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Conserved domains on  [gi|1804235952|ref|WP_161868573|]
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transcriptional regulator NrdR [Enterococcus diestrammenae]

Protein Classification

transcriptional regulator NrdR( domain architecture ID 11442498)

transcriptional regulator NrdR represses transcription of the class Ib ribonucleotide reductase (RNR) genes nrdHIEF, but has a much smaller effect on the transcription of class Ia RNR genes nrdAB and class III RNR genes nrdDG

Gene Ontology:  GO:0045892|GO:0003690|GO:0005524|GO:0008270
PubMed:  35577776|15949864

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NrdR COG1327
Transcriptional regulator NrdR, contains Zn-ribbon and ATP-cone domains [Transcription];
1-153 2.37e-87

Transcriptional regulator NrdR, contains Zn-ribbon and ATP-cone domains [Transcription];


:

Pssm-ID: 440938 [Multi-domain]  Cd Length: 153  Bit Score: 251.92  E-value: 2.37e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1804235952   1 MRCPKCHHNASRVIDSRQTDDGRTIRRRRECENCGFRFTTFERIEETPLLVIKKDGKREEFTREKILRGLIRSAEKRPVA 80
Cdd:COG1327     1 MRCPFCGHEDTKVIDSRPSEDGTAIRRRRECLACGKRFTTYERVELVPLMVIKKDGRREPFDREKLLRGLLRACEKRPVS 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1804235952  81 MEQMEQIVDEVEERVRSLGENEVSTILIGEYVMEALKDVDEISYIRFASVYRQFKDMSVFLKELQEIVEKAKN 153
Cdd:COG1327    81 AEQIEAAVDRIERELRASGEREVPSREIGELVMEELKKLDEVAYVRFASVYRSFKDVDDFREELEELLKEKEK 153
 
Name Accession Description Interval E-value
NrdR COG1327
Transcriptional regulator NrdR, contains Zn-ribbon and ATP-cone domains [Transcription];
1-153 2.37e-87

Transcriptional regulator NrdR, contains Zn-ribbon and ATP-cone domains [Transcription];


Pssm-ID: 440938 [Multi-domain]  Cd Length: 153  Bit Score: 251.92  E-value: 2.37e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1804235952   1 MRCPKCHHNASRVIDSRQTDDGRTIRRRRECENCGFRFTTFERIEETPLLVIKKDGKREEFTREKILRGLIRSAEKRPVA 80
Cdd:COG1327     1 MRCPFCGHEDTKVIDSRPSEDGTAIRRRRECLACGKRFTTYERVELVPLMVIKKDGRREPFDREKLLRGLLRACEKRPVS 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1804235952  81 MEQMEQIVDEVEERVRSLGENEVSTILIGEYVMEALKDVDEISYIRFASVYRQFKDMSVFLKELQEIVEKAKN 153
Cdd:COG1327    81 AEQIEAAVDRIERELRASGEREVPSREIGELVMEELKKLDEVAYVRFASVYRSFKDVDDFREELEELLKEKEK 153
TIGR00244 TIGR00244
transcriptional regulator NrdR; Members of this almost entirely bacterial family contain an ...
 1-147 7.32e-57

transcriptional regulator NrdR; Members of this almost entirely bacterial family contain an ATP cone domain (pfam03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes. [Regulatory functions, DNA interactions]


Pssm-ID: 129347 [Multi-domain]  Cd Length: 147  Bit Score: 174.63  E-value: 7.32e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1804235952   1 MRCPKCHHNASRVIDSRQTDDGRTIRRRRECENCGFRFTTFERIEETPLLVIKKDGKREEFTREKILRGLIRSAEKRPVA 80
Cdd:TIGR00244   1 MHCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAELLPPTVIKQDGVREPFNREKLLRGMVRACEKRPVS 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1804235952  81 MEQMEQIVDEVEERVRSLGENEVSTILIGEYVMEALKDVDEISYIRFASVYRQFKDMSVFLKELQEI 147
Cdd:TIGR00244  81 FDDLEHAINHIEAQLRAQGEREVPSELIGQMVMQYLKKLDEVAYIRFASVYRSFQDIADFVDELEQL 147
ATP-cone pfam03477
ATP cone domain;
49-137 5.34e-18

ATP cone domain;


Pssm-ID: 397513 [Multi-domain]  Cd Length: 86  Bit Score: 73.45  E-value: 5.34e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1804235952  49 LLVIKKDGKREEFTREKILRGLIRSAEKrpvAMEQMEQIVDEVEERVRSLGENEVSTILIGEYVMEALKDVDEISYIRFA 128
Cdd:pfam03477   1 MKVIKRDGRREPFDKEKIRRAIEKACEK---SPDQADELASEVEEELEKSLEDGISTEEIQDLVEKTLAEHPDYAVARAY 77


                  ....*....
gi 1804235952 129 SVYRQFKDM 137
Cdd:pfam03477  78 ILYRNLRKE 86
PRK06406 PRK06406
vitamin B12-dependent ribonucleotide reductase;
45-148 6.94e-04

vitamin B12-dependent ribonucleotide reductase;


Pssm-ID: 235796 [Multi-domain]  Cd Length: 771  Bit Score: 38.68  E-value: 6.94e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1804235952  45 EETPLLVIKKDGKREEFTREKILRGLIRSA-EKRPVAMEQMEQIVDEVEERVRSLGENEVSTI--LIGEYVMEalKDVDE 121
Cdd:PRK06406    1 EKMVKEVIKRDGTVVPFDKKKIAMAIYKAMlSVKNGSMEDAEELTDKVVERLKKYERPTVEQIqdIVEKVLMT--KKING 78

                          90       100
                  ....*....|....*....|....*..
gi 1804235952 122 ISYIRFASVYRQFKDMSVFLKELQEIV 148
Cdd:PRK06406   79 KDFTDVAKSYILYREKRRKIREEKELI 105
Zn-ribbon_RPA12 cd10507
C-terminal zinc ribbon domain of RPA12 subunit of RNA polymerase I; The C-terminal zinc ribbon ...
 2-40 1.00e-03

C-terminal zinc ribbon domain of RPA12 subunit of RNA polymerase I; The C-terminal zinc ribbon domain (C-ribbon) of subunit A12 (Zn-ribbon_RPA12) in RNA polymerase (Pol) I is involved in intrinsic transcript cleavage. Eukaryote genomes are transcribed by three nuclear RNA polymerases (Pol I, II and III) that share some subunits. RPA12 in Pol I, RPB9 in Pol II, RPC11 in Pol III and TFS in archaea are distantly related to each other and to the TFIIS elongation factor of Pol II. RPA12 has two zinc-binding domains separated by a flexible linker.


Pssm-ID: 259792  Cd Length: 47  Bit Score: 35.26  E-value: 1.00e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1804235952   2 RCPKCHHNASRVIdSRQT---DDGRTIRRrrECENCGFRFTT 40
Cdd:cd10507     8 KCPKCGHDEMTYS-TLQLrsaDEGQTVFY--ECPKCGHRFSE 46
 
Name Accession Description Interval E-value
NrdR COG1327
Transcriptional regulator NrdR, contains Zn-ribbon and ATP-cone domains [Transcription];
1-153 2.37e-87

Transcriptional regulator NrdR, contains Zn-ribbon and ATP-cone domains [Transcription];


Pssm-ID: 440938 [Multi-domain]  Cd Length: 153  Bit Score: 251.92  E-value: 2.37e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1804235952   1 MRCPKCHHNASRVIDSRQTDDGRTIRRRRECENCGFRFTTFERIEETPLLVIKKDGKREEFTREKILRGLIRSAEKRPVA 80
Cdd:COG1327     1 MRCPFCGHEDTKVIDSRPSEDGTAIRRRRECLACGKRFTTYERVELVPLMVIKKDGRREPFDREKLLRGLLRACEKRPVS 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1804235952  81 MEQMEQIVDEVEERVRSLGENEVSTILIGEYVMEALKDVDEISYIRFASVYRQFKDMSVFLKELQEIVEKAKN 153
Cdd:COG1327    81 AEQIEAAVDRIERELRASGEREVPSREIGELVMEELKKLDEVAYVRFASVYRSFKDVDDFREELEELLKEKEK 153
TIGR00244 TIGR00244
transcriptional regulator NrdR; Members of this almost entirely bacterial family contain an ...
 1-147 7.32e-57

transcriptional regulator NrdR; Members of this almost entirely bacterial family contain an ATP cone domain (pfam03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes. [Regulatory functions, DNA interactions]


Pssm-ID: 129347 [Multi-domain]  Cd Length: 147  Bit Score: 174.63  E-value: 7.32e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1804235952   1 MRCPKCHHNASRVIDSRQTDDGRTIRRRRECENCGFRFTTFERIEETPLLVIKKDGKREEFTREKILRGLIRSAEKRPVA 80
Cdd:TIGR00244   1 MHCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAELLPPTVIKQDGVREPFNREKLLRGMVRACEKRPVS 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1804235952  81 MEQMEQIVDEVEERVRSLGENEVSTILIGEYVMEALKDVDEISYIRFASVYRQFKDMSVFLKELQEI 147
Cdd:TIGR00244  81 FDDLEHAINHIEAQLRAQGEREVPSELIGQMVMQYLKKLDEVAYIRFASVYRSFQDIADFVDELEQL 147
ATP-cone pfam03477
ATP cone domain;
49-137 5.34e-18

ATP cone domain;


Pssm-ID: 397513 [Multi-domain]  Cd Length: 86  Bit Score: 73.45  E-value: 5.34e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1804235952  49 LLVIKKDGKREEFTREKILRGLIRSAEKrpvAMEQMEQIVDEVEERVRSLGENEVSTILIGEYVMEALKDVDEISYIRFA 128
Cdd:pfam03477   1 MKVIKRDGRREPFDKEKIRRAIEKACEK---SPDQADELASEVEEELEKSLEDGISTEEIQDLVEKTLAEHPDYAVARAY 77


                  ....*....
gi 1804235952 129 SVYRQFKDM 137
Cdd:pfam03477  78 ILYRNLRKE 86
NrdD COG1328
Anaerobic ribonucleoside-triphosphate reductase [Nucleotide transport and metabolism]; ...
 47-156 4.69e-07

Anaerobic ribonucleoside-triphosphate reductase [Nucleotide transport and metabolism]; Anaerobic ribonucleoside-triphosphate reductase is part of the Pathway/BioSystem: Thymidylate biosynthesis


Pssm-ID: 440939 [Multi-domain]  Cd Length: 671  Bit Score: 47.99  E-value: 4.69e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1804235952  47 TPLLVIKKDGKREEFTREKILRGLIRSA---EKRPVAMEQMEQIVDEVEERVRSLGENEVSTI-LIGEYVMEALKDVDEI 122
Cdd:COG1328     1 MMLKVIKRDGRVVPFDPEKIANAIKKAAkavGGEDRDEELAEEIADEVEKELERLGGGGTITVeEIQDIVEKVLMESGHP 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1804235952 123 ----SYIrfasVYRQFKDM-----SVFLKELQEIVEKAKNSDN 156
Cdd:COG1328    81 evakAYI----LYREQRTRlrearTTLVDDIELLDEYDDWRVN 119
PRK06406 PRK06406
vitamin B12-dependent ribonucleotide reductase;
45-148 6.94e-04

vitamin B12-dependent ribonucleotide reductase;


Pssm-ID: 235796 [Multi-domain]  Cd Length: 771  Bit Score: 38.68  E-value: 6.94e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1804235952  45 EETPLLVIKKDGKREEFTREKILRGLIRSA-EKRPVAMEQMEQIVDEVEERVRSLGENEVSTI--LIGEYVMEalKDVDE 121
Cdd:PRK06406    1 EKMVKEVIKRDGTVVPFDKKKIAMAIYKAMlSVKNGSMEDAEELTDKVVERLKKYERPTVEQIqdIVEKVLMT--KKING 78

                          90       100
                  ....*....|....*....|....*..
gi 1804235952 122 ISYIRFASVYRQFKDMSVFLKELQEIV 148
Cdd:PRK06406   79 KDFTDVAKSYILYREKRRKIREEKELI 105
Zn-ribbon_RPA12 cd10507
C-terminal zinc ribbon domain of RPA12 subunit of RNA polymerase I; The C-terminal zinc ribbon ...
 2-40 1.00e-03

C-terminal zinc ribbon domain of RPA12 subunit of RNA polymerase I; The C-terminal zinc ribbon domain (C-ribbon) of subunit A12 (Zn-ribbon_RPA12) in RNA polymerase (Pol) I is involved in intrinsic transcript cleavage. Eukaryote genomes are transcribed by three nuclear RNA polymerases (Pol I, II and III) that share some subunits. RPA12 in Pol I, RPB9 in Pol II, RPC11 in Pol III and TFS in archaea are distantly related to each other and to the TFIIS elongation factor of Pol II. RPA12 has two zinc-binding domains separated by a flexible linker.


Pssm-ID: 259792  Cd Length: 47  Bit Score: 35.26  E-value: 1.00e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1804235952   2 RCPKCHHNASRVIdSRQT---DDGRTIRRrrECENCGFRFTT 40
Cdd:cd10507     8 KCPKCGHDEMTYS-TLQLrsaDEGQTVFY--ECPKCGHRFSE 46
PRK09263 PRK09263
anaerobic ribonucleoside triphosphate reductase; Provisional
 47-136 7.40e-03

anaerobic ribonucleoside triphosphate reductase; Provisional


Pssm-ID: 236436 [Multi-domain]  Cd Length: 711  Bit Score: 35.62  E-value: 7.40e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1804235952  47 TPLLVIKKDGKREEFTREKILRGLIRSAEKRPVAMEQM-EQIVDEVEERVrsLGENEVSTILIGEYVMEALKDVDEISYI 125
Cdd:PRK09263    1 MMPKVIKRDGRKVPFDSEKIKNAIEKAAKAVEVDDEDYcATVAAEIASRV--EGRDEVDIEEIQDAVENQLMAGPYKALA 78

                          90
                  ....*....|.
gi 1804235952 126 RFASVYRQFKD 136
Cdd:PRK09263   79 RAYIEYRHDRD 89
 
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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