ID: 274161 [Multi-domain]  Cd Length: 154  Bit Score: 214.52  E-value: 1.63e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395585017   2 NYDRFYPCDFVNGPGCRTVLFVTGCLHKCEGCYNKSTWNARNGVPFTGETLEQLIECLN-NDYIEGLTITGGDPLYPDNR 80
Cdd:TIGR02491   1 NYMNIKPDDIVNGEGIRVSLFVAGCKHHCEGCFNKETWNFNGGKEFTEALEKEIIRDLNdNPLIDGLTLSGGDPLYPRNV 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2395585017  81 DVIHSVVQTIKNLYPNKSIWLWTGYKFEDI----KQLEMLKYVDVIIDGKYEKNLPTKKL-WRGSDNQRLWSNT 149
Cdd:TIGR02491  81 EELIELVKKIKAEFPEKDIWLWTGYTWEEIledeKHLEVLKYIDVLVDGKFELSKKDLKLkFRGSSNQRIIDLK 154
Fer4_12 pfam13353
4Fe-4S single cluster domain; This family includes proteins containing domains which bind to ...
 12-146 6.91e-64

4Fe-4S single cluster domain; This family includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. The structure of the domain is an alpha-antiparallel beta sandwich.


Pssm-ID: 433138 [Multi-domain]  Cd Length: 137  Bit Score: 192.00  E-value: 6.91e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395585017  12 VNGPGCRTVLFVTGCLHKCEGCYNKSTWNARNGVPFTGETLEQLIECLNNDYIEGLTITGGDPLYpdNRDVIHSVVQTIK 91
Cdd:pfam13353   1 VNGPGVRCSLFVSGCNHHCKGCFNPETWDFKYGKPFTEELEDEIIEDLAKPYIQGLTLSGGEPLL--NAEALLELVKRVR 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2395585017  92 NLYPNKSIWLWTGYKFEDI---KQLEMLKYVDVIIDGKYEKNLPTKKL-WRGSDNQRLW 146
Cdd:pfam13353  79 EECPEKDIWLWTGYTFEELqskDQLELLKLIDVLVDGKFEQSLKDPSLrFRGSSNQRII 137
nrdG PRK11121
anaerobic ribonucleoside-triphosphate reductase-activating protein;
1-143 2.98e-61

anaerobic ribonucleoside-triphosphate reductase-activating protein;


Pssm-ID: 236853  Cd Length: 154  Bit Score: 185.97  E-value: 2.98e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395585017   1 MNYDRFYPCDFVNGPGCRTVLFVTGCLHKCEGCYNKSTWNARNGVPFTGETLEQLIECLNNDYI--EGLTITGGDPLYPD 78
Cdd:PRK11121    1 MNYHQYYPVDVVNGPGTRCTLFVSGCVHQCPGCYNKSTWRLNSGHPFTKEMEDQIIADLNDTRIkrQGLSLSGGDPLHPQ 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2395585017  79 NRDVIHSVVQTIKNLYPNKSIWLWTGYKFEDI--KQLEMLKYVDVIIDGKYEKNLPTKKL-WRGSDNQ 143
Cdd:PRK11121   81 NVPDILKLVQRVKAECPGKDIWVWTGYKLDELnaAQRQVVDLIDVLVDGKFVQDLADPSLiWRGSSNQ 148
Fer4_14 pfam13394
4Fe-4S single cluster domain;
21-126 2.58e-32

4Fe-4S single cluster domain;


Pssm-ID: 433171 [Multi-domain]  Cd Length: 115  Bit Score: 111.30  E-value: 2.58e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395585017  21 LFVTGCLHKCEGCYNKSTWNARNGVPFTGETLEQLIECLNNDYIE--GLTITGGDPLYPDNRDVIHSVVQTIKNLYPNKS 98
Cdd:pfam13394   1 LFVSGCNHSCPGCDNKETWKFNYGEPFTEELEDQIIADLKDSYIKrqGLVLTGGEPLHPWNLPVLLKLLKRVKEEYPSKD 80

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2395585017  99 IWLWTGYKFEDI-------KQLEMLKYVDVIIDGK 126
Cdd:pfam13394  81 IWLETGYTLAIDfeypdteEQLFTLSVIDVLVDGK 115
PflA COG1180
Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, ...
 5-124 4.30e-08

Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440793 [Multi-domain]  Cd Length: 242  Bit Score: 50.57  E-value: 4.30e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395585017   5 RFY---PCDFVNGPG-CRTVLFVTGCLHKCEGCYNKSTWNARNGVPFTGETLEQLIECLNNDYI-----EGLTITGGDPL 75
Cdd:COG1180     6 RIYgisPFSTVDGPGsIRLSVFTQGCNLRCPYCHNPEISQGRPDAAGRELSPEELVEEALKDRGfldscGGVTFSGGEPT 85

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395585017  76 -YPDN-RDV--------IHSVVQTikNLYPNKSIWlwtgykfedikqLEMLKYVD-VIID 124
Cdd:COG1180    86 lQPEFlLDLaklakelgLHTALDT--NGYIPEEAL------------EELLPYLDaVNID 131
pflA PRK11145
pyruvate formate lyase 1-activating protein;
6-52 9.09e-07

pyruvate formate lyase 1-activating protein;


Pssm-ID: 182994 [Multi-domain]  Cd Length: 246  Bit Score: 46.94  E-value: 9.09e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2395585017   6 FYPCDFVNGPGCRTVLFVTGCLHKCEGCYNKSTWNARNGVPFTGETL 52
Cdd:PRK11145   10 FESCGTVDGPGIRFITFFQGCLMRCLYCHNRDTWDTHGGKEVTVEEL 56
Radical_SAM pfam04055
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
 22-92 2.08e-05

Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual methylations, isomerization, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation.


Pssm-ID: 427681 [Multi-domain]  Cd Length: 159  Bit Score: 42.13  E-value: 2.08e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2395585017  22 FVTGCLHKCEGCYNKSTWNARNGVPFTGETLEQLIECLNNDYIEGLTITGGDPLYPDNRDVIHSVVQTIKN 92
Cdd:pfam04055   1 ITRGCNLRCTYCAFPSIRARGKGRELSPEEILEEAKELKRLGVEVVILGGGEPLLLPDLVELLERLLKLEL 71
Radical_SAM cd01335
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
 20-83 4.52e-05

Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster. Mechanistically, they share the transfer of a single electron from the iron-sulfur cluster to SAM, which leads to its reductive cleavage to methionine and a 5'-deoxyadenosyl radical, which, in turn, abstracts a hydrogen from the appropriately positioned carbon atom. Depending on the enzyme, SAM is consumed during this process or it is restored and reused. Radical SAM enzymes catalyze steps in metabolism, DNA repair, the biosynthesis of vitamins and coenzymes, and the biosynthesis of many antibiotics. Examples are biotin synthase (BioB), lipoyl synthase (LipA), pyruvate formate-lyase (PFL), coproporphyrinogen oxidase (HemN), lysine 2,3-aminomutase (LAM), anaerobic ribonucleotide reductase (ARR), and MoaA, an enzyme of the biosynthesis of molybdopterin.


Pssm-ID: 100105 [Multi-domain]  Cd Length: 204  Bit Score: 41.55  E-value: 4.52e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2395585017  20 VLFVTGCLHKCEGCYNKSTWNARNGVPFTGETLEQLIECLNNDYIEGLTITGGDPL-YPDNRDVI 83
Cdd:cd01335     1 LELTRGCNLNCGFCSNPASKGRGPESPPEIEEILDIVLEAKERGVEVVILTGGEPLlYPELAELL 65
COG2108 COG2108
Uncharacterized radical SAM domain-containing protein [Function unknown];
15-117 5.01e-05

Uncharacterized radical SAM domain-containing protein [Function unknown];


Pssm-ID: 441711 [Multi-domain]  Cd Length: 361  Bit Score: 41.87  E-value: 5.01e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2395585017  15 PGCR-------TVLFVTGclhKC-EGCYNKSTWNARNG--VPFTGE----TLEQLIEclnndYIE-----GLTITGGDPL 75
Cdd:COG2108    18 PGCRlcrkgakLVLFITG---LCnRNCFYCPLSEERKGkdVIYANErpveSDEDVIE-----EARrmgalGAGITGGEPL 89

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2395585017  76 YPDNRdVIHsVVQTIKNLY-PNKSIWLWTGYKFEDIKQLEMLK 117
Cdd:COG2108    90 LVLDR-TLE-YIRLLKEEFgPDHHIHLYTNGILADEDVLRKLA 130
QueE COG0602
Organic radical activating enzyme NrdG/QueE [Coenzyme transport and metabolism]; Organic ...
 16-83 1.97e-04

Organic radical activating enzyme NrdG/QueE [Coenzyme transport and metabolism]; Organic radical activating enzyme NrdG/QueE is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 440367 [Multi-domain]  Cd Length: 205  Bit Score: 39.74  E-value: 1.97e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2395585017  16 GCRTVlFV--TGCLHKCEGCYNKSTWNARNGVPFTGETLEQLIECLNNDYIeglTITGGDPL-YPDNRDVI 83
Cdd:COG0602    19 GRPAV-FVrlAGCNLRCSWCDTKYAWDGEGGKRMSAEEILEEVAALGARHV---VITGGEPLlQDDLAELL 85
 
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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