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Conserved domains on  [gi|2033713664|pdb|7EGB|V]
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Chain V, Transcription initiation factor IIE subunit beta

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TFIIE_beta_winged_helix cd07977
TFIIE_beta_winged_helix domain, located at the central core region of TFIIE beta, with ...
 68-146 2.21e-34

TFIIE_beta_winged_helix domain, located at the central core region of TFIIE beta, with double-stranded DNA binding activity; Transcription Factor IIE (TFIIE) beta winged-helix (or forkhead) domain is located at the central core region of TFIIE beta. The winged-helix is a form of helix-turn-helix (HTH) domain which typically binds DNA with the 3rd helix. The winged-helix domain is distinguished by the presence of a C-terminal beta-strand hairpin unit (the wing) that packs against the cleft of the tri-helical core. Although most winged-helix domains are multi-member families, TFIIE beta winged-helix domain is typically found as a single orthologous group. TFIIE is one of the six eukaryotic general transcription factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH) that are required for transcription initiation of protein-coding genes. TFIIE is a heterotetramer consisting of two copies each of alpha and beta subunits. TFIIE beta contains several functional domains, an N-terminal serine-rich region, a central core domain exhibiting a winged-helix structure capable of binding double-stranded DNA, a leucine repeat, a sigma3 region, and a C-terminal domain containing two basic regions. The assembly of transcription preinitiation complex (PIC) includes the general transcription factors and RNA polymerase II (pol II) initiated by the binding of the TBP subunit of TFIID to the TATA box, followed by either the sequential assembly of other general transcription factors and pol II or a preassembled pol II holoenzyme pathway. TFIIE interacts directly with TFIIF, TFIIB, pol II, and promoter DNA. TFIIE recruits TFIIH and regulates its activities. TFIIE and TFIIH are also important for the transition from initiation to elongation.


:

Pssm-ID: 153423  Cd Length: 75  Bit Score: 119.65  E-value: 2.21e-34
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
7EGB_V       68 SGSSGYKFGVLAKIVNYMKTRHQrgdtHPLTLDEILDETQHLDIGLKQKQWLMTEALVNNPKIEVIDGKYAFKPKYNVR 146
Cdd:cd07977   1 TGSGTHVFTQLAKIVDYMKKRHQ----HPLTLDEILDYLSLLDIGPKLKEWLKSEALVNNPKIDPKDGTFSFKPKYNIR 75
TFA2_Winged_2 pfam18121
TFA2 Winged helix domain 2; This is the second winged helix domain can be found in TFA2 ...
 146-204 4.76e-07

TFA2 Winged helix domain 2; This is the second winged helix domain can be found in TFA2 proteins present in Saccharomyces cerevisiae. In form 2, the domain interacts directly with Rad3, a DNA helicase.


:

Pssm-ID: 465658  Cd Length: 61  Bit Score: 45.95  E-value: 4.76e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
7EGB_V        146 RDKKALLRLLDQHDQRglGGILLEDIEEALPNSQKAVKALGDQ----ILFVNRPDKKKILFFN 204
Cdd:pfam18121   1 RNKEDLLALLQKQSTA--GGIPVKDLKDSWPDVEEAIEELEAEgkilVLRTKKDGKPRIVFYN 61
 
Name Accession Description Interval E-value
TFIIE_beta_winged_helix cd07977
TFIIE_beta_winged_helix domain, located at the central core region of TFIIE beta, with ...
 68-146 2.21e-34

TFIIE_beta_winged_helix domain, located at the central core region of TFIIE beta, with double-stranded DNA binding activity; Transcription Factor IIE (TFIIE) beta winged-helix (or forkhead) domain is located at the central core region of TFIIE beta. The winged-helix is a form of helix-turn-helix (HTH) domain which typically binds DNA with the 3rd helix. The winged-helix domain is distinguished by the presence of a C-terminal beta-strand hairpin unit (the wing) that packs against the cleft of the tri-helical core. Although most winged-helix domains are multi-member families, TFIIE beta winged-helix domain is typically found as a single orthologous group. TFIIE is one of the six eukaryotic general transcription factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH) that are required for transcription initiation of protein-coding genes. TFIIE is a heterotetramer consisting of two copies each of alpha and beta subunits. TFIIE beta contains several functional domains, an N-terminal serine-rich region, a central core domain exhibiting a winged-helix structure capable of binding double-stranded DNA, a leucine repeat, a sigma3 region, and a C-terminal domain containing two basic regions. The assembly of transcription preinitiation complex (PIC) includes the general transcription factors and RNA polymerase II (pol II) initiated by the binding of the TBP subunit of TFIID to the TATA box, followed by either the sequential assembly of other general transcription factors and pol II or a preassembled pol II holoenzyme pathway. TFIIE interacts directly with TFIIF, TFIIB, pol II, and promoter DNA. TFIIE recruits TFIIH and regulates its activities. TFIIE and TFIIH are also important for the transition from initiation to elongation.


Pssm-ID: 153423  Cd Length: 75  Bit Score: 119.65  E-value: 2.21e-34
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
7EGB_V       68 SGSSGYKFGVLAKIVNYMKTRHQrgdtHPLTLDEILDETQHLDIGLKQKQWLMTEALVNNPKIEVIDGKYAFKPKYNVR 146
Cdd:cd07977   1 TGSGTHVFTQLAKIVDYMKKRHQ----HPLTLDEILDYLSLLDIGPKLKEWLKSEALVNNPKIDPKDGTFSFKPKYNIR 75
TFIIE_beta pfam02186
TFIIE beta subunit core domain; General transcription factor TFIIE consists of two subunits, ...
 74-145 2.42e-19

TFIIE beta subunit core domain; General transcription factor TFIIE consists of two subunits, TFIIE alpha pfam02002 and TFIIE beta. TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. The structure of the DNA binding core region has been solved and has a winged helix fold.


Pssm-ID: 460479  Cd Length: 66  Bit Score: 79.89  E-value: 2.42e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
7EGB_V         74 KFGVLAKIVNYMKTRHqrgdtHPLTLDEILDETQhLDIGlkQKQWLMTEALVNNPKIEV--IDGKYAFKPKYNV 145
Cdd:pfam02186   1 LFTQLHKAVEYLKKQD-----GPLTLEEILDYLS-LDLG--DKNWLLLEALKNNPKIEYdpKTGTFSYKPLYNI 66
TFA2 COG5174
Transcription initiation factor IIE, beta subunit [Transcription];
81-285 2.14e-15

Transcription initiation factor IIE, beta subunit [Transcription];


Pssm-ID: 227501 [Multi-domain]  Cd Length: 285  Bit Score: 74.64  E-value: 2.14e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
7EGB_V       81 IVNYMKTRHQrgdthPLTLDEILDetqHLDIGLKQKQWLMTEALvNNPKIEVIDGKYAFKPKYNVRDKKALLRLLDQhdQ 160
Cdd:COG5174  88 AIEYLKQHDR-----PLSFEEIKD---YLSIDLHNNYVLLLKKK-RRIRIDATHSTFMFKPLYSIRSVEDLLKVLRS--Q 156

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
7EGB_V      161 RGLGGILLEDIEEALPNSQKAVKALGDQ---ILFVNRPDK-KKILFFNDKSCQFSVDEEFQKLWRSVtvdsmdeeKIEEY 236
Cdd:COG5174 157 GTEEGLSMKKLMDGWPNVVPFVEELEKSneiLILRTDKDGsPVVVWNNTQNLECPVDPEFKSLWNQV--------RIPTY 228

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....*.
7EGB_V      237 LKRqgISSMQESG--PKKVAP--IQRRKKPASQKK---RRFKTHNEHLAGVLKDYS 285
Cdd:COG5174 229 HDL--IRELNTAGlkPTSVDPntKKRPTIKIKKKKrsrRKGKITNTHVKGILLDYS 282
TFA2_Winged_2 pfam18121
TFA2 Winged helix domain 2; This is the second winged helix domain can be found in TFA2 ...
 146-204 4.76e-07

TFA2 Winged helix domain 2; This is the second winged helix domain can be found in TFA2 proteins present in Saccharomyces cerevisiae. In form 2, the domain interacts directly with Rad3, a DNA helicase.


Pssm-ID: 465658  Cd Length: 61  Bit Score: 45.95  E-value: 4.76e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
7EGB_V        146 RDKKALLRLLDQHDQRglGGILLEDIEEALPNSQKAVKALGDQ----ILFVNRPDKKKILFFN 204
Cdd:pfam18121   1 RNKEDLLALLQKQSTA--GGIPVKDLKDSWPDVEEAIEELEAEgkilVLRTKKDGKPRIVFYN 61
 
Name Accession Description Interval E-value
TFIIE_beta_winged_helix cd07977
TFIIE_beta_winged_helix domain, located at the central core region of TFIIE beta, with ...
 68-146 2.21e-34

TFIIE_beta_winged_helix domain, located at the central core region of TFIIE beta, with double-stranded DNA binding activity; Transcription Factor IIE (TFIIE) beta winged-helix (or forkhead) domain is located at the central core region of TFIIE beta. The winged-helix is a form of helix-turn-helix (HTH) domain which typically binds DNA with the 3rd helix. The winged-helix domain is distinguished by the presence of a C-terminal beta-strand hairpin unit (the wing) that packs against the cleft of the tri-helical core. Although most winged-helix domains are multi-member families, TFIIE beta winged-helix domain is typically found as a single orthologous group. TFIIE is one of the six eukaryotic general transcription factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH) that are required for transcription initiation of protein-coding genes. TFIIE is a heterotetramer consisting of two copies each of alpha and beta subunits. TFIIE beta contains several functional domains, an N-terminal serine-rich region, a central core domain exhibiting a winged-helix structure capable of binding double-stranded DNA, a leucine repeat, a sigma3 region, and a C-terminal domain containing two basic regions. The assembly of transcription preinitiation complex (PIC) includes the general transcription factors and RNA polymerase II (pol II) initiated by the binding of the TBP subunit of TFIID to the TATA box, followed by either the sequential assembly of other general transcription factors and pol II or a preassembled pol II holoenzyme pathway. TFIIE interacts directly with TFIIF, TFIIB, pol II, and promoter DNA. TFIIE recruits TFIIH and regulates its activities. TFIIE and TFIIH are also important for the transition from initiation to elongation.


Pssm-ID: 153423  Cd Length: 75  Bit Score: 119.65  E-value: 2.21e-34
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
7EGB_V       68 SGSSGYKFGVLAKIVNYMKTRHQrgdtHPLTLDEILDETQHLDIGLKQKQWLMTEALVNNPKIEVIDGKYAFKPKYNVR 146
Cdd:cd07977   1 TGSGTHVFTQLAKIVDYMKKRHQ----HPLTLDEILDYLSLLDIGPKLKEWLKSEALVNNPKIDPKDGTFSFKPKYNIR 75
TFIIE_beta pfam02186
TFIIE beta subunit core domain; General transcription factor TFIIE consists of two subunits, ...
 74-145 2.42e-19

TFIIE beta subunit core domain; General transcription factor TFIIE consists of two subunits, TFIIE alpha pfam02002 and TFIIE beta. TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. The structure of the DNA binding core region has been solved and has a winged helix fold.


Pssm-ID: 460479  Cd Length: 66  Bit Score: 79.89  E-value: 2.42e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
7EGB_V         74 KFGVLAKIVNYMKTRHqrgdtHPLTLDEILDETQhLDIGlkQKQWLMTEALVNNPKIEV--IDGKYAFKPKYNV 145
Cdd:pfam02186   1 LFTQLHKAVEYLKKQD-----GPLTLEEILDYLS-LDLG--DKNWLLLEALKNNPKIEYdpKTGTFSYKPLYNI 66
TFA2 COG5174
Transcription initiation factor IIE, beta subunit [Transcription];
81-285 2.14e-15

Transcription initiation factor IIE, beta subunit [Transcription];


Pssm-ID: 227501 [Multi-domain]  Cd Length: 285  Bit Score: 74.64  E-value: 2.14e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
7EGB_V       81 IVNYMKTRHQrgdthPLTLDEILDetqHLDIGLKQKQWLMTEALvNNPKIEVIDGKYAFKPKYNVRDKKALLRLLDQhdQ 160
Cdd:COG5174  88 AIEYLKQHDR-----PLSFEEIKD---YLSIDLHNNYVLLLKKK-RRIRIDATHSTFMFKPLYSIRSVEDLLKVLRS--Q 156

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
7EGB_V      161 RGLGGILLEDIEEALPNSQKAVKALGDQ---ILFVNRPDK-KKILFFNDKSCQFSVDEEFQKLWRSVtvdsmdeeKIEEY 236
Cdd:COG5174 157 GTEEGLSMKKLMDGWPNVVPFVEELEKSneiLILRTDKDGsPVVVWNNTQNLECPVDPEFKSLWNQV--------RIPTY 228

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....*.
7EGB_V      237 LKRqgISSMQESG--PKKVAP--IQRRKKPASQKK---RRFKTHNEHLAGVLKDYS 285
Cdd:COG5174 229 HDL--IRELNTAGlkPTSVDPntKKRPTIKIKKKKrsrRKGKITNTHVKGILLDYS 282
TFA2_Winged_2 pfam18121
TFA2 Winged helix domain 2; This is the second winged helix domain can be found in TFA2 ...
 146-204 4.76e-07

TFA2 Winged helix domain 2; This is the second winged helix domain can be found in TFA2 proteins present in Saccharomyces cerevisiae. In form 2, the domain interacts directly with Rad3, a DNA helicase.


Pssm-ID: 465658  Cd Length: 61  Bit Score: 45.95  E-value: 4.76e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
7EGB_V        146 RDKKALLRLLDQHDQRglGGILLEDIEEALPNSQKAVKALGDQ----ILFVNRPDKKKILFFN 204
Cdd:pfam18121   1 RNKEDLLALLQKQSTA--GGIPVKDLKDSWPDVEEAIEELEAEgkilVLRTKKDGKPRIVFYN 61
 
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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