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Conserved domains on  [gi|878900966|emb|CIX53750|]
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organic radical activating chaperone [Streptococcus pneumoniae]

Protein Classification

4Fe-4S single cluster domain-containing protein( domain architecture ID 12135473)

4Fe-4S single cluster domain-containing protein binds iron-sulfur clusters

Gene Ontology:  GO:0051539
PubMed:  29601957

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Fer4_12 pfam13353
4Fe-4S single cluster domain; This family includes proteins containing domains which bind to ...
 28-166 7.25e-82

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: 239.00  E-value: 7.25e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 878900966   28 VDGEGVRNSLYVSGCMFHCEGCYNVATWSFNAGILYTAELEEQIMADLAQPYVQGLTLLGGEPFLNTGILLPLVKRIRKE 107
Cdd:pfam13353   1 VNGPGVRCSLFVSGCNHHCKGCFNPETWDFKYGKPFTEELEDEIIEDLAKPYIQGLTLSGGEPLLNAEALLELVKRVREE 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 878900966  108 LPDKDIWSWTGYTWEEMMLEtpDKLELLSLIDILVDGRYDRTKRNLMLQFRGSSNQRII 166
Cdd:pfam13353  81 CPEKDIWLWTGYTFEELQSK--DQLELLKLIDVLVDGKFEQSLKDPSLRFRGSSNQRII 137
 
Name Accession Description Interval E-value
Fer4_12 pfam13353
4Fe-4S single cluster domain; This family includes proteins containing domains which bind to ...
 28-166 7.25e-82

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: 239.00  E-value: 7.25e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 878900966   28 VDGEGVRNSLYVSGCMFHCEGCYNVATWSFNAGILYTAELEEQIMADLAQPYVQGLTLLGGEPFLNTGILLPLVKRIRKE 107
Cdd:pfam13353   1 VNGPGVRCSLFVSGCNHHCKGCFNPETWDFKYGKPFTEELEDEIIEDLAKPYIQGLTLSGGEPLLNAEALLELVKRVREE 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 878900966  108 LPDKDIWSWTGYTWEEMMLEtpDKLELLSLIDILVDGRYDRTKRNLMLQFRGSSNQRII 166
Cdd:pfam13353  81 CPEKDIWLWTGYTFEELQSK--DQLELLKLIDVLVDGKFEQSLKDPSLRFRGSSNQRII 137
NrdG TIGR02491
anaerobic ribonucleoside-triphosphate reductase activating protein; This enzyme is a member of ...
 18-168 2.53e-76

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: 225.69  E-value: 2.53e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 878900966   18 RIIDYKAFNFVDGEGVRNSLYVSGCMFHCEGCYNVATWSFNAGILYTAELEEQIMADLAQ-PYVQGLTLLGGEPFL--NT 94
Cdd:TIGR02491   1 NYMNIKPDDIVNGEGIRVSLFVAGCKHHCEGCFNKETWNFNGGKEFTEALEKEIIRDLNDnPLIDGLTLSGGDPLYprNV 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 878900966   95 GILLPLVKRIRKELPDKDIWSWTGYTWEEMMLEtPDKLELLSLIDILVDGRYDRTKRNLMLQFRGSSNQRIIDV 168
Cdd:TIGR02491  81 EELIELVKKIKAEFPEKDIWLWTGYTWEEILED-EKHLEVLKYIDVLVDGKFELSKKDLKLKFRGSSNQRIIDL 153
nrdG PRK11121
anaerobic ribonucleoside-triphosphate reductase-activating protein;
22-165 1.97e-55

anaerobic ribonucleoside-triphosphate reductase-activating protein;


Pssm-ID: 236853  Cd Length: 154  Bit Score: 172.87  E-value: 1.97e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 878900966  22 YKAFNFVDGEGVRNSLYVSGCMFHCEGCYNVATWSFNAGILYTAELEEQIMADLAQPYV--QGLTLLGGEPFL--NTGIL 97
Cdd:PRK11121   6 YYPVDVVNGPGTRCTLFVSGCVHQCPGCYNKSTWRLNSGHPFTKEMEDQIIADLNDTRIkrQGLSLSGGDPLHpqNVPDI 85

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 878900966  98 LPLVKRIRKELPDKDIWSWTGYTWEEMmleTPDKLELLSLIDILVDGRYDRTKRNLMLQFRGSSNQRI 165
Cdd:PRK11121  86 LKLVQRVKAECPGKDIWVWTGYKLDEL---NAAQRQVVDLIDVLVDGKFVQDLADPSLIWRGSSNQVI 150
PflA COG1180
Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, ...
 16-193 1.09e-12

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


Pssm-ID: 440793 [Multi-domain]  Cd Length: 242  Bit Score: 64.44  E-value: 1.09e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 878900966  16 QGRIIDYKAFNFVDGEG-VRNSLYVSGCMFHCEGCYNVATWSFN---AGILYT-AELEEQIMADLAQPY-VQGLTLLGGE 89
Cdd:COG1180    4 RGRIYGISPFSTVDGPGsIRLSVFTQGCNLRCPYCHNPEISQGRpdaAGRELSpEELVEEALKDRGFLDsCGGVTFSGGE 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 878900966  90 PFLNTGILLPLVKRIRKelpdKDI---WSWTGYTWEEMMletpdkLELLSLID-ILVD------GRYDR-Tkrnlmlqfr 158
Cdd:COG1180   84 PTLQPEFLLDLAKLAKE----LGLhtaLDTNGYIPEEAL------EELLPYLDaVNIDlkafddEFYRKlT--------- 144

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 878900966 159 GSSNQRIID-VQKSLKSGQ------VVIWDkLNDGKESYEQV 193
Cdd:COG1180  145 GVSLEPVLEnLELLAESGVhveirtLVIPG-LNDSEEELEAI 185
Radical_SAM cd01335
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
 41-151 4.32e-08

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: 51.18  E-value: 4.32e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 878900966  41 GCMFHCEGCYNVATWSFNAGILYTAELEEQIMADLAQPYVQGLTLLGGEPFLNTGiLLPLVKRIRKELPDKDI-WSWTGY 119
Cdd:cd01335    6 GCNLNCGFCSNPASKGRGPESPPEIEEILDIVLEAKERGVEVVILTGGEPLLYPE-LAELLRRLKKELPGFEIsIETNGT 84

                         90       100       110
                 ....*....|....*....|....*....|..
gi 878900966 120 TWEEMMLETPDKLELLSlIDILVDGRYDRTKR 151
Cdd:cd01335   85 LLTEELLKELKELGLDG-VGVSLDSGDEEVAD 115
 
Name Accession Description Interval E-value
Fer4_12 pfam13353
4Fe-4S single cluster domain; This family includes proteins containing domains which bind to ...
 28-166 7.25e-82

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: 239.00  E-value: 7.25e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 878900966   28 VDGEGVRNSLYVSGCMFHCEGCYNVATWSFNAGILYTAELEEQIMADLAQPYVQGLTLLGGEPFLNTGILLPLVKRIRKE 107
Cdd:pfam13353   1 VNGPGVRCSLFVSGCNHHCKGCFNPETWDFKYGKPFTEELEDEIIEDLAKPYIQGLTLSGGEPLLNAEALLELVKRVREE 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 878900966  108 LPDKDIWSWTGYTWEEMMLEtpDKLELLSLIDILVDGRYDRTKRNLMLQFRGSSNQRII 166
Cdd:pfam13353  81 CPEKDIWLWTGYTFEELQSK--DQLELLKLIDVLVDGKFEQSLKDPSLRFRGSSNQRII 137
NrdG TIGR02491
anaerobic ribonucleoside-triphosphate reductase activating protein; This enzyme is a member of ...
 18-168 2.53e-76

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: 225.69  E-value: 2.53e-76
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 878900966   18 RIIDYKAFNFVDGEGVRNSLYVSGCMFHCEGCYNVATWSFNAGILYTAELEEQIMADLAQ-PYVQGLTLLGGEPFL--NT 94
Cdd:TIGR02491   1 NYMNIKPDDIVNGEGIRVSLFVAGCKHHCEGCFNKETWNFNGGKEFTEALEKEIIRDLNDnPLIDGLTLSGGDPLYprNV 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 878900966   95 GILLPLVKRIRKELPDKDIWSWTGYTWEEMMLEtPDKLELLSLIDILVDGRYDRTKRNLMLQFRGSSNQRIIDV 168
Cdd:TIGR02491  81 EELIELVKKIKAEFPEKDIWLWTGYTWEEILED-EKHLEVLKYIDVLVDGKFELSKKDLKLKFRGSSNQRIIDL 153
nrdG PRK11121
anaerobic ribonucleoside-triphosphate reductase-activating protein;
22-165 1.97e-55

anaerobic ribonucleoside-triphosphate reductase-activating protein;


Pssm-ID: 236853  Cd Length: 154  Bit Score: 172.87  E-value: 1.97e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 878900966  22 YKAFNFVDGEGVRNSLYVSGCMFHCEGCYNVATWSFNAGILYTAELEEQIMADLAQPYV--QGLTLLGGEPFL--NTGIL 97
Cdd:PRK11121   6 YYPVDVVNGPGTRCTLFVSGCVHQCPGCYNKSTWRLNSGHPFTKEMEDQIIADLNDTRIkrQGLSLSGGDPLHpqNVPDI 85

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 878900966  98 LPLVKRIRKELPDKDIWSWTGYTWEEMmleTPDKLELLSLIDILVDGRYDRTKRNLMLQFRGSSNQRI 165
Cdd:PRK11121  86 LKLVQRVKAECPGKDIWVWTGYKLDEL---NAAQRQVVDLIDVLVDGKFVQDLADPSLIWRGSSNQVI 150
Fer4_14 pfam13394
4Fe-4S single cluster domain;
37-145 1.42e-43

4Fe-4S single cluster domain;


Pssm-ID: 433171 [Multi-domain]  Cd Length: 115  Bit Score: 141.35  E-value: 1.42e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 878900966   37 LYVSGCMFHCEGCYNVATWSFNAGILYTAELEEQIMADLAQPYV--QGLTLLGGEPF--LNTGILLPLVKRIRKELPDKD 112
Cdd:pfam13394   1 LFVSGCNHSCPGCDNKETWKFNYGEPFTEELEDQIIADLKDSYIkrQGLVLTGGEPLhpWNLPVLLKLLKRVKEEYPSKD 80

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 878900966  113 IWSWTGYTWEE--MMLETPDKLELLSLIDILVDGR 145
Cdd:pfam13394  81 IWLETGYTLAIdfEYPDTEEQLFTLSVIDVLVDGK 115
PflA COG1180
Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, ...
 16-193 1.09e-12

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


Pssm-ID: 440793 [Multi-domain]  Cd Length: 242  Bit Score: 64.44  E-value: 1.09e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 878900966  16 QGRIIDYKAFNFVDGEG-VRNSLYVSGCMFHCEGCYNVATWSFN---AGILYT-AELEEQIMADLAQPY-VQGLTLLGGE 89
Cdd:COG1180    4 RGRIYGISPFSTVDGPGsIRLSVFTQGCNLRCPYCHNPEISQGRpdaAGRELSpEELVEEALKDRGFLDsCGGVTFSGGE 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 878900966  90 PFLNTGILLPLVKRIRKelpdKDI---WSWTGYTWEEMMletpdkLELLSLID-ILVD------GRYDR-Tkrnlmlqfr 158
Cdd:COG1180   84 PTLQPEFLLDLAKLAKE----LGLhtaLDTNGYIPEEAL------EELLPYLDaVNIDlkafddEFYRKlT--------- 144

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 878900966 159 GSSNQRIID-VQKSLKSGQ------VVIWDkLNDGKESYEQV 193
Cdd:COG1180  145 GVSLEPVLEnLELLAESGVhveirtLVIPG-LNDSEEELEAI 185
Radical_SAM cd01335
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
 41-151 4.32e-08

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: 51.18  E-value: 4.32e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 878900966  41 GCMFHCEGCYNVATWSFNAGILYTAELEEQIMADLAQPYVQGLTLLGGEPFLNTGiLLPLVKRIRKELPDKDI-WSWTGY 119
Cdd:cd01335    6 GCNLNCGFCSNPASKGRGPESPPEIEEILDIVLEAKERGVEVVILTGGEPLLYPE-LAELLRRLKKELPGFEIsIETNGT 84

                         90       100       110
                 ....*....|....*....|....*....|..
gi 878900966 120 TWEEMMLETPDKLELLSlIDILVDGRYDRTKR 151
Cdd:cd01335   85 LLTEELLKELKELGLDG-VGVSLDSGDEEVAD 115
Radical_SAM pfam04055
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
 41-148 2.84e-07

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: 48.29  E-value: 2.84e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 878900966   41 GCMFHCEGCYNVATWSFNAGILYTAELEEQIMADLAQPYVQGLTLLGGEPFLNTGILLpLVKRIRKELPDKDIwswtgyt 120
Cdd:pfam04055   4 GCNLRCTYCAFPSIRARGKGRELSPEEILEEAKELKRLGVEVVILGGGEPLLLPDLVE-LLERLLKLELAEGI------- 75

                          90       100
                  ....*....|....*....|....*...
gi 878900966  121 weEMMLETPDKLELLSLIDILVDGRYDR 148
Cdd:pfam04055  76 --RITLETNGTLLDEELLELLKEAGLDR 101
pflA PRK11145
pyruvate formate lyase 1-activating protein;
17-92 2.11e-06

pyruvate formate lyase 1-activating protein;


Pssm-ID: 182994 [Multi-domain]  Cd Length: 246  Bit Score: 46.56  E-value: 2.11e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 878900966  17 GRIIDYKAFNFVDGEGVRNSLYVSGCMFHCEGCYNVATWSFNAGilytAELE-EQIMADLA--QPYVQ----GLTLLGGE 89
Cdd:PRK11145   5 GRIHSFESCGTVDGPGIRFITFFQGCLMRCLYCHNRDTWDTHGG----KEVTvEELMKEVVtyRHFMNasggGVTASGGE 80


                 ...
gi 878900966  90 PFL 92
Cdd:PRK11145  81 AIL 83
SkfB COG0535
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
 42-106 1.96e-03

Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, chromosome partitioning, Coenzyme transport and metabolism];


Pssm-ID: 440301 [Multi-domain]  Cd Length: 159  Bit Score: 37.19  E-value: 1.96e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 878900966  42 CMFHCEGCYNvatwsfNAGILYTAELE----EQIMADLAQPYVQGLTLLGGEPFLNTGIlLPLVKRIRK 106
Cdd:COG0535   10 CNLRCKHCYA------DAGPKRPGELSteeaKRILDELAELGVKVVGLTGGEPLLRPDL-FELVEYAKE 71
 
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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