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Conserved domains on  [gi|1092402962|pdb|5JUB|A]
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Chain A, Transcriptional regulator

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ComR_TPR pfam18710
ComR tetratricopeptide; In Gram-positive bacteria, cell-to-cell communication mainly relies on ...
 75-294 2.33e-87

ComR tetratricopeptide; In Gram-positive bacteria, cell-to-cell communication mainly relies on extracellular signaling peptides. ComR is a member of the RNPP family, which positively controls competence for natural DNA transformation in streptococci. It is directly activated by the binding of its associated pheromone XIP. The crystal structure analysis of ComR shows that it contains an N-terminal helix-turn-helix (HTH), DNA binding domain (DBD) and a C-terminal tetratricopeptide repeat (TPR) domain. The TPR domain is composed of 11 alpha-helices forming 5 TPR motifs followed by an additional C-terminal alpha-helix 16 called CAP. The pheromone XIP binding site is found in the TPR region. Biochemical and mutational analysis indicate that, if the interacting XIP is accepted it can then trigger the conformational change of the TPR domain to open the DBD-TPR interface to allow dimer formation that is required to bind DNA.


:

Pssm-ID: 436683  Cd Length: 222  Bit Score: 260.65  E-value: 2.33e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5JUB_A         75 PDEYYEMKNRLIKFPTYRNPDRIKSKLTLIEEVYEKFFDILPEEELLTLDILENILSFTSWEESPKVEEIYEDLFEQVKR 154
Cdd:pfam18710   1 PDRYLELKYRLLRTPTYGDKDRLEQKEELFDEIYEKYYDDLPEEEQLAIDLLQSILDVYNTENIPFGEEILEEYFEQVKK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5JUB_A        155 KRKFSTNDLLVIDYYFF--HLYGRKQYDKKLFERIIKRVLNQEIWTDDVYNIVLFNDLMAIAALKIFHNSFSDFLTVVDK 232
Cdd:pfam18710  81 KKKYSLNDLLIIDLYLTyvESFKSKLFDKKLFEKLERKLLNQEESLDDEDLFLLRDVLLSALGVLLLHKDYEKILELLKV 160

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
5JUB_A        233 ALAVIEKSQLYSYKPSVFVLKAKYELLHKENKKEAAENYDKAIVFASVLEDSVLEESIKAGK 294
Cdd:pfam18710 161 LRKIMDKTQDFQKKPIVFMLEWKYYLYVEKDFDKAKELYQQAIMFAKLIGDEVLAEKLEEEW 222
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
2-77 4.96e-10

Transcriptional regulator, contains XRE-family HTH domain [Transcription];


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 55.39  E-value: 4.96e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
5JUB_A        2 NLKDSIGLRIKTERERQQMSREVLClDGAELTVRQLIRIEKGESLPSLDRLSYIAKRLGKSMTELLDQDNITIPDE 77
Cdd:COG1396   3 TLKKALGERLRELRKARGLTQEELA-ERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEELPEA 77
 
Name Accession Description Interval E-value
ComR_TPR pfam18710
ComR tetratricopeptide; In Gram-positive bacteria, cell-to-cell communication mainly relies on ...
 75-294 2.33e-87

ComR tetratricopeptide; In Gram-positive bacteria, cell-to-cell communication mainly relies on extracellular signaling peptides. ComR is a member of the RNPP family, which positively controls competence for natural DNA transformation in streptococci. It is directly activated by the binding of its associated pheromone XIP. The crystal structure analysis of ComR shows that it contains an N-terminal helix-turn-helix (HTH), DNA binding domain (DBD) and a C-terminal tetratricopeptide repeat (TPR) domain. The TPR domain is composed of 11 alpha-helices forming 5 TPR motifs followed by an additional C-terminal alpha-helix 16 called CAP. The pheromone XIP binding site is found in the TPR region. Biochemical and mutational analysis indicate that, if the interacting XIP is accepted it can then trigger the conformational change of the TPR domain to open the DBD-TPR interface to allow dimer formation that is required to bind DNA.


Pssm-ID: 436683  Cd Length: 222  Bit Score: 260.65  E-value: 2.33e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5JUB_A         75 PDEYYEMKNRLIKFPTYRNPDRIKSKLTLIEEVYEKFFDILPEEELLTLDILENILSFTSWEESPKVEEIYEDLFEQVKR 154
Cdd:pfam18710   1 PDRYLELKYRLLRTPTYGDKDRLEQKEELFDEIYEKYYDDLPEEEQLAIDLLQSILDVYNTENIPFGEEILEEYFEQVKK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5JUB_A        155 KRKFSTNDLLVIDYYFF--HLYGRKQYDKKLFERIIKRVLNQEIWTDDVYNIVLFNDLMAIAALKIFHNSFSDFLTVVDK 232
Cdd:pfam18710  81 KKKYSLNDLLIIDLYLTyvESFKSKLFDKKLFEKLERKLLNQEESLDDEDLFLLRDVLLSALGVLLLHKDYEKILELLKV 160

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
5JUB_A        233 ALAVIEKSQLYSYKPSVFVLKAKYELLHKENKKEAAENYDKAIVFASVLEDSVLEESIKAGK 294
Cdd:pfam18710 161 LRKIMDKTQDFQKKPIVFMLEWKYYLYVEKDFDKAKELYQQAIMFAKLIGDEVLAEKLEEEW 222
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
2-77 4.96e-10

Transcriptional regulator, contains XRE-family HTH domain [Transcription];


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 55.39  E-value: 4.96e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
5JUB_A        2 NLKDSIGLRIKTERERQQMSREVLClDGAELTVRQLIRIEKGESLPSLDRLSYIAKRLGKSMTELLDQDNITIPDE 77
Cdd:COG1396   3 TLKKALGERLRELRKARGLTQEELA-ERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEELPEA 77
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 8-66 3.32e-06

Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.


Pssm-ID: 238045 [Multi-domain]  Cd Length: 58  Bit Score: 43.70  E-value: 3.32e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
5JUB_A        8 GLRIKTERERQQMSREVLClDGAELTVRQLIRIEKGESLPSLDRLSYIAKRLGKSMTEL 66
Cdd:cd00093   1 GERLKELRKEKGLTQEELA-EKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
10-66 3.15e-05

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 40.96  E-value: 3.15e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
5JUB_A          10 RIKTERERQQMSREVLClDGAELTVRQLIRIEKGESLPSLDRLSYIAKRLGKSMTEL 66
Cdd:smart00530   1 RLKELREEKGLTQEELA-EKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 11-66 8.50e-05

Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and CI. Within the protein Swiss:Q5F9C2, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be that of a DNA-binding regulator, the function of most other members, so is not necessarily characteriztic of the whole family.


Pssm-ID: 460181 [Multi-domain]  Cd Length: 55  Bit Score: 39.45  E-value: 8.50e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
5JUB_A         11 IKTERERQQMSREVLClDGAELTVRQLIRIEKGESLPSLDRLSYIAKRLGKSMTEL 66
Cdd:pfam01381   1 LKELREELGLSQEELA-EKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
 
Name Accession Description Interval E-value
ComR_TPR pfam18710
ComR tetratricopeptide; In Gram-positive bacteria, cell-to-cell communication mainly relies on ...
 75-294 2.33e-87

ComR tetratricopeptide; In Gram-positive bacteria, cell-to-cell communication mainly relies on extracellular signaling peptides. ComR is a member of the RNPP family, which positively controls competence for natural DNA transformation in streptococci. It is directly activated by the binding of its associated pheromone XIP. The crystal structure analysis of ComR shows that it contains an N-terminal helix-turn-helix (HTH), DNA binding domain (DBD) and a C-terminal tetratricopeptide repeat (TPR) domain. The TPR domain is composed of 11 alpha-helices forming 5 TPR motifs followed by an additional C-terminal alpha-helix 16 called CAP. The pheromone XIP binding site is found in the TPR region. Biochemical and mutational analysis indicate that, if the interacting XIP is accepted it can then trigger the conformational change of the TPR domain to open the DBD-TPR interface to allow dimer formation that is required to bind DNA.


Pssm-ID: 436683  Cd Length: 222  Bit Score: 260.65  E-value: 2.33e-87
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5JUB_A         75 PDEYYEMKNRLIKFPTYRNPDRIKSKLTLIEEVYEKFFDILPEEELLTLDILENILSFTSWEESPKVEEIYEDLFEQVKR 154
Cdd:pfam18710   1 PDRYLELKYRLLRTPTYGDKDRLEQKEELFDEIYEKYYDDLPEEEQLAIDLLQSILDVYNTENIPFGEEILEEYFEQVKK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5JUB_A        155 KRKFSTNDLLVIDYYFF--HLYGRKQYDKKLFERIIKRVLNQEIWTDDVYNIVLFNDLMAIAALKIFHNSFSDFLTVVDK 232
Cdd:pfam18710  81 KKKYSLNDLLIIDLYLTyvESFKSKLFDKKLFEKLERKLLNQEESLDDEDLFLLRDVLLSALGVLLLHKDYEKILELLKV 160

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
5JUB_A        233 ALAVIEKSQLYSYKPSVFVLKAKYELLHKENKKEAAENYDKAIVFASVLEDSVLEESIKAGK 294
Cdd:pfam18710 161 LRKIMDKTQDFQKKPIVFMLEWKYYLYVEKDFDKAKELYQQAIMFAKLIGDEVLAEKLEEEW 222
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
2-77 4.96e-10

Transcriptional regulator, contains XRE-family HTH domain [Transcription];


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 55.39  E-value: 4.96e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
5JUB_A        2 NLKDSIGLRIKTERERQQMSREVLClDGAELTVRQLIRIEKGESLPSLDRLSYIAKRLGKSMTELLDQDNITIPDE 77
Cdd:COG1396   3 TLKKALGERLRELRKARGLTQEELA-ERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEELPEA 77
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 3-65 2.76e-07

Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and HTH domains [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441418 [Multi-domain]  Cd Length: 70  Bit Score: 47.24  E-value: 2.76e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
5JUB_A        3 LKDSIGLRIKTERERQQMSREVLcldGAELTVRQ--LIRIEKGESLPSLDRLSYIAKRLGKSMTE 65
Cdd:COG1813   9 LVEDYGERIREAREARGLSQEEL---AEKLGVSEstIRRIERGEATPSLDTLRKLEKALGISLAE 70
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
4-71 8.41e-07

DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 45.61  E-value: 8.41e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
5JUB_A        4 KDSIGLRIKTERERQQMSREVLClDGAELTVRQLIRIEKGESLPSLDRLSYIAKRLGKSMTELLDQDN 71
Cdd:COG1476   2 KKKLGNRLKELRKERGLTQEELA-ELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLEE 68
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 8-66 3.32e-06

Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.


Pssm-ID: 238045 [Multi-domain]  Cd Length: 58  Bit Score: 43.70  E-value: 3.32e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
5JUB_A        8 GLRIKTERERQQMSREVLClDGAELTVRQLIRIEKGESLPSLDRLSYIAKRLGKSMTEL 66
Cdd:cd00093   1 GERLKELRKEKGLTQEELA-EKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
10-66 3.15e-05

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 40.96  E-value: 3.15e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
5JUB_A          10 RIKTERERQQMSREVLClDGAELTVRQLIRIEKGESLPSLDRLSYIAKRLGKSMTEL 66
Cdd:smart00530   1 RLKELREEKGLTQEELA-EKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 11-66 8.50e-05

Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and CI. Within the protein Swiss:Q5F9C2, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be that of a DNA-binding regulator, the function of most other members, so is not necessarily characteriztic of the whole family.


Pssm-ID: 460181 [Multi-domain]  Cd Length: 55  Bit Score: 39.45  E-value: 8.50e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
5JUB_A         11 IKTERERQQMSREVLClDGAELTVRQLIRIEKGESLPSLDRLSYIAKRLGKSMTEL 66
Cdd:pfam01381   1 LKELREELGLSQEELA-EKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 5-71 3.85e-03

Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain CBS pair) [Transcription];


Pssm-ID: 442838 [Multi-domain]  Cd Length: 95  Bit Score: 36.15  E-value: 3.85e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
5JUB_A        5 DSIGLRIKTERERQQMSREVLcLDGAELTVRQLIRIEKGESLPSLDRLSYIAKRLGKSMTELLDQDN 71
Cdd:COG3620  16 DTLGEALRLMRKELGLSQLPV-AELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAVLVVDD 81
 
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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