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Conserved domains on  [gi|1262259917|gb|PFO88150|]
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ribonucleoside-diphosphate reductase [Bacillus cereus]

Protein Classification

ferritin family protein( domain architecture ID 38)

ferritin family protein similar to rubrerythrin, a non-heme di-iron that is involved in oxidative stress defense as a peroxide scavenger in a wide range of organisms

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Ferritin_like super family cl00264
Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Ferritin-like, ...
 3-131 4.82e-71

Ferritin-like superfamily of diiron-containing four-helix-bundle proteins; Ferritin-like, diiron-carboxylate proteins participate in a range of functions including iron regulation, mono-oxygenation, and reactive radical production. These proteins are characterized by the fact that they catalyze dioxygen-dependent oxidation-hydroxylation reactions within diiron centers; one exception is manganese catalase, which catalyzes peroxide-dependent oxidation-reduction within a dimanganese center. Diiron-carboxylate proteins are further characterized by the presence of duplicate metal ligands, glutamates and histidines (ExxH) and two additional glutamates within a four-helix bundle. Outside of these conserved residues there is little obvious homology. Members include bacterioferritin, ferritin, rubrerythrin, aromatic and alkene monooxygenase hydroxylases (AAMH), ribonucleotide reductase R2 (RNRR2), acyl-ACP-desaturases (Acyl_ACP_Desat), manganese (Mn) catalases, demethoxyubiquinone hydroxylases (DMQH), DNA protecting proteins (DPS), and ubiquinol oxidases (AOX), and the aerobic cyclase system, Fe-containing subunit (ACSF).


The actual alignment was detected with superfamily member TIGR04171:

Pssm-ID: 469698  Cd Length: 313  Bit Score: 215.11  E-value: 4.82e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262259917   3 VKDESIHGVFVGILAQQIFAELSVEEQQEVQKETQELLMELYEIEMAYTEEIYTSIGLVEDVNRFVRYNANKGLMNLGLE 82
Cdd:TIGR04171 184 IRDESIHGVYIGYKAQEGFNKLSEEEQEELKDWMYDLLYELYENEEKYTEELYDEVGLTEDVKKFVRYNANKALMNLGFE 263

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1262259917  83 PKFEEE--EINPIVLNGLRTDTKNHDFFSVKGNGYVKAtNVEKLADDDFVF 131
Cdd:TIGR04171 264 PLFPEEatDVNPIVLNGLSTETKNHDFFSGKGNGYVKG-KVEALEDDDFDF 313
 
Name Accession Description Interval E-value
RNR_1b_NrdF TIGR04171
ribonucleoside-diphosphate reductase, class 1b, beta subunit; Members of this family are NrdF, ...
 3-131 4.82e-71

ribonucleoside-diphosphate reductase, class 1b, beta subunit; Members of this family are NrdF, the beta subunit of class 1b ribonucleotide reductase. This form uses a dimanganese moiety associated with a tyrosine radical to reduce the cellular requirement for iron. [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism]


Pssm-ID: 275027  Cd Length: 313  Bit Score: 215.11  E-value: 4.82e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262259917   3 VKDESIHGVFVGILAQQIFAELSVEEQQEVQKETQELLMELYEIEMAYTEEIYTSIGLVEDVNRFVRYNANKGLMNLGLE 82
Cdd:TIGR04171 184 IRDESIHGVYIGYKAQEGFNKLSEEEQEELKDWMYDLLYELYENEEKYTEELYDEVGLTEDVKKFVRYNANKALMNLGFE 263

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1262259917  83 PKFEEE--EINPIVLNGLRTDTKNHDFFSVKGNGYVKAtNVEKLADDDFVF 131
Cdd:TIGR04171 264 PLFPEEatDVNPIVLNGLSTETKNHDFFSGKGNGYVKG-KVEALEDDDFDF 313
nrdF PRK09614
ribonucleotide-diphosphate reductase subunit beta; Reviewed
 3-131 1.91e-52

ribonucleotide-diphosphate reductase subunit beta; Reviewed


Pssm-ID: 236591 [Multi-domain]  Cd Length: 324  Bit Score: 168.08  E-value: 1.91e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262259917   3 VKDESIHGVFVGILAQQIFAELSVEEQQEVQKETQELLMELYEIEMAYTEEIYTSIGLVEDVNRFVRYNANKGLMNLGLE 82
Cdd:PRK09614  195 IRDESLHGYYIGYLFQEGLEELPELEQEELKDEIYDLLYELYENEEAYTELLYDIVGLAEDVKKYIRYNANKRLMNLGLE 274

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1262259917  83 PKFE-EEEINPIVLNGLR-TDTKNHDFFSVKGNGYVKATnVEKLADDDFVF 131
Cdd:PRK09614  275 PLFPeEEEVNPIWLNGLSnNADENHDFFEGKGTSYVKGA-TEATEDDDWDF 324
NrdB COG0208
Ribonucleotide reductase beta subunit, ferritin-like domain [Nucleotide transport and ...
 3-128 9.35e-38

Ribonucleotide reductase beta subunit, ferritin-like domain [Nucleotide transport and metabolism]; Ribonucleotide reductase beta subunit, ferritin-like domain is part of the Pathway/BioSystem: Pyrimidine salvage


Pssm-ID: 439978 [Multi-domain]  Cd Length: 326  Bit Score: 129.90  E-value: 9.35e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262259917   3 VKDESIHGVFVGILAQQIFAELSVEEQQEVQKETQELLMELYEIEMAYTEEIYTS--IGL-VEDVNRFVRYNANKGLMNL 79
Cdd:COG0208   199 LRDESLHGNFGIYLINTIREENPELFTEELKEEIYELLKEAVELEKEYADDLFPDgiLGLnAEDVKQYIRYIANKRLMNL 278

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1262259917  80 GLEPKFEEEEiNPI--VLNGLRTDtKNHDFFSVKGNGYVKAtNVEKLADDD 128
Cdd:COG0208   279 GLEPLFEGDV-NPFpwMSEGLDLN-KKTDFFETRVTEYQKG-GVESTFDED 326
RNRR2 cd01049
Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Ribonucleotide ...
 4-101 3.11e-25

Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Ribonucleotide Reductase, R2/beta subunit (RNRR2) is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins. The RNR protein catalyzes the conversion of ribonucleotides to deoxyribonucleotides and is found in all eukaryotes, many prokaryotes, several viruses, and few archaea. The catalytically active form of RNR is a proposed alpha2-beta2 tetramer. The homodimeric alpha subunit (R1) contains the active site and redox active cysteines as well as the allosteric binding sites. The beta subunit (R2) contains a diiron cluster that, in its reduced state, reacts with dioxygen to form a stable tyrosyl radical and a diiron(III) cluster. This essential tyrosyl radical is proposed to generate a thiyl radical, located on a cysteine residue in the R1 active site that initiates ribonucleotide reduction. The beta subunit is composed of 10-13 helices, the 8 longest helices form an alpha-helical bundle; some have 2 addition beta strands. Yeast is unique in that it assembles both homodimers and heterodimers of RNRR2. The yeast heterodimer, Y2Y4, contains R2 (Y2) and a R2 homolog (Y4) that lacks the diiron center and is proposed to only assist in cofactor assembly, and perhaps stabilize R1 (Y1) in its active conformation.


Pssm-ID: 153108 [Multi-domain]  Cd Length: 288  Bit Score: 96.54  E-value: 3.11e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262259917   4 KDESIHGVFVGILAQQIFAELSVEEQQEVQKETQELLMELYEIEMAYTEEIYT--SIGL-VEDVNRFVRYNANKGLMNLG 80
Cdd:cd01049   188 RDESLHGDFACLLIRELLNENPELFTEEFKEEVYELIKEAVELEKEFARDLLPdgILGLnKEDMKQYIEYVANRRLENLG 267

                          90       100
                  ....*....|....*....|.
gi 1262259917  81 LEPKFEEEEINPIVLNGLRTD 101
Cdd:cd01049   268 LEKLFNVEDKNPFDWMELISD 288
Ribonuc_red_sm pfam00268
Ribonucleotide reductase, small chain;
4-92 6.89e-24

Ribonucleotide reductase, small chain;


Pssm-ID: 425568 [Multi-domain]  Cd Length: 276  Bit Score: 92.95  E-value: 6.89e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262259917   4 KDESIHGVFVGILAQQIFAELSVEEQQEVQKETQELLMELYEIEMAYTEEIY--TSIGL-VEDVNRFVRYNANKGLMNLG 80
Cdd:pfam00268 186 RDEGLHGDFACLLFQHLKEENPELETKELKEEVYDLIKEAVELEKEFLDDALpvGLLGMnAEDVKQYIEYVADRRLMNLG 265

                          90
                  ....*....|..
gi 1262259917  81 LEPKFEEEEiNP 92
Cdd:pfam00268 266 YEKLYNVEV-NP 276
 
Name Accession Description Interval E-value
RNR_1b_NrdF TIGR04171
ribonucleoside-diphosphate reductase, class 1b, beta subunit; Members of this family are NrdF, ...
 3-131 4.82e-71

ribonucleoside-diphosphate reductase, class 1b, beta subunit; Members of this family are NrdF, the beta subunit of class 1b ribonucleotide reductase. This form uses a dimanganese moiety associated with a tyrosine radical to reduce the cellular requirement for iron. [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism]


Pssm-ID: 275027  Cd Length: 313  Bit Score: 215.11  E-value: 4.82e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262259917   3 VKDESIHGVFVGILAQQIFAELSVEEQQEVQKETQELLMELYEIEMAYTEEIYTSIGLVEDVNRFVRYNANKGLMNLGLE 82
Cdd:TIGR04171 184 IRDESIHGVYIGYKAQEGFNKLSEEEQEELKDWMYDLLYELYENEEKYTEELYDEVGLTEDVKKFVRYNANKALMNLGFE 263

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1262259917  83 PKFEEE--EINPIVLNGLRTDTKNHDFFSVKGNGYVKAtNVEKLADDDFVF 131
Cdd:TIGR04171 264 PLFPEEatDVNPIVLNGLSTETKNHDFFSGKGNGYVKG-KVEALEDDDFDF 313
nrdF PRK09614
ribonucleotide-diphosphate reductase subunit beta; Reviewed
 3-131 1.91e-52

ribonucleotide-diphosphate reductase subunit beta; Reviewed


Pssm-ID: 236591 [Multi-domain]  Cd Length: 324  Bit Score: 168.08  E-value: 1.91e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262259917   3 VKDESIHGVFVGILAQQIFAELSVEEQQEVQKETQELLMELYEIEMAYTEEIYTSIGLVEDVNRFVRYNANKGLMNLGLE 82
Cdd:PRK09614  195 IRDESLHGYYIGYLFQEGLEELPELEQEELKDEIYDLLYELYENEEAYTELLYDIVGLAEDVKKYIRYNANKRLMNLGLE 274

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1262259917  83 PKFE-EEEINPIVLNGLR-TDTKNHDFFSVKGNGYVKATnVEKLADDDFVF 131
Cdd:PRK09614  275 PLFPeEEEVNPIWLNGLSnNADENHDFFEGKGTSYVKGA-TEATEDDDWDF 324
NrdB COG0208
Ribonucleotide reductase beta subunit, ferritin-like domain [Nucleotide transport and ...
 3-128 9.35e-38

Ribonucleotide reductase beta subunit, ferritin-like domain [Nucleotide transport and metabolism]; Ribonucleotide reductase beta subunit, ferritin-like domain is part of the Pathway/BioSystem: Pyrimidine salvage


Pssm-ID: 439978 [Multi-domain]  Cd Length: 326  Bit Score: 129.90  E-value: 9.35e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262259917   3 VKDESIHGVFVGILAQQIFAELSVEEQQEVQKETQELLMELYEIEMAYTEEIYTS--IGL-VEDVNRFVRYNANKGLMNL 79
Cdd:COG0208   199 LRDESLHGNFGIYLINTIREENPELFTEELKEEIYELLKEAVELEKEYADDLFPDgiLGLnAEDVKQYIRYIANKRLMNL 278

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1262259917  80 GLEPKFEEEEiNPI--VLNGLRTDtKNHDFFSVKGNGYVKAtNVEKLADDD 128
Cdd:COG0208   279 GLEPLFEGDV-NPFpwMSEGLDLN-KKTDFFETRVTEYQKG-GVESTFDED 326
PRK13965 PRK13965
ribonucleotide-diphosphate reductase subunit beta; Provisional
 3-131 1.85e-35

ribonucleotide-diphosphate reductase subunit beta; Provisional


Pssm-ID: 184425 [Multi-domain]  Cd Length: 335  Bit Score: 124.50  E-value: 1.85e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262259917   3 VKDESIHGVFVGILAQQIFAELSVEEQQEVQKETQELLMELYEIEMAYTEEIYTSIGLVEDVNRFVRYNANKGLMNLGLE 82
Cdd:PRK13965  205 LRDKVIHNYYSGYKYQQKVARLSPEKQAEMKAFVFDLLYELIDLEKAYLRELYAGFDLAEDAIRFSLYNAGKFLQNLGYE 284

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1262259917  83 PKFEEEE--INPIVLNGLRTDT-KNHDFFSVKGNGYVKATnVEKLADDDFVF 131
Cdd:PRK13965  285 SPFTEEEtrVSPEVFAQLSARAdENHDFFSGNGSSYVMGI-TEETTDDDWEF 335
nrdF2 PRK13966
ribonucleotide-diphosphate reductase subunit beta; Provisional
 3-131 6.20e-32

ribonucleotide-diphosphate reductase subunit beta; Provisional


Pssm-ID: 140022  Cd Length: 324  Bit Score: 115.20  E-value: 6.20e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262259917   3 VKDESIHGVFVGILAQQIFAELSVEEQQEVQKETQELLMELYEIEMAYTEEIYTSIGLVEDVNRFVRYNANKGLMNLGLE 82
Cdd:PRK13966  194 IRDEAVHGYYIGYKFQRGLALVDDVTRAELKDYTYELLFELYDNEVEYTQDLYDEVGLTEDVKKFLRYNANKALMNLGYE 273

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1262259917  83 PKF--EEEEINPIVLNGLRTDT-KNHDFFSVKGNGYV--KATNVEklaDDDFVF 131
Cdd:PRK13966  274 ALFprDETDVNPAILSALSPNAdENHDFFSGSGSSYVigKAVVTE---DDDWDF 324
RNRR2 cd01049
Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Ribonucleotide ...
 4-101 3.11e-25

Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Ribonucleotide Reductase, R2/beta subunit (RNRR2) is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins. The RNR protein catalyzes the conversion of ribonucleotides to deoxyribonucleotides and is found in all eukaryotes, many prokaryotes, several viruses, and few archaea. The catalytically active form of RNR is a proposed alpha2-beta2 tetramer. The homodimeric alpha subunit (R1) contains the active site and redox active cysteines as well as the allosteric binding sites. The beta subunit (R2) contains a diiron cluster that, in its reduced state, reacts with dioxygen to form a stable tyrosyl radical and a diiron(III) cluster. This essential tyrosyl radical is proposed to generate a thiyl radical, located on a cysteine residue in the R1 active site that initiates ribonucleotide reduction. The beta subunit is composed of 10-13 helices, the 8 longest helices form an alpha-helical bundle; some have 2 addition beta strands. Yeast is unique in that it assembles both homodimers and heterodimers of RNRR2. The yeast heterodimer, Y2Y4, contains R2 (Y2) and a R2 homolog (Y4) that lacks the diiron center and is proposed to only assist in cofactor assembly, and perhaps stabilize R1 (Y1) in its active conformation.


Pssm-ID: 153108 [Multi-domain]  Cd Length: 288  Bit Score: 96.54  E-value: 3.11e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262259917   4 KDESIHGVFVGILAQQIFAELSVEEQQEVQKETQELLMELYEIEMAYTEEIYT--SIGL-VEDVNRFVRYNANKGLMNLG 80
Cdd:cd01049   188 RDESLHGDFACLLIRELLNENPELFTEEFKEEVYELIKEAVELEKEFARDLLPdgILGLnKEDMKQYIEYVANRRLENLG 267

                          90       100
                  ....*....|....*....|.
gi 1262259917  81 LEPKFEEEEINPIVLNGLRTD 101
Cdd:cd01049   268 LEKLFNVEDKNPFDWMELISD 288
nrdF1 PRK13967
ribonucleotide-diphosphate reductase subunit beta; Provisional
 3-131 9.48e-25

ribonucleotide-diphosphate reductase subunit beta; Provisional


Pssm-ID: 140023  Cd Length: 322  Bit Score: 95.95  E-value: 9.48e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262259917   3 VKDESIHGVFVGILAQQIFAELSVEEQQEVQKETQELLMELYEIEMAYTEEIYTSIGLVEDVNRFVRYNANKGLMNLGLE 82
Cdd:PRK13967  192 IRDEAVHGYYIGYKCQRGLADLTDAERADHREYTCELLHTLYANEIDYAHDLYDELGWTDDVLPYMRYNANKALANLGYQ 271

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1262259917  83 PKFEEE--EINPIVLNGLRTDT-KNHDFFSVKGNGYVKATNvEKLADDDFVF 131
Cdd:PRK13967  272 PAFDRDtcQVNPAVRAALDPGAgENHDFFSGSGSSYVMGTH-QPTTDTDWDF 322
Ribonuc_red_sm pfam00268
Ribonucleotide reductase, small chain;
4-92 6.89e-24

Ribonucleotide reductase, small chain;


Pssm-ID: 425568 [Multi-domain]  Cd Length: 276  Bit Score: 92.95  E-value: 6.89e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262259917   4 KDESIHGVFVGILAQQIFAELSVEEQQEVQKETQELLMELYEIEMAYTEEIY--TSIGL-VEDVNRFVRYNANKGLMNLG 80
Cdd:pfam00268 186 RDEGLHGDFACLLFQHLKEENPELETKELKEEVYDLIKEAVELEKEFLDDALpvGLLGMnAEDVKQYIEYVADRRLMNLG 265

                          90
                  ....*....|..
gi 1262259917  81 LEPKFEEEEiNP 92
Cdd:pfam00268 266 YEKLYNVEV-NP 276
PRK07209 PRK07209
ribonucleotide-diphosphate reductase subunit beta; Validated
 4-92 1.87e-04

ribonucleotide-diphosphate reductase subunit beta; Validated


Pssm-ID: 235968  Cd Length: 369  Bit Score: 39.59  E-value: 1.87e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1262259917   4 KDESIHGVFvGI-LAQQIFAELSVEEQQEVQKETQELLMELYEIEMAYTEEIYTS--IGLVEDVNR-FVRYNANKGLMNL 79
Cdd:PRK07209  246 RDESMHLNF-GIdLINQIKLENPHLWTAEFQAEIRELIKEAVELEYRYARDTMPRgvLGLNASMFKdYLRFIANRRLQQI 324

                          90
                  ....*....|...
gi 1262259917  80 GLEPKFEEEEiNP 92
Cdd:PRK07209  325 GLKPQYPGTE-NP 336
 
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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