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Conserved domains on  [gi|6322915|ref|NP_012988|]
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transcription factor TFIIE subunit TFA2 [Saccharomyces cerevisiae S288C]

Protein Classification

transcription initiation factor IIE subunit beta family protein( domain architecture ID 10790965)

transcription initiation factor IIE (TFIIE) subunit beta binds to the region where the promoter starts to open upon transcription initiation by RNA polymerase II and plays a role in double-stranded DNA binding of TFIIE .

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TFA2 COG5174
Transcription initiation factor IIE, beta subunit [Transcription];
1-328 1.76e-139

Transcription initiation factor IIE, beta subunit [Transcription];


:

Pssm-ID: 227501 [Multi-domain]  Cd Length: 285  Bit Score: 396.29  E-value: 1.76e-139
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322915    1 MSKNRDpllaNLNAFKSKVKSAPVIAPAKvgqkktndtvitidgntRKRTASERAQENTLNSAKnpvlvdikkeagSNSS 80
Cdd:COG5174   1 MSKNRD----NLNAFKSKVKSAPVIAPAQ-----------------KKRMASPCHFEVGLNSND------------GHSS 47

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322915   81 NAISLddddddedfGSSPSKKVRPGSIAAAALQANQTDISkSHDSSKLLWATEYIQKKGKPVLVNELLDYLSMKKDDKVI 160
Cdd:COG5174  48 TAWSK---------GSSPTKKARIPRMDRDRIQSIDRGVQ-RHTNSYLHAAIEYLKQHDRPLSFEEIKDYLSIDLHNNYV 117

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322915  161 ELLKKLDRIEFDPKKGTFKYLSTYDVHSPSELLKLLRSQVTFKGISCKDLKDGWPQCDETINQLEEDSKILVLRTKKDKT 240
Cdd:COG5174 118 LLLKKKRRIRIDATHSTFMFKPLYSIRSVEDLLKVLRSQGTEEGLSMKKLMDGWPNVVPFVEELEKSNEILILRTDKDGS 197

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322915  241 PRYVWYNSGgNLKC-IDEEFVKMWENVQLPQFAELPRKLQDLGLKPASVDPATIKRQTKRVEVKKKRQRKGKITNTHMTG 319
Cdd:COG5174 198 PVVVWNNTQ-NLECpVDPEFKSLWNQVRIPTYHDLIRELNTAGLKPTSVDPNTKKRPTIKIKKKKRSRRKGKITNTHVKG 276


                ....*....
gi 6322915  320 ILKDYSHRV 328
Cdd:COG5174 277 ILLDYSQDE 285
 
Name Accession Description Interval E-value
TFA2 COG5174
Transcription initiation factor IIE, beta subunit [Transcription];
1-328 1.76e-139

Transcription initiation factor IIE, beta subunit [Transcription];


Pssm-ID: 227501 [Multi-domain]  Cd Length: 285  Bit Score: 396.29  E-value: 1.76e-139
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322915    1 MSKNRDpllaNLNAFKSKVKSAPVIAPAKvgqkktndtvitidgntRKRTASERAQENTLNSAKnpvlvdikkeagSNSS 80
Cdd:COG5174   1 MSKNRD----NLNAFKSKVKSAPVIAPAQ-----------------KKRMASPCHFEVGLNSND------------GHSS 47

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322915   81 NAISLddddddedfGSSPSKKVRPGSIAAAALQANQTDISkSHDSSKLLWATEYIQKKGKPVLVNELLDYLSMKKDDKVI 160
Cdd:COG5174  48 TAWSK---------GSSPTKKARIPRMDRDRIQSIDRGVQ-RHTNSYLHAAIEYLKQHDRPLSFEEIKDYLSIDLHNNYV 117

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322915  161 ELLKKLDRIEFDPKKGTFKYLSTYDVHSPSELLKLLRSQVTFKGISCKDLKDGWPQCDETINQLEEDSKILVLRTKKDKT 240
Cdd:COG5174 118 LLLKKKRRIRIDATHSTFMFKPLYSIRSVEDLLKVLRSQGTEEGLSMKKLMDGWPNVVPFVEELEKSNEILILRTDKDGS 197

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322915  241 PRYVWYNSGgNLKC-IDEEFVKMWENVQLPQFAELPRKLQDLGLKPASVDPATIKRQTKRVEVKKKRQRKGKITNTHMTG 319
Cdd:COG5174 198 PVVVWNNTQ-NLECpVDPEFKSLWNQVRIPTYHDLIRELNTAGLKPTSVDPNTKKRPTIKIKKKKRSRRKGKITNTHVKG 276


                ....*....
gi 6322915  320 ILKDYSHRV 328
Cdd:COG5174 277 ILLDYSQDE 285
TFA2_Winged_2 pfam18121
TFA2 Winged helix domain 2; This is the second winged helix domain can be found in TFA2 ...
 187-247 8.42e-23

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: 89.48  E-value: 8.42e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 6322915    187 HSPSELLKLLRSQVTFKGISCKDLKDGWPQCDETINQLEEDSKILVLRTKKDKTPRYVWYN 247
Cdd:pfam18121   1 RNKEDLLALLQKQSTAGGIPVKDLKDSWPDVEEAIEELEAEGKILVLRTKKDGKPRIVFYN 61
TFIIE_beta_winged_helix cd07977
TFIIE_beta_winged_helix domain, located at the central core region of TFIIE beta, with ...
 119-187 2.50e-13

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: 64.18  E-value: 2.50e-13
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 6322915  119 ISKSHDSSKLLWATEYIQKKG-KPVLVNELLDYLS-MKKDDKVIELLKKLDRI---EFDPKKGTFKYLSTYDVH 187
Cdd:cd07977   2 GSGTHVFTQLAKIVDYMKKRHqHPLTLDEILDYLSlLDIGPKLKEWLKSEALVnnpKIDPKDGTFSFKPKYNIR 75
 
Name Accession Description Interval E-value
TFA2 COG5174
Transcription initiation factor IIE, beta subunit [Transcription];
1-328 1.76e-139

Transcription initiation factor IIE, beta subunit [Transcription];


Pssm-ID: 227501 [Multi-domain]  Cd Length: 285  Bit Score: 396.29  E-value: 1.76e-139
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322915    1 MSKNRDpllaNLNAFKSKVKSAPVIAPAKvgqkktndtvitidgntRKRTASERAQENTLNSAKnpvlvdikkeagSNSS 80
Cdd:COG5174   1 MSKNRD----NLNAFKSKVKSAPVIAPAQ-----------------KKRMASPCHFEVGLNSND------------GHSS 47

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322915   81 NAISLddddddedfGSSPSKKVRPGSIAAAALQANQTDISkSHDSSKLLWATEYIQKKGKPVLVNELLDYLSMKKDDKVI 160
Cdd:COG5174  48 TAWSK---------GSSPTKKARIPRMDRDRIQSIDRGVQ-RHTNSYLHAAIEYLKQHDRPLSFEEIKDYLSIDLHNNYV 117

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322915  161 ELLKKLDRIEFDPKKGTFKYLSTYDVHSPSELLKLLRSQVTFKGISCKDLKDGWPQCDETINQLEEDSKILVLRTKKDKT 240
Cdd:COG5174 118 LLLKKKRRIRIDATHSTFMFKPLYSIRSVEDLLKVLRSQGTEEGLSMKKLMDGWPNVVPFVEELEKSNEILILRTDKDGS 197

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322915  241 PRYVWYNSGgNLKC-IDEEFVKMWENVQLPQFAELPRKLQDLGLKPASVDPATIKRQTKRVEVKKKRQRKGKITNTHMTG 319
Cdd:COG5174 198 PVVVWNNTQ-NLECpVDPEFKSLWNQVRIPTYHDLIRELNTAGLKPTSVDPNTKKRPTIKIKKKKRSRRKGKITNTHVKG 276


                ....*....
gi 6322915  320 ILKDYSHRV 328
Cdd:COG5174 277 ILLDYSQDE 285
TFA2_Winged_2 pfam18121
TFA2 Winged helix domain 2; This is the second winged helix domain can be found in TFA2 ...
 187-247 8.42e-23

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: 89.48  E-value: 8.42e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 6322915    187 HSPSELLKLLRSQVTFKGISCKDLKDGWPQCDETINQLEEDSKILVLRTKKDKTPRYVWYN 247
Cdd:pfam18121   1 RNKEDLLALLQKQSTAGGIPVKDLKDSWPDVEEAIEELEAEGKILVLRTKKDGKPRIVFYN 61
TFIIE_beta pfam02186
TFIIE beta subunit core domain; General transcription factor TFIIE consists of two subunits, ...
 125-186 3.50e-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: 3.50e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 6322915    125 SSKLLWATEYIQKKGKPVLVNELLDYLSMKKDDK---VIELLKKLDRIEFDPKKGTFKYLSTYDV 186
Cdd:pfam02186   2 FTQLHKAVEYLKKQDGPLTLEEILDYLSLDLGDKnwlLLEALKNNPKIEYDPKTGTFSYKPLYNI 66
TFIIE_beta_winged_helix cd07977
TFIIE_beta_winged_helix domain, located at the central core region of TFIIE beta, with ...
 119-187 2.50e-13

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: 64.18  E-value: 2.50e-13
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 6322915  119 ISKSHDSSKLLWATEYIQKKG-KPVLVNELLDYLS-MKKDDKVIELLKKLDRI---EFDPKKGTFKYLSTYDVH 187
Cdd:cd07977   2 GSGTHVFTQLAKIVDYMKKRHqHPLTLDEILDYLSlLDIGPKLKEWLKSEALVnnpKIDPKDGTFSFKPKYNIR 75
 
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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