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Conserved domains on  [gi|491323132|ref|WP_005181098|]
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MULTISPECIES: metal/formaldehyde-sensitive transcriptional repressor [Acinetobacter]

Protein Classification

metal/formaldehyde-sensitive transcriptional repressor( domain architecture ID 10178356)

metal/formaldehyde-sensitive transcriptional repressor, similar to E. coli RncR that represses expression of the gene encoding the nickel and cobalt-efflux protein RcnA, and E. coli FrmR that regulates the formaldehyde degradation frmRAB operon

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RcnR-FrmR-like_DUF156 cd10153
Transcriptional regulators RcnR and FrmR, and related domains; this domain family was ...
 3-87 1.04e-28

Transcriptional regulators RcnR and FrmR, and related domains; this domain family was previously known as part of DUF156; This domain family includes various transcriptional regulators that respond to different stressors. It includes Escherichia coli RncR (formally known as YohL, nickel and cobalt-sensitive), and E. coli FrmR (formally known as YaiN, formaldehyde sensitive). Escherichia coli RncR represses expression of the gene encoding the nickel and cobalt-efflux protein RcnA; RcnA may act through modulating NikR, to repress the NIkABCDE nickel transporter. In vitro, purified RncR binds to the rncA promoter DNA fragment in the absence of Ni2+ or Co2+, and the affinity of RncR for this promoter is reduced in the presence of excess nickel. Escherichia coli FrmR regulates the formaldehyde degradation frmRAB operon. This family belongs to a larger superfamily that includes CsoRs (copper-sensitive operon repressors). CsoRs form homotetramers (dimer of dimers). In Mycobacterium tuberculosis CsoR, within each dimer, two Cys residues on opposite subunits, along with a His residue, bind the Cu(I) ion (forming a triagonal S2N coordination complex, C-H-C). These residues are conserved in the majority of members of this superfamily. In this family, however, not all these residues are conserved; in E.coli RcnR and FrmR there is a His or a Thr instead of the second Cys (C-H-H or C-H-T) respectively. For E. coli FrmR, an N-terminal His residue, not conserved in all members of this family, is also involved in metal binding (H-C-H-H). A conserved Tyr and a Glu residue that facilitate allosteric regulation of DNA binding for CsoRs are poorly conserved in this family.


:

Pssm-ID: 197388  Cd Length: 88  Bit Score: 98.39  E-value: 1.04e-28
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491323132  3 HLHTDK-KVLNRIKRLQGQISAVEQSIhDPEKSCIEVLQQVAAIKGAVNGLMNELIESHLRHHVIGDEV--EVNEVELDE 79
Cdd:cd10153   1 HTPKEKkKLLARVRRIRGQVEALERAL-EAEADCAAVLQQIAAVRGAVNGLMAEVLESHLREHVADPELsdAERAQAAEE 79


                ....*...
gi 491323132 80 FLKLLKRY 87
Cdd:cd10153  80 LIEVLRSY 87
 
Name Accession Description Interval E-value
RcnR-FrmR-like_DUF156 cd10153
Transcriptional regulators RcnR and FrmR, and related domains; this domain family was ...
 3-87 1.04e-28

Transcriptional regulators RcnR and FrmR, and related domains; this domain family was previously known as part of DUF156; This domain family includes various transcriptional regulators that respond to different stressors. It includes Escherichia coli RncR (formally known as YohL, nickel and cobalt-sensitive), and E. coli FrmR (formally known as YaiN, formaldehyde sensitive). Escherichia coli RncR represses expression of the gene encoding the nickel and cobalt-efflux protein RcnA; RcnA may act through modulating NikR, to repress the NIkABCDE nickel transporter. In vitro, purified RncR binds to the rncA promoter DNA fragment in the absence of Ni2+ or Co2+, and the affinity of RncR for this promoter is reduced in the presence of excess nickel. Escherichia coli FrmR regulates the formaldehyde degradation frmRAB operon. This family belongs to a larger superfamily that includes CsoRs (copper-sensitive operon repressors). CsoRs form homotetramers (dimer of dimers). In Mycobacterium tuberculosis CsoR, within each dimer, two Cys residues on opposite subunits, along with a His residue, bind the Cu(I) ion (forming a triagonal S2N coordination complex, C-H-C). These residues are conserved in the majority of members of this superfamily. In this family, however, not all these residues are conserved; in E.coli RcnR and FrmR there is a His or a Thr instead of the second Cys (C-H-H or C-H-T) respectively. For E. coli FrmR, an N-terminal His residue, not conserved in all members of this family, is also involved in metal binding (H-C-H-H). A conserved Tyr and a Glu residue that facilitate allosteric regulation of DNA binding for CsoRs are poorly conserved in this family.


Pssm-ID: 197388  Cd Length: 88  Bit Score: 98.39  E-value: 1.04e-28
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491323132  3 HLHTDK-KVLNRIKRLQGQISAVEQSIhDPEKSCIEVLQQVAAIKGAVNGLMNELIESHLRHHVIGDEV--EVNEVELDE 79
Cdd:cd10153   1 HTPKEKkKLLARVRRIRGQVEALERAL-EAEADCAAVLQQIAAVRGAVNGLMAEVLESHLREHVADPELsdAERAQAAEE 79


                ....*...
gi 491323132 80 FLKLLKRY 87
Cdd:cd10153  80 LIEVLRSY 87
Trns_repr_metal pfam02583
Metal-sensitive transcriptional repressor; This is a family of metal-sensitive repressors, ...
 8-86 9.83e-25

Metal-sensitive transcriptional repressor; This is a family of metal-sensitive repressors, involved in resistance to metal ions. Members of this family bind copper, nickel or cobalt ions via conserved cysteine and histidine residues. In the absence of metal ions, these proteins bind to promoter regions and repress transcription. When bound to metal ions they are unable to bind DNA, leading to transcriptional derepression.


Pssm-ID: 426851  Cd Length: 80  Bit Score: 87.88  E-value: 9.83e-25
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 491323132   8 KKVLNRIKRLQGQISAVEQSIHDpEKSCIEVLQQVAAIKGAVNGLMNELIESHLRHHVIGDEVEVNEVELDEFLKLLKR 86
Cdd:pfam02583  3 KKLLNRLKRIEGQVRGIERMIEE-DRYCIDILTQLAAVRSALNGVGKEILEDHLRHCVVEAIEEGREEKIEELIELLKK 80
FrmR COG1937
DNA-binding transcriptional regulator, FrmR family [Transcription];
5-85 7.99e-22

DNA-binding transcriptional regulator, FrmR family [Transcription];


Pssm-ID: 441540  Cd Length: 82  Bit Score: 80.56  E-value: 7.99e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491323132  5 HTDKKVLNRIKRLQGQISAVEQSIHDpEKSCIEVLQQVAAIKGAVNGLMNELIESHLRHHVIGDEVEVN-EVELDEFLKL 83
Cdd:COG1937   2 EDKKKLLNRLKRIEGQVRGIIRMIEE-DRYCIDILTQLAAVRSALNKVGLELLEDHLRHCVVEAIESGDrEEKIEELLKL 80


                ..
gi 491323132 84 LK 85
Cdd:COG1937  81 LK 82
PRK11352 PRK11352
formaldehyde-responsive transcriptional repressor FrmR;
8-87 1.84e-17

formaldehyde-responsive transcriptional repressor FrmR;


Pssm-ID: 183095  Cd Length: 91  Bit Score: 69.86  E-value: 1.84e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491323132  8 KKVLNRIKRLQGQISAVEQSIHDpEKSCIEVLQQVAAIKGAVNGLMNELIESHLRHHVIGDEVEVNEVE--LDEFLKLLK 85
Cdd:PRK11352  9 KKVLTRVRRIRGQIDALERSLEG-DAECRAILQQIAAVRGAANGLMAEVLESHIRETFDRNDCYSREVSqsVDDTIELVR 87


                ..
gi 491323132 86 RY 87
Cdd:PRK11352 88 AY 89
 
Name Accession Description Interval E-value
RcnR-FrmR-like_DUF156 cd10153
Transcriptional regulators RcnR and FrmR, and related domains; this domain family was ...
 3-87 1.04e-28

Transcriptional regulators RcnR and FrmR, and related domains; this domain family was previously known as part of DUF156; This domain family includes various transcriptional regulators that respond to different stressors. It includes Escherichia coli RncR (formally known as YohL, nickel and cobalt-sensitive), and E. coli FrmR (formally known as YaiN, formaldehyde sensitive). Escherichia coli RncR represses expression of the gene encoding the nickel and cobalt-efflux protein RcnA; RcnA may act through modulating NikR, to repress the NIkABCDE nickel transporter. In vitro, purified RncR binds to the rncA promoter DNA fragment in the absence of Ni2+ or Co2+, and the affinity of RncR for this promoter is reduced in the presence of excess nickel. Escherichia coli FrmR regulates the formaldehyde degradation frmRAB operon. This family belongs to a larger superfamily that includes CsoRs (copper-sensitive operon repressors). CsoRs form homotetramers (dimer of dimers). In Mycobacterium tuberculosis CsoR, within each dimer, two Cys residues on opposite subunits, along with a His residue, bind the Cu(I) ion (forming a triagonal S2N coordination complex, C-H-C). These residues are conserved in the majority of members of this superfamily. In this family, however, not all these residues are conserved; in E.coli RcnR and FrmR there is a His or a Thr instead of the second Cys (C-H-H or C-H-T) respectively. For E. coli FrmR, an N-terminal His residue, not conserved in all members of this family, is also involved in metal binding (H-C-H-H). A conserved Tyr and a Glu residue that facilitate allosteric regulation of DNA binding for CsoRs are poorly conserved in this family.


Pssm-ID: 197388  Cd Length: 88  Bit Score: 98.39  E-value: 1.04e-28
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491323132  3 HLHTDK-KVLNRIKRLQGQISAVEQSIhDPEKSCIEVLQQVAAIKGAVNGLMNELIESHLRHHVIGDEV--EVNEVELDE 79
Cdd:cd10153   1 HTPKEKkKLLARVRRIRGQVEALERAL-EAEADCAAVLQQIAAVRGAVNGLMAEVLESHLREHVADPELsdAERAQAAEE 79


                ....*...
gi 491323132 80 FLKLLKRY 87
Cdd:cd10153  80 LIEVLRSY 87
Trns_repr_metal pfam02583
Metal-sensitive transcriptional repressor; This is a family of metal-sensitive repressors, ...
 8-86 9.83e-25

Metal-sensitive transcriptional repressor; This is a family of metal-sensitive repressors, involved in resistance to metal ions. Members of this family bind copper, nickel or cobalt ions via conserved cysteine and histidine residues. In the absence of metal ions, these proteins bind to promoter regions and repress transcription. When bound to metal ions they are unable to bind DNA, leading to transcriptional derepression.


Pssm-ID: 426851  Cd Length: 80  Bit Score: 87.88  E-value: 9.83e-25
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 491323132   8 KKVLNRIKRLQGQISAVEQSIHDpEKSCIEVLQQVAAIKGAVNGLMNELIESHLRHHVIGDEVEVNEVELDEFLKLLKR 86
Cdd:pfam02583  3 KKLLNRLKRIEGQVRGIERMIEE-DRYCIDILTQLAAVRSALNGVGKEILEDHLRHCVVEAIEEGREEKIEELIELLKK 80
FrmR COG1937
DNA-binding transcriptional regulator, FrmR family [Transcription];
5-85 7.99e-22

DNA-binding transcriptional regulator, FrmR family [Transcription];


Pssm-ID: 441540  Cd Length: 82  Bit Score: 80.56  E-value: 7.99e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491323132  5 HTDKKVLNRIKRLQGQISAVEQSIHDpEKSCIEVLQQVAAIKGAVNGLMNELIESHLRHHVIGDEVEVN-EVELDEFLKL 83
Cdd:COG1937   2 EDKKKLLNRLKRIEGQVRGIIRMIEE-DRYCIDILTQLAAVRSALNKVGLELLEDHLRHCVVEAIESGDrEEKIEELLKL 80


                ..
gi 491323132 84 LK 85
Cdd:COG1937  81 LK 82
CsoR-like_DUF156 cd10148
Transcriptional regulators CsoR (copper-sensitive operon repressor), RcnR, and FrmR, and ...
 8-86 3.42e-18

Transcriptional regulators CsoR (copper-sensitive operon repressor), RcnR, and FrmR, and related domains; this domain superfamily was previously known as DUF156; This superfamily includes various transcriptional regulators that respond to stressors including Cu(I), Ni(I), sulfite, and formaldehyde. It includes CsoR (copper-sensitive operon repressor) from Mycobacterium tuberculosis (MtCsoR), Bacillus subtilis (BsCsoR), Thermus thermophilus (TthCsoR), and Staphylococcus aureus (SaCsoR), Mycobacterium tuberculosis RicR (regulated in copper repressor, MtRicR), Escherichia coli RncR (formally known as YohL, nickel and cobalt-sensitive), Alcaligenes xylosoxidans NreA (nickel-sensitive), E. coli FrmR (formally known as YaiN, formaldehyde sensitive), and Staphylococcus aureus CstR (CsoR-like sulfur transferase repressor, NWMN_0026.5, SaCstR). CsoR is Cu(I)-inducible, and regulates the expression of genes involved in copper homeostasis. For example, TthCsoR binds the promoter region of the copZ-csoR-copA operon, and represses expression of these genes, which encode the copper chaperone CopZ, CsoR, and the copper efflux P-type ATPase CopA, respectively. In the presence of excess Cu(I), TthCsoR binds this ion, and is released from the DNA, allowing expression of the downstream genes. TthCsoR also senses other metal ions such as Cu(II), Zn(II), Ag(I), Cd(II) and Ni(II). CsoRs form a homotetramer (dimer of dimers). In the case of MtCsoR, two Cys residues on opposite subunits within each dimer, along with a His residue, bind the Cu(I) ion. These residues are conserved in the majority of members of this superfamily. Exceptions include the functionally uncharacterized Bacillus subtilis YrkD where there is an Asn instead of His (C-N-C), E.coli RcnR where there is a Thr instead of the second Cys (C-H-T), or TthCsoR and E.coli FrmR where there is a His instead of the second Cys and which have an additional N-terminal His (not found in those family members having C-H-C) that may also be involved in metal binding (H-C-H-H). A conserved Tyr and a Glu residue facilitate allosteric regulation of DNA binding. SaCstR regulates genes predicted to function in sulfur metabolism; it is thought that oxidation of the intersubunit Cys pair to a mixture of disulphide and trisulphide linkages by sulfite, results in a reduced affinity of SaCstR for the operator DNA. SaCstR exists as a mixture of oligomeric states, including dimers, tetramers and octamers. The sequence of SaCstR was not available at the time this hierarchy was curated and therefore was not included. Escherichia coli RncR represses expression of the gene encoding the nickel and cobalt-efflux protein RcnA. The gene encoding Alcaligenes xylosoxidans NreA is part of the nre nickel resistance locus located on the pTOM9 plasmid from thisbacteria. Escherichia coli FrmR regulates the formaldehyde degradation frmRAB operon.


Pssm-ID: 197385  Cd Length: 80  Bit Score: 71.38  E-value: 3.42e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491323132  8 KKVLNRIKRLQGQISAVEQSIHDpEKSCIEVLQQVAAIKGAVNGLMNELIESHLRHHVI-GDEVEVNEVELDEFLKLLKR 86
Cdd:cd10148   2 KDLLKRLRRIEGQVRGIQRMIEE-DRYCVDILTQLAAVRSALDKVGLLILEDHLKHCVAeAIESGEAEEKIEELLKLLKK 80
PRK11352 PRK11352
formaldehyde-responsive transcriptional repressor FrmR;
8-87 1.84e-17

formaldehyde-responsive transcriptional repressor FrmR;


Pssm-ID: 183095  Cd Length: 91  Bit Score: 69.86  E-value: 1.84e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491323132  8 KKVLNRIKRLQGQISAVEQSIHDpEKSCIEVLQQVAAIKGAVNGLMNELIESHLRHHVIGDEVEVNEVE--LDEFLKLLK 85
Cdd:PRK11352  9 KKVLTRVRRIRGQIDALERSLEG-DAECRAILQQIAAVRGAANGLMAEVLESHIRETFDRNDCYSREVSqsVDDTIELVR 87


                ..
gi 491323132 86 RY 87
Cdd:PRK11352 88 AY 89
PRK15039 PRK15039
Ni(II)/Co(II)-binding transcriptional repressor RcnR;
1-87 2.46e-15

Ni(II)/Co(II)-binding transcriptional repressor RcnR;


Pssm-ID: 184999  Cd Length: 90  Bit Score: 64.62  E-value: 2.46e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491323132  1 MGHLHTDKKVLN-RIKRLQGQISAVEQSIHDPEKsCIEVLQQVAAIKGAVNGLMNELIESHLRHHVIGDEVEVN-EVELD 78
Cdd:PRK15039  1 MSHTIRDKQKLKaRASKIQGQVVALKKMLDEPHE-CAAVLQQIAAIRGAVNGLMREVIKGHLTEHIVHQGDELKrEEDLD 79


                ....*....
gi 491323132 79 EFLKLLKRY 87
Cdd:PRK15039 80 VVLKVLDSY 88
FpFrmR-Cterm-like_DUF156 cd10156
C-terminal domain of Faecalibacterium prausnitzii A2-165 FrmR , and related domains; this ...
 8-86 6.28e-12

C-terminal domain of Faecalibacterium prausnitzii A2-165 FrmR , and related domains; this domain family was previously known as part of DUF156; This domain family contains the C-terminal domain of the functionally uncharacterized protein Faecalibacterium prausnitzii A2-165 FrmR, and related domains. This family is part of a larger superfamily that contains various transcriptional regulators that respond to different stressors such as Cu(I), Ni(I), sulfite, and formaldehyde, and includes CsoRs (copper-sensitive operon repressors). CsoRs form homotetramers (dimer of dimers). In Mycobacterium tuberculosis CsoR, within each dimer, two Cys residues on opposite subunits, along with a His residue, bind the Cu(I) ion (forming a triagonal S2N coordination complex, C-H-C). These residues are conserved in the majority of members of this superfamily, including this family, and a conserved Tyr and a Glu residue that facilitate allosteric regulation of DNA binding for CsoRs are also conserved.


Pssm-ID: 197391  Cd Length: 86  Bit Score: 55.79  E-value: 6.28e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 491323132  8 KKVLNRIKRLQGQISAVEQSIHDpEKSCIEVLQQVAAIKGAVNGLMNELIESHLRHHVIGDEVEVNEVELDEFLKLLKR 86
Cdd:cd10156   7 KDLINRLNRIEGQIRGIKKMLEE-DRYCGDILVQVAAVESALNSFNKELLQNHIRTCVVEDIRNGNEEVVDELMDLLQK 84
SaCsoR-like_DUF156 cd10152
Staphylococcus aureus copper-sensitive operon repressor (CsoR), and related domains; this ...
 8-86 2.25e-11

Staphylococcus aureus copper-sensitive operon repressor (CsoR), and related domains; this family was previously known as part of DUF156; This domain family includes Staphylococcus aureus CsoR (SaCsoR). SaCsoR is Cu(I)-inducible, and regulates the expression of genes involved in copper homeostasis; it represses a genetically unlinked copA-copZ operon. copA encodes a copper efflux P-type ATPase, and copZ, a copper chaperone. This family belongs to a larger superfamily that contains various transcriptional regulators that respond to different stressors such as Cu(I), Ni(I), sulfite, and formaldehyde, and includes Mycobacterium tuberculosis CsoR (MtCsoR), Bacillus subtilis CsoR, and Thermus thermophilus CsoR. The latter three proteins do not belong to this family. CsoRs form homotetramers (dimer of dimers). In MtCsoR, within each dimer, two Cys residues on opposite subunits, along with a His residue, bind the Cu(I) ion (forming a triagonal S2N coordination complex, C-H-C). These residues are conserved in the majority of members of this superfamily, including this family, and a conserved Tyr and a Glu residue that facilitate allosteric regulation of DNA binding for CsoRs are also well conserved.


Pssm-ID: 197387  Cd Length: 82  Bit Score: 54.30  E-value: 2.25e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 491323132  8 KKVLNRIKRLQGQISAVEQSIhDPEKSCIEVLQQVAAIKGAVNGLMNELIESHLRHHVIGDEVEVNEVELDEFLKLLKR 86
Cdd:cd10152   2 KNLINRLNRIEGQIRGIKGMI-ENDVYCDDVLNQIASVKSALDGVSKLLLESHIKSCVVEQIKEGEEEVVEELLYTINK 79
CsoR-like_DUF156_1 cd10158
Uncharacterized family 1; belongs to a superfamily containing the transcriptional regulators ...
 7-87 3.78e-10

Uncharacterized family 1; belongs to a superfamily containing the transcriptional regulators CsoR (copper-sensitive operon repressor), RcnR, and FrmR, and related domains; this family was previously known as part of DUF156; Uncharacterized family 1, belonging to a larger superfamily that contains various transcriptional regulators that respond to different stressors such as Cu(I), Ni(I), sulfite, and formaldehyde, and includes CsoRs (copper-sensitive operon repressors). CsoRs form homotetramers (dimer of dimers). In Mycobacterium tuberculosis CsoR, within each dimer, two Cys residues on opposite subunits, along with a His residue, bind the Cu(I) ion (forming a triagonal S2N coordination complex, C-H-C). These residues are conserved in the majority of members of this superfamily, including this family; however, a conserved Tyr and a Glu residue that facilitates allosteric regulation of DNA binding for CsoRs are poorly conserved.


Pssm-ID: 197393  Cd Length: 81  Bit Score: 51.09  E-value: 3.78e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491323132  7 DKKVLNRIKRLQGQISAVEQSIHDpEKSCIEVLQQVAAIKGAVNGLMNELIESHLRHHVIgDEVEVN-EVELDEFLKLLK 85
Cdd:cd10158   1 RKKVINRLARIIGHLRSVKRMVEE-DRDCSEVLIQIAAVRSALNNVAKVILKDHLEHCIV-EAVEENdEEAIEELNEAID 78


                ..
gi 491323132 86 RY 87
Cdd:cd10158  79 KF 80
BsYrkD-like_DUF156 cd10155
Uncharacterized protein YrkD from Bacillus subtilis and related domains; this domain ...
 7-84 6.66e-09

Uncharacterized protein YrkD from Bacillus subtilis and related domains; this domain superfamily was previously known as part of DUF156; This domain family contains an uncharacterized protein YrkD from Bacillus subtilis and related proteins. This family is part of a larger superfamily that contains various transcriptional regulators that respond to different stressors such as Cu(I), Ni(I), sulfite, and formaldehyde, and includes CsoRs (copper-sensitive operon repressors). CsoRs form homotetramers (dimer of dimers). In Mycobacterium tuberculosis CsoR, within each dimer, two Cys residues on opposite subunits, along with a His residue, bind the Cu(I) ion (forming a triagonal S2N coordination complex, C-H-C). These residues are conserved in the majority of members of this superfamily. In this family, however, not all these residues are conserved, there is an Asn instead of the His (C-N-C); also a conserved Tyr and a Glu residue that facilitates allosteric regulation of DNA binding for CsoRs are very poorly conserved.


Pssm-ID: 197390  Cd Length: 82  Bit Score: 48.02  E-value: 6.66e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491323132  7 DKKVLNRIKRLQGQISAVEQSIhDPEKSCIEVLQQVAAIKGAVNGLMNELIESHLRHHVI--GDEVEVNEVELDEFLKLL 84
Cdd:cd10155   1 DKKIKNRLKRAEGQLRGILKMM-EEGKECKDVVTQLSAVRSSVDRAIGLIVAENLEECVReeEEDGEDQEEKIQEAINLL 79
BsCsoR-like_DUF156 cd10157
Bacillus subtilis copper-sensitive operon repressor (BsCsoR), and related domains; this family ...
 8-88 6.44e-08

Bacillus subtilis copper-sensitive operon repressor (BsCsoR), and related domains; this family was previously known as part of DUF156; This domain family includes Bacillus subtilis CsoR (BsCsoR). CsoRs are Cu(I)-inducible, and regulate the expression of genes involved in copper homeostasis. BsCsoR regulates the copZA operon which encodes the copper chaperone CopZ, and the copper efflux P-type ATPase CopA. This family belongs to a larger superfamily that contains various transcriptional regulators that respond to different stressors such as Cu(I), Ni(I), sulfite, and formaldehyde, and includes Mycobacterium tuberculosis CsoR (MtCsoR), Thermus thermophilus CsoR, and Staphylococcus aureus CsoR. The latter three proteins do not belong to this family. CsoRs regulate the expression of genes involved in copper homeostasis. CsoRs form homotetramers (dimer of dimers). In MtCsoR, within each dimer, two Cys residues on opposite subunits, along with a His residue, bind the Cu(I) ion (forming a triagonal S2N coordination complex, C-H-C). These residues are conserved in the majority of members of this superfamily, including this family, and the conserved Tyr and a Glu residue that facilitate allosteric regulation of DNA binding for CsoRs are also well conserved.


Pssm-ID: 197392  Cd Length: 85  Bit Score: 45.56  E-value: 6.44e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491323132  8 KKVLNRIKRLQGQISAVEQSIHDpEKSCIEVLQQVAAIKGAVNGLMNELIESHLRHHVIGDEVEVNEVE-LDEFLKLLKR 86
Cdd:cd10157   4 DALLNRLKRIEGQVRGLQKMVED-DRYCIDILVQISAIQAALKQVGLQVLEDHTSHCVADAIKNGDGEEsIKELMKVIKQ 82


                ..
gi 491323132 87 YT 88
Cdd:cd10157  83 FS 84
NreA-like_DUF156 cd10154
Alcaligenes xylosoxidans NreA and related domains; this domain family was previously known as ...
 6-87 6.29e-07

Alcaligenes xylosoxidans NreA and related domains; this domain family was previously known as part of DUF156; This domain family includes Alcaligenes xylosoxidans NreA, Psudomonas putida MreA, and related domains. The gene encoding Alcaligenes xylosoxidans NreA is part of the nre nickel resistance locus located on the pTOM9 plasmid from this bacteria; it confers low-level nickel resistance on both Ralstonia and Escherichia coli strains. The Pseudomonas putida MreA gene is found in association with a gene encoding mrdH, a heavy metal efflux transporter of broad specificity. MreA may have a role in cadmium and nickel resistance. This family is part of a larger superfamily that contains various transcriptional regulators that respond to different stressors such as Cu(I), Ni(I), sulfite, and formaldehyde, and includes CsoRs (copper-sensitive operon repressors). CsoRs form homotetramers (dimer of dimers). In Mycobacterium tuberculosis CsoR, within each dimer, two Cys residues on opposite subunits, along with a His residue, bind the Cu(I) ion (forming a triagonal S2N coordination complex, C-H-C). These residues are conserved in the majority of members of this superfamily, including members of this family; however, a conserved Tyr and a Glu residue that facilitates allosteric regulation of DNA binding for CsoRs are poorly conserved.


Pssm-ID: 197389  Cd Length: 86  Bit Score: 43.14  E-value: 6.29e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491323132  6 TDKKVLNRIKRLQGQISAVEQSIHDpEKSCIEVLQQVAAIKGAVNGLMNELIESHLRH---HVIGDEVEVNEVELDEFlK 82
Cdd:cd10154   3 SHPDIIKRLKRAEGHLRSIITMIEE-GRPCVDIAQQLHAVEKAITQAKRTLIHDHIDHcleEAVGDLPRDERSVLAEF-K 80


                ....*
gi 491323132 83 LLKRY 87
Cdd:cd10154  81 AITKY 85
TthCsoR-like_DUF156 cd10151
Thermus thermophilus CsoR, a Cu(I)-sensing transcriptional regulator, and related domains; ...
 8-86 7.77e-07

Thermus thermophilus CsoR, a Cu(I)-sensing transcriptional regulator, and related domains; this domain family was previously known as part of DUF156; This domain family contains various Cu(I)-inducible transcriptional regulators including CsoR (copper-sensitive operon repressor) from Mycobacterium tuberculosis (MtCsoR), and Thermus thermophilus (TthCsoR). CsoR regulates the expression of genes involved in copper homeostasis. For example, TthCsoR binds the promoter region of the copZ-csoR-copA operon, and represses expression of these genes, which encode the copper chaperone CopZ, CsoR, and the copper efflux P-type ATPase CopA, respectively. In the presence of excess Cu(I), TthCsoR binds this ion, and is released from the DNA, allowing expression of the downstream genes. TthCsoR also senses other metal ions such as Cu(II), Zn(II), Ag(I), Cd(II) and Ni(II). MtCsoR regulates an operon that includes CsoR and a putative copper transporter gene, ctpV (cation transporter P-type ATPase). CsoRs form a homotetramer (dimer of dimers). In MtCsoR, within each dimer, two Cys residues on opposite subunits, along with a His residue, bind the Cu(I) ion (forming a triagonal S2N coordination complex, C-H-C). These residues are conserved in some but not all members of this family; for example, for TthCsoR, there is a His instead of the second Cys as well as an N-terminal His (not found in those family members having C-H-C) which may also be involved in metal binding (H-C-H-H). A conserved Tyr and a Glu residue facilitate allosteric regulation of DNA binding.


Pssm-ID: 197386  Cd Length: 82  Bit Score: 42.70  E-value: 7.77e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491323132  8 KKVLNRIKRLQGQISAVEQSIHDPeKSCIEVLQQVAAIKGAVNGLMNELIESHLRHHVIGdEVEVNEVE--LDEFLKLLK 85
Cdd:cd10151   4 EDALRRLKIIEGHLEGIQKMLEED-KYCVDVLRQIKAVQSALEKVSDLILEGHLESCVTT-AIERGEREevIEELMEAFK 81


                .
gi 491323132 86 R 86
Cdd:cd10151  82 Y 82
CsoR-like_DUF156_3 cd10160
Uncharacterized family 3; belongs to a superfamily containing the transcriptional regulators ...
 13-88 3.18e-05

Uncharacterized family 3; belongs to a superfamily containing the transcriptional regulators CsoR (copper-sensitive operon repressor), RcnR, and FrmR, and related domains; this family was previously known as part of DUF156; Uncharacterized family 3, belonging to a larger superfamily that contains various transcriptional regulators that respond to different stressors such as Cu(I), Ni(I), sulfite, and formaldehyde, and includes CsoRs (copper-sensitive operon repressors). CsoRs form homotetramers (dimer of dimers). In Mycobacterium tuberculosis CsoR, within each dimer, two Cys residues on opposite subunits, along with a His residue, bind the Cu(I) ion (forming a triagonal S2N coordination complex, C-H-C). These residues are conserved in the majority of members of this superfamily, including this family; however, a conserved Tyr and a Glu residue that facilitate allosteric regulation of DNA binding for CsoRs are not conserved.


Pssm-ID: 197395  Cd Length: 85  Bit Score: 38.55  E-value: 3.18e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 491323132 13 RIKRLQGQISAVEQSIhDPEKSCIEVLQQVAAIKGAVNGLMNELIESHLrHHVIGDEVEVNEVE--LDEFLKLLKRYT 88
Cdd:cd10160   8 RLKKIIGQVNAIDRMI-DEDVPCEDVLIQINAAKSALHKVGQIVLEGHL-NHCVRDGIEHGDADetIEDFSKAIEYFS 83
CsoR-like_DUF156_4 cd10161
Uncharacterized family 4; belongs to a superfamily containing the transcriptional regulators ...
 8-50 1.95e-04

Uncharacterized family 4; belongs to a superfamily containing the transcriptional regulators CsoR (copper-sensitive operon repressor), RcnR, and FrmR, and related domains; this family was previously known as part of DUF156; Uncharacterized family 4, belonging to a larger superfamily that contains various transcriptional regulators that respond to different stressors such as Cu(I), Ni(I), sulfite, and formaldehyde, and includes CsoRs (copper-sensitive operon repressors). CsoRs form homotetramers (dimer of dimers). In Mycobacterium tuberculosis CsoR, within each dimer, two Cys residues on opposite subunits, along with a His residue, bind the Cu(I) ion (forming a triagonal S2N coordination complex, C-H-C). These residues are conserved in the majority of members of this superfamily. In this family, however, only one of these residues is conserved (the first Cys); and a conserved Tyr and a Glu residue that facilitate allosteric regulation of DNA binding for CsoRs are also not conserved.


Pssm-ID: 197396  Cd Length: 82  Bit Score: 36.29  E-value: 1.95e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 491323132  8 KKVLNRIKRLQGQISAVEQSIHDPEkSCIEVLQQVAAIKGAVN 50
Cdd:cd10161   2 TGLLNRLARVEGQIRGIQRMIEEGE-DCESIAQQMSASRKALD 43
CsoR-like_DUF156_2 cd10159
Uncharacterized family 2; belongs to a superfamily containing transcriptional regulators CsoR ...
 8-87 3.15e-04

Uncharacterized family 2; belongs to a superfamily containing transcriptional regulators CsoR (copper-sensitive operon repressor), RcnR, and FrmR, and related domains; this family was previously known as part of DUF156; Uncharacterized family 2, belonging to a larger superfamily that contains various transcriptional regulators that respond to different stressors such as Cu(I), Ni(I), sulfite, and formaldehyde, and includes CsoRs (copper-sensitive operon repressors). CsoRs form homotetramers (dimer of dimers). In Mycobacterium tuberculosis CsoR, within each dimer, two Cys residues on opposite subunits, along with a His residue, bind the Cu(I) ion (forming a triagonal S2N coordination complex, C-H-C). These residues are conserved in the majority of members of this superfamily, including this family, and a conserved Tyr and a Glu residue that facilitate allosteric regulation of DNA binding for CsoRs are also conserved.


Pssm-ID: 197394  Cd Length: 82  Bit Score: 36.03  E-value: 3.15e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491323132  8 KKVLNRIKRLQGQISAVEQSIHDpEKSCIEVLQQVAAIKGAVNGLMNELIESHLrHHVIGDEVEVNEVE--LDEFLKLLK 85
Cdd:cd10159   3 KKALRLLKTARGQIDGIIKMIEE-DRYCIDISNQILATQALLKKANKEILSAHM-KHCVKEAVESEDAEekIEEIIELLD 80


                ..
gi 491323132 86 RY 87
Cdd:cd10159  81 KL 82
 
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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